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"*" +[[package]] +name = "nvidia-cudnn-cu12" +version = "9.10.2.21" +description = "cuDNN runtime libraries" +optional = false +python-versions = ">=3" +groups = ["main"] +markers = "platform_system == \"Linux\" and platform_machine == \"x86_64\" and python_version < \"3.14\"" +files = [ + {file = "nvidia_cudnn_cu12-9.10.2.21-py3-none-manylinux_2_27_aarch64.whl", hash = "sha256:c9132cc3f8958447b4910a1720036d9eff5928cc3179b0a51fb6d167c6cc87d8"}, + {file = "nvidia_cudnn_cu12-9.10.2.21-py3-none-manylinux_2_27_x86_64.whl", hash = "sha256:949452be657fa16687d0930933f032835951ef0892b37d2d53824d1a84dc97a8"}, + {file = "nvidia_cudnn_cu12-9.10.2.21-py3-none-win_amd64.whl", hash = "sha256:c6288de7d63e6cf62988f0923f96dc339cea362decb1bf5b3141883392a7d65e"}, +] + +[package.dependencies] +nvidia-cublas-cu12 = "*" + [[package]] name = "nvidia-cufft-cu12" version = "11.3.0.4" @@ -3663,7 +3078,7 @@ description = "CUFFT native runtime libraries" optional = false python-versions = ">=3" groups = ["main"] -markers = "platform_system == \"Linux\" and platform_machine == \"x86_64\"" +markers = "platform_system == \"Linux\" and platform_machine == \"x86_64\" and python_version >= \"3.14\"" files = [ {file = "nvidia_cufft_cu12-11.3.0.4-py3-none-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:d16079550df460376455cba121db6564089176d9bac9e4f360493ca4741b22a6"}, {file = "nvidia_cufft_cu12-11.3.0.4-py3-none-manylinux2014_aarch64.whl", hash = "sha256:8510990de9f96c803a051822618d42bf6cb8f069ff3f48d93a8486efdacb48fb"}, @@ -3675,6 +3090,23 @@ files = [ [package.dependencies] nvidia-nvjitlink-cu12 = "*" +[[package]] +name = "nvidia-cufft-cu12" +version = "11.3.3.83" +description = "CUFFT native runtime libraries" +optional = false +python-versions = ">=3" +groups = ["main"] +markers = "platform_system == \"Linux\" and platform_machine == \"x86_64\" and python_version < \"3.14\"" +files = [ + {file = 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platform_machine == \"x86_64\"" +markers = "platform_system == \"Linux\" and platform_machine == \"x86_64\" and python_version >= \"3.14\"" files = [ {file = "nvidia_nccl_cu12-2.26.2-py3-none-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:5c196e95e832ad30fbbb50381eb3cbd1fadd5675e587a548563993609af19522"}, {file = "nvidia_nccl_cu12-2.26.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:694cf3879a206553cc9d7dbda76b13efaf610fdb70a50cba303de1b0d1530ac6"}, ] +[[package]] +name = "nvidia-nccl-cu12" +version = "2.27.3" +description = "NVIDIA Collective Communication Library (NCCL) Runtime" +optional = false +python-versions = ">=3" +groups = ["main"] +markers = "platform_system == \"Linux\" and platform_machine == \"x86_64\" and python_version < \"3.14\"" +files = [ + {file = "nvidia_nccl_cu12-2.27.3-py3-none-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:9ddf1a245abc36c550870f26d537a9b6087fb2e2e3d6e0ef03374c6fd19d984f"}, + {file 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(>=1.17) ; python_version >= \"3.13\" and platform_python_implementation != \"PyPy\""] [metadata] lock-version = "2.1" python-versions = "^3.12" -content-hash = "8d7212070e6a14f472e3fb95bac71fc6380405a383d8f8d9602109c67b4d3705" +content-hash = "70ce2a6a771ecefd5e6b22ebc37180593311f4cbad2543b7aa0ceaf17a03f743" diff --git a/fieldExtraction/pyproject.toml b/fieldExtraction/pyproject.toml index 6666d9d..65e3245 100644 --- a/fieldExtraction/pyproject.toml +++ b/fieldExtraction/pyproject.toml @@ -1,5 +1,5 @@ [tool.poetry] -name = "doczy-smart-chunking" +name = "doczy-field-extraction" version = "0.1.0" description = "" authors = ["Alex Galarce "] @@ -19,7 +19,6 @@ openpyxl = "^3.1.5" pytest-mock = "^3.14.0" langchain = "^0.3.14" langchainhub = "^0.1.21" -langchain-chroma = "^0.2.0" langchain-aws = "^0.2.11" langchain-text-splitters = "^0.3.5" langchain-community = "^0.3.15" diff --git a/fieldExtraction/src/investment/file_processing.py b/fieldExtraction/src/investment/file_processing.py index 1c44a02..e0cad4a 100644 --- a/fieldExtraction/src/investment/file_processing.py +++ b/fieldExtraction/src/investment/file_processing.py @@ -1,4 +1,5 @@ import pandas as pd +import logging import src.codes.code_funcs as code_funcs import src.investment.aarete_derived as aarete_derived @@ -22,7 +23,7 @@ from src.utils.string_utils import datetime_str def process_file(file_object, constants: Constants, run_timestamp): filename, contract_text = file_object - print(f"{datetime_str()} Processing {filename}...") + logging.info(f"{datetime_str()} Processing {filename}...") ################## PREPROCESS ################## contract_text = preprocess.clean_text(contract_text) @@ -33,7 +34,7 @@ def process_file(file_object, constants: Constants, run_timestamp): exhibit_dict, all_exhibit_headers = preprocess.one_to_n_exhibit_chunking( text_dict, constants.EXHIBIT_HEADER_MARKERS, filename ) - print(f"{datetime_str()} Preprocessing Complete - {filename}") + logging.info(f"{datetime_str()} Preprocessing Complete - {filename}") ################## ONE TO N ################## if string_utils.contains_reimbursement(contract_text): @@ -44,11 +45,11 @@ def process_file(file_object, constants: Constants, run_timestamp): one_to_n_results = postprocessing_funcs.generate_reimb_ids( one_to_n_results ) # Add reimb_id - print(f"{datetime_str()} One to N Complete - {filename}") + logging.info(f"{datetime_str()} One to N Complete - {filename}") else: one_to_n_results = pd.DataFrame([{"FILE_NAME": filename}]) dynamic_one_to_one_fields = FieldSet() - print(f"{datetime_str()} No One to N Found, Skipping - {filename}") + logging.info(f"{datetime_str()} No One to N Found, Skipping - {filename}") ################## ONE TO ONE ################## one_to_one_results = run_one_to_one_prompts( @@ -60,7 +61,7 @@ def process_file(file_object, constants: Constants, run_timestamp): constants, ) # Return dict one_to_one_results["FILE_NAME"] = filename - print(f"{datetime_str()} One to One Complete - {filename}") + logging.info(f"{datetime_str()} One to One Complete - {filename}") ################## MERGE ################## merged_results = row_funcs.merge_one_to_one_into_one_to_n( @@ -69,13 +70,13 @@ def process_file(file_object, constants: Constants, run_timestamp): ################## CODES ################## results_with_code = code_funcs.code_breakout(merged_results, constants) - print(f"{datetime_str()} Codes Complete - {filename}") + logging.info(f"{datetime_str()} Codes Complete - {filename}") final_results = code_funcs.grouper_breakout(results_with_code) ################## POSTPROCESS ################## final_df = postprocess.postprocess(final_results, constants) - print(f"{datetime_str()} Postprocessing Complete - {filename}") + logging.info(f"{datetime_str()} Postprocessing Complete - {filename}") ################## WRITE INDIVIDUAL ################## if config.WRITE_TO_S3: @@ -83,7 +84,7 @@ def process_file(file_object, constants: Constants, run_timestamp): else: io_utils.write_local(final_df, filename, "", "individual") - print(f"{datetime_str()} Writing Complete - {filename}") + logging.info(f"{datetime_str()} Writing Complete - {filename}") return final_df @@ -180,7 +181,9 @@ def run_one_to_n_prompts(filename, exhibit_dict, all_exhibit_headers, constants) one_to_n_results = aarete_derived.get_crosswalk_fields(one_to_n_results) ################## Determine LOB Relationship ################## - one_to_n_results = one_to_n_funcs.get_lob_relationship(one_to_n_results, exhibit_dict, filename) + one_to_n_results = one_to_n_funcs.get_lob_relationship( + one_to_n_results, exhibit_dict, filename + ) ################## Fill NA Mapping ################## one_to_n_results = aarete_derived.fill_na_mapping(one_to_n_results) diff --git a/fieldExtraction/src/investment/main.py b/fieldExtraction/src/investment/main.py index 85c6c5a..0fb8b29 100644 --- a/fieldExtraction/src/investment/main.py +++ b/fieldExtraction/src/investment/main.py @@ -90,7 +90,7 @@ def main(testing=False, test_params={}): k: v for k, v in input_dict.items() if k in test_params["input_files"] } - print(f"Total Input Files : {len(input_dict)}") + logging.info(f"Total Input Files : {len(input_dict)}") # Process files with run_timestamp successful_results = [] @@ -114,7 +114,7 @@ def main(testing=False, test_params={}): except ( Exception ) as e: # When there's an issue with the future itself (not the processing inside the future) - print(f"Error processing future: {str(e)}") + logging.error(f"Error processing future: {str(e)}") # Coerce this to the format expected by pd.concat (so a single-row dataframe) error_results.append(pd.DataFrame([{"error": str(e)}])) diff --git a/fieldExtraction/src/investment/one_to_n_funcs.py b/fieldExtraction/src/investment/one_to_n_funcs.py index 3f2d320..14428e7 100644 --- a/fieldExtraction/src/investment/one_to_n_funcs.py +++ b/fieldExtraction/src/investment/one_to_n_funcs.py @@ -1176,7 +1176,7 @@ def split_reimb_dates(one_to_n_results: list, filename: str) -> list: """ if not one_to_n_results or not isinstance(one_to_n_results, list): - print("No valid data to process") + logging.info("No valid data to process") return one_to_n_results # Filter records that have non-empty REIMB_DATES @@ -1195,7 +1195,7 @@ def split_reimb_dates(one_to_n_results: list, filename: str) -> list: records_to_process.append((i, record)) if not records_to_process: - print("No valid date ranges to process") + logging.info("No valid date ranges to process") # Still remove the REIMB_DATES field from all records for record in one_to_n_results: if "REIMB_DATES" in record: @@ -1225,13 +1225,13 @@ def split_reimb_dates(one_to_n_results: list, filename: str) -> list: if "end_date" in llm_output_cleaned: record["REIMB_TERMINATION_DT"] = llm_output_cleaned["end_date"] else: - print( + logging.error( f"Invalid LLM output format for index {index}: {llm_output_cleaned}" ) except Exception as e: # Broader exception handling for LLM calls and JSON parsing - print(f"Error processing dates for index {index}: {str(e)}") + logging.error(f"Error processing dates for index {index}: {str(e)}") # Continue processing other records even if one fails continue @@ -1386,14 +1386,13 @@ def run_grouper_breakout(service: str, methodology: str, filename: str) -> dict: grouper_questions = FieldSet( file_path=config.FIELD_JSON_PATH, field_type="grouper" ).print_prompt_dict() - prompt = prompt_templates.GROUPER_BREAKOUT( - service, methodology, grouper_questions - ) + prompt = prompt_templates.GROUPER_BREAKOUT(service, methodology, grouper_questions) logging.debug(f"Running GROUPER breakout in {filename} with prompt: {prompt}") llm_response = llm_utils.invoke_claude(prompt, "sonnet_latest", filename) logging.debug(f"LLM Response for GROUPER breakout in {filename}: {llm_response}") return string_utils.universal_json_load(llm_response) or {} + def run_outliers_breakout(service: str, methodology: str, filename: str) -> dict: """ Runs focused OUTLIERS analysis using specialized prompt. diff --git a/fieldExtraction/src/investment/one_to_one_funcs.py b/fieldExtraction/src/investment/one_to_one_funcs.py index e774e0e..6d79f38 100644 --- a/fieldExtraction/src/investment/one_to_one_funcs.py +++ b/fieldExtraction/src/investment/one_to_one_funcs.py @@ -94,7 +94,7 @@ def filter_payer_from_providers( if similarity_score < threshold: filtered_providers.append(provider) else: - print( + logging.info( f"Filtered out provider that matched payer: '{provider_name}' similar to '{payer_name}' with score {similarity_score}" ) @@ -210,7 +210,7 @@ def run_smart_chunked_fields( answers_dict[field.field_name] = field_answer except Exception as e: - print(f"Error processing field {field}: {type(e)}, {str(e)}") + logging.error(f"Error processing field {field}: {type(e)}, {str(e)}") for field in fields: answers_dict[field.field_name] = f"Error: {str(e)}" @@ -300,7 +300,7 @@ def run_full_context_fields( ) full_context_answers_dict = string_utils.universal_json_load(claude_answer_raw) except Exception as e: - print(f"Error processing high accuracy fields: {str(e)}") + logging.error(f"Error processing high accuracy fields: {str(e)}") full_context_answers_dict = {} for field in full_context_fields.list_fields(): full_context_answers_dict[field] = f"Error: {str(e)}" diff --git a/fieldExtraction/src/investment/table_funcs.py b/fieldExtraction/src/investment/table_funcs.py index bc0ca0b..25b66b4 100644 --- a/fieldExtraction/src/investment/table_funcs.py +++ b/fieldExtraction/src/investment/table_funcs.py @@ -96,7 +96,7 @@ def convert_str_to_dataframe(text: str, is_continuation: bool = False) -> pd.Dat # Empty list - return empty DataFrame return pd.DataFrame() except (SyntaxError, ValueError): - print(f"Invalid list format: {list_str}") + logging.error(f"Invalid list format: {list_str}") # Fall back to dict format (old format) - but warn about deprecation dict_match = re.search(DICTIONARY_PATTERN, text) @@ -111,7 +111,7 @@ def convert_str_to_dataframe(text: str, is_continuation: bool = False) -> pd.Dat # No need to set the headers explicitly, DataFrame will use keys as column names return pd.DataFrame(parsed_data, dtype=str) except (SyntaxError, ValueError): - print(f"Invalid dictionary format: {dict_str}") + logging.error(f"Invalid dictionary format: {dict_str}") return pd.DataFrame() # Return empty DataFrame if no valid format found @@ -136,7 +136,7 @@ def convert_str_to_dict(text: str) -> Dict[str, Any]: try: return ast.literal_eval(dict_str) except (SyntaxError, ValueError): - print(f"Invalid dictionary format: {dict_str}") + logging.error(f"Invalid dictionary format: {dict_str}") return {} diff --git a/fieldExtraction/src/investment/tin_npi_funcs.py b/fieldExtraction/src/investment/tin_npi_funcs.py index d8eda84..01df973 100644 --- a/fieldExtraction/src/investment/tin_npi_funcs.py +++ b/fieldExtraction/src/investment/tin_npi_funcs.py @@ -1,4 +1,5 @@ import json +import logging import re from typing import Optional @@ -309,7 +310,9 @@ def identify_group_provider( return new_group_provider except Exception as e: - print(f"Error parsing group provider response: {response}. Exception: {e}") + logging.error( + f"Error parsing group provider response: {response}. Exception: {e}" + ) return None # Fallback: if no match found, return None @@ -400,7 +403,7 @@ def get_provider_info(text_dict: dict, page_num: str, filename: str) -> list: providers = [providers] elif not isinstance(providers, list): # If not a list or dict, create a default list with error info - print( + logging.warning( f"Warning: Unexpected format in provider info response: {type(providers)}" ) providers = [ @@ -423,8 +426,8 @@ def get_provider_info(text_dict: dict, page_num: str, filename: str) -> list: return providers except ValueError as e: # Handle JSON parsing error - print(f"Error parsing JSON response from LLM: {str(e)}") - print(f"Raw response: {claude_answer_raw}") + logging.error(f"Error parsing JSON response from LLM: {str(e)}") + logging.error(f"Raw response: {claude_answer_raw}") # Return a default value return [ { diff --git a/fieldExtraction/src/investment/vision_funcs.py b/fieldExtraction/src/investment/vision_funcs.py index 9a4246f..6151460 100644 --- a/fieldExtraction/src/investment/vision_funcs.py +++ b/fieldExtraction/src/investment/vision_funcs.py @@ -1,5 +1,6 @@ import base64 from io import BytesIO +import logging from typing import List import fitz # PyMuPDF @@ -115,5 +116,5 @@ def process_pdf_pages_to_base64_images( return base64_images except (ValueError, fitz.FileDataError) as e: - print(f"Error processing PDF pages: {str(e)}") + logging.error(f"Error processing PDF pages: {str(e)}") raise diff --git a/fieldExtraction/src/utils/io_utils.py b/fieldExtraction/src/utils/io_utils.py index c00b15e..f70a934 100644 --- a/fieldExtraction/src/utils/io_utils.py +++ b/fieldExtraction/src/utils/io_utils.py @@ -1,3 +1,4 @@ +import logging import os import tempfile from io import StringIO @@ -26,21 +27,23 @@ def read_local(file_path): # io_utils.py return file_contents except UnicodeDecodeError: # If ANSI also fails, log an error message or handle it accordingly - print(f"Failed to decode {file_path} with UTF-8 and cp1252 encodings.") + logging.error( + f"Failed to decode {file_path} with UTF-8 and cp1252 encodings." + ) if os.path.isfile(file_path) and file_path.endswith(".csv"): try: df = pd.read_csv(file_path) return df except Exception: - print("Failed to read .csv file.") + logging.error("Failed to read .csv file.") if os.path.isfile(file_path) and file_path.endswith(".xlsx"): try: df = pd.read_excel(file_path) return df except Exception: - print("Failed to read .xlsx file.") + logging.error("Failed to read .xlsx file.") def list_s3_files(prefix=config.S3_PREFIX, bucket=config.S3_BUCKET): # io_utils.py @@ -72,7 +75,7 @@ def read_s3_pdf(pdf_path): temp_pdf_path = temp_pdf.name return temp_pdf_path except ClientError as e: - print(f"Error fetching PDF from S3: {e}") + logging.error(f"Error fetching PDF from S3: {e}") return None @@ -108,7 +111,7 @@ def read_s3(): files = {} for contract in contract_list: - print(f"Reading {contract}") + logging.info(f"Reading {contract}") try: data = s3_client.get_object(Bucket=bucket, Key=contract) if contract.endswith(".txt"): @@ -135,7 +138,7 @@ def read_s3_csv(csv_path): # io_utils.py df = pd.read_csv(StringIO(response["Body"].read().decode("utf-8"))) return df except ClientError as e: - print(f"Error listing S3 objects: {e}") + logging.error(f"Error listing S3 objects: {e}") def read_input(local_path=config.LOCAL_PATH): # io_utils.py @@ -178,11 +181,13 @@ def filter_already_processed(input_dict, input_dict_b): # io_utils.py k: v for k, v in input_dict_b.items() if k not in already_processed_b } - print(f"Filtering based on S3 master tracking for batch {config.BATCH_ID}:") - print( + logging.info( + f"Filtering based on S3 master tracking for batch {config.BATCH_ID}:" + ) + logging.info( f"AC: Found {len(already_processed_ac)} already processed, {len(input_dict_ac)} remaining" ) - print( + logging.info( f"B: Found {len(already_processed_b)} already processed, {len(input_dict_b)} remaining" ) @@ -205,11 +210,11 @@ def filter_already_processed(input_dict, input_dict_b): # io_utils.py k: v for k, v in input_dict_b.items() if k not in already_processed_b } - print(f"Filtering based on local output directory:") - print( + logging.info(f"Filtering based on local output directory:") + logging.info( f"AC: Found {len(already_processed_ac)} already processed, {len(input_dict_ac)} remaining" ) - print( + logging.info( f"B: Found {len(already_processed_b)} already processed, {len(input_dict_b)} remaining" ) @@ -298,9 +303,9 @@ def write_s3(df, filename, run_timestamp, output_type): Bucket=config.S3_OUTPUT_BUCKET, Key=output_path, Body=csv_buffer ) except ClientError as e: - print(f"Error uploading to S3: {e}") + logging.error(f"Error uploading to S3: {e}") if output_type == "final": - print(f"Saved batch output file: {output_path}") + logging.info(f"Saved batch output file: {output_path}") elif output_type == "individual": - print(f"Saved individual output file: {output_path}") + logging.info(f"Saved individual output file: {output_path}") diff --git a/fieldExtraction/src/utils/llm_utils.py b/fieldExtraction/src/utils/llm_utils.py index 0544279..4886216 100644 --- a/fieldExtraction/src/utils/llm_utils.py +++ b/fieldExtraction/src/utils/llm_utils.py @@ -161,7 +161,7 @@ def invoke_claude( else: raise ValueError(f"Unsupported model_id: {model_id}") else: - print("Usage: python local_main.py <-local> OR python main.py ") + logging.error("Usage: python local_main.py <-local> OR python main.py ") raise # Store response in cache with LRU eviction @@ -185,7 +185,6 @@ def invoke_claude_with_image_array( prompt, model_id, filename, base64_images, max_tokens=4096 ): cache_key = get_cache_key_with_image_array(prompt, model_id, base64_images) - # print(f"Cache key for {filename}: {cache_key}") # printing for debugging # Check cache first - use get() method from LRUCache if cache_key in claude_cache: claude_cache.move_to_end(cache_key) # Mark as recently used @@ -218,7 +217,7 @@ def invoke_claude_with_image_array( ) else: - print("Usage: python local_main.py <-local> OR python main.py ") + logging.error("Usage: python local_main.py <-local> OR python main.py ") raise # Store response in cache with LRU eviction @@ -584,21 +583,21 @@ def ec2_claude_3_and_up( ]: if attempt < max_retries - 1: delay = (2**attempt + random.uniform(0, 1)) * initial_delay - print( + logging.info( f"Attempt {attempt + 1} failed. Retrying in {delay:.2f} seconds..." ) time.sleep(delay) else: - print( + logging.info( f"Switching to next runtime due to {error_code}: {str(e)}." ) break # Switch to the next runtime else: - print(f"Unexpected error: {str(e)}") + logging.error(f"Unexpected error: {str(e)}") raise # Reraise other exceptions except Exception as e: - print(f"Unexpected error: {str(e)}") + logging.error(f"Unexpected error: {str(e)}") raise else: # Runtime rotation is disabled for attempt in range(max_retries): @@ -639,7 +638,7 @@ def ec2_claude_3_and_up( # Timeout errors should probably retry if attempt < max_retries - 1: delay = (2**attempt + random.uniform(0, 1)) * initial_delay - print( + logging.info( f"Attempt {attempt + 1} failed due to timeout. Retrying in {delay:.2f} seconds..." ) time.sleep(delay) @@ -650,18 +649,18 @@ def ec2_claude_3_and_up( if error_code in ["ThrottlingException", "TooManyRequestsException"]: if attempt < max_retries - 1: delay = (2**attempt + random.uniform(0, 1)) * initial_delay - print( + logging.info( f"Attempt {attempt + 1} failed due to rate limiting. Retrying in {delay:.2f} seconds..." ) time.sleep(delay) else: raise else: - print(f"Unexpected error: {str(e)}") + logging.error(f"Unexpected error: {str(e)}") raise # Non-throttling client errors should fail immediately except Exception as e: - print(f"Unexpected error: {str(e)}") + logging.error(f"Unexpected error: {str(e)}") raise raise Exception(f"Max retries ({max_retries}) exceeded for model {model_id}.") diff --git a/fieldExtraction/src/utils/string_utils.py b/fieldExtraction/src/utils/string_utils.py index 90b03d2..db972cb 100644 --- a/fieldExtraction/src/utils/string_utils.py +++ b/fieldExtraction/src/utils/string_utils.py @@ -1,4 +1,5 @@ import json +import logging import re import traceback import warnings @@ -206,9 +207,9 @@ def universal_json_load(string_dict: str): try: return json.loads(matched_str) except json.JSONDecodeError as e: - print(f"Failed to parse JSON: {e}") - print(f"Original string: {string_dict}") - print(f"Traceback: {traceback.format_exc()}") + logging.error(f"Failed to parse JSON: {e}") + logging.error(f"Original string: {string_dict}") + logging.error(f"Traceback: {traceback.format_exc()}") # Use placeholders to preserve JSON structure characters for CSV compatibility csv_safe_string = ( string_dict.replace(",", "[COMMA]") @@ -230,9 +231,9 @@ def universal_json_load(string_dict: str): ) # Replace single quotes with double quotes return json.loads(cleaned_str) except json.JSONDecodeError as e: - print(f"Failed to parse list: {e}") - print(f"Original string: {string_dict}") - print(f"Traceback: {traceback.format_exc()}") + logging.error(f"Failed to parse list: {e}") + logging.error(f"Original string: {string_dict}") + logging.error(f"Traceback: {traceback.format_exc()}") # Use placeholders to preserve JSON structure characters for CSV compatibility csv_safe_string = ( string_dict.replace(",", "[COMMA]") @@ -275,7 +276,7 @@ def contains_reimbursement(text, page="1", method="keyword"): elif isinstance(text, str): text_to_check = text.lower() else: - print("contains_reimbursement - Invalid data type") + logging.warning("contains_reimbursement - Invalid data type") return False return any(keyword in text_to_check for keyword in reimbursement_strings) elif method == "regex": diff --git a/fieldExtraction/src/utils/table_utils.py b/fieldExtraction/src/utils/table_utils.py deleted file mode 100644 index e5e8c45..0000000 --- a/fieldExtraction/src/utils/table_utils.py +++ /dev/null @@ -1,517 +0,0 @@ -import ast -import copy -import math -import re -from collections import defaultdict -from typing import Any, Dict, List, Optional, Pattern, Tuple, Union - -import pandas as pd - -import src.utils.llm_utils as llm_utils -import src.utils.string_utils as string_utils -from src import config -from src.prompts import preprocessing_prompts - -# Table regex patterns -START_PAGE_PATTERN: Pattern[str] = re.compile( - r"^(?!None\n).+\n\{.*?\}", re.DOTALL -) # Regex for start page - shouldn't have literal `None` -CONTINUATION_PAGE_PATTERN: Pattern[str] = re.compile( - r"^None\n\{.*?\}", re.DOTALL -) # Regex for continuation page - has literal `None` present at the start -START_PAGE_NUM_PATTERN: str = r"\n\d+\n?" -CONTINUATION_PAGE_NUM_PATTERN: str = r"\d+\n" -DICTIONARY_PATTERN: str = r"\{.*\}" - -# Markers for table start and end -START_MARKER: str = "-------Table Start--------" -END_MARKER: str = "-------Table End--------" - - -def count_tables(exhibit_text: str) -> int: - """Count number of tables found in an exhibit, through use of a - regex that catches the table start and end strings. - - Args: - exhibit_text (str): Input page text - - Returns: - int: Number of tables - """ - pattern = r"-Table Start-" # Source text contains "-------Table Start--------" but in case hyphen count is unreliable, just looking for one - matches = re.findall(pattern, exhibit_text) - return len(matches) - - -def extract_first_table_from_page(text: str) -> str: - """ - Extracts the first table from a given page of text based on predefined start and end markers. - - Args: - text (str): The text content of the page from which the table needs to be extracted. - - Returns: - str: The extracted table content as a string. If the start or end markers are not found, returns an empty string. - """ - if START_MARKER not in text or END_MARKER not in text: - return "" - - start_index: int = text.find(START_MARKER) + len(START_MARKER) - end_index: int = text.find(END_MARKER) - filtered_page: str = text[start_index:end_index].strip() - - return filtered_page - - -def extract_snippets_between_markers(text: str) -> List[str]: - """ - Extracts all snippets from the input text that are enclosed between START_MARKER and END_MARKER. - - Args: - text (str): The input text from which to extract the snippets. - - Returns: - list: A list of substrings found between START_MARKER and END_MARKER in the input text. - """ - return re.findall(rf"{START_MARKER}(.+?){END_MARKER}", text, re.DOTALL) - - -def get_str_dictionaries_from_text( - text: str, only_first: bool = True -) -> Union[List[str], str]: - """ - Extracts dictionary-like strings from the given text using a predefined pattern. - - Args: - text (str): The input text from which to extract dictionary-like strings. - only_first (bool, optional): If True, returns only the first match. If False, returns all matches. Defaults to True. - - Returns: - list or str: A list of all matched dictionary-like strings if only_first is False, otherwise the first matched string. - """ - matches = re.findall(DICTIONARY_PATTERN, text) - if not matches: - return "" - return matches[0] if only_first else matches - - -def page_contains_multiple_tables(text: str) -> bool: - """ - Checks if the given text contains multiple tables. - - Args: - text (str): The text to be checked for multiple tables. - - Returns: - bool: True if the text contains more than one table, False otherwise. - """ - return len(re.findall(rf"{START_MARKER}", text)) > 1 - - -def get_page_metadata(page: str) -> Union[List[str], List[Tuple]]: - """ - Extracts and returns metadata from a given page. - - If the page contains a single table, it returns the common metadata for the table. - If the page contains multiple tables, it returns a list of metadata for each table (ordered by position in the page). - If the page contains no tables (or contains a malformed table), it returns an empty list. - - Args: - page (str): The content of the page from which metadata is to be extracted. - - Returns: - List[str]: A list containing metadata. If the page contains a single table, - the list contains one element with the common metadata. If the - page contains multiple tables, the list contains tuples where - each tuple consists of the metadata and the matched dictionary pattern (the corresponding table). - """ - # if the page does not contain a table (or contains a malformed table), return an empty list - if not re.search(START_MARKER, page) or not re.search(END_MARKER, page): - print("Malformed table in get_page_metadata!") - return [] - - # return the common metadata for the table (or the group of tables starting with this one) - if not page_contains_multiple_tables(page): - group_metadata = page[: page.find(START_MARKER)].strip() - group_metadata = re.sub( - START_PAGE_NUM_PATTERN, "\n", group_metadata - ) # Remove page number marker - return [group_metadata] - else: # if the page contains multiple tables - all_tables = extract_snippets_between_markers(page) - table_metadata_map = [] - - for table in all_tables: - match = re.search(DICTIONARY_PATTERN, table, re.DOTALL) - if match: - metadata = table.replace(match.group(0), "").strip() - table_metadata_map.append((metadata, match.group(0))) - - return table_metadata_map - - -def convert_str_to_dict(text: str) -> Dict[str, Any]: - """ - Converts a string representation of a dictionary to an actual dictionary. - - This function searches for a dictionary pattern within the given text and - converts the matched string to a dictionary using `ast.literal_eval`. - - Args: - text (str): The input string that potentially contains a dictionary. - - Returns: - dict: The dictionary extracted from the input string. If no dictionary - pattern is found, an empty dictionary is returned. - """ - match = re.search(DICTIONARY_PATTERN, text) - if match: - dict_str: str = match.group(0) - try: - return ast.literal_eval(dict_str) - except (SyntaxError, ValueError): - print(f"Invalid dictionary format: {dict_str}") - return {} - - -def group_pages_containing_tables( - text_dict: Dict[str, str] -) -> Dict[str, Dict[str, Any]]: - # TODO: add test cases for this function - """ - Groups pages containing tables into start and continuation groups based on patterns. - - Args: - text_dict (Dict[str, str]): A dictionary where keys are page numbers (as strings) and values are the page contents. - - Returns: - Dict[str, Dict[str, Any]]: A dictionary where keys are the start page numbers of groups, and values are dictionaries containing: - - "metadata": Metadata of the start page. - - "group": List of page numbers in the group. - - The function processes each page in the input dictionary, identifies if the page contains a table that matches a start or continuation pattern, - and groups the pages accordingly. If a page does not match any pattern, it is not included in any group. - """ - groups: Dict[str, Dict[str, Any]] = defaultdict(dict) - current_group: List[str] = [] - group_metadata: Optional[str] = None - for page_num, page_content in text_dict.items(): - # We can have one or more tables present on a page. The first table (ONLY) on the page decides if the page will be a start or continuation page. - - first_table_on_page = extract_first_table_from_page(page_content) - - if re.search( - START_PAGE_PATTERN, first_table_on_page - ): # Check if the page matches the start pattern - if current_group: # if a group is already established previously - group_start_page: str = current_group[0] - groups[group_start_page] = { - "metadata": group_metadata, - "group": current_group, - } - current_group = ( - [] - ) # reset the current group, because we've found the start pattern - group_metadata = None - current_group = [page_num] - group_metadata = get_page_metadata(page_content) - elif re.search( - CONTINUATION_PAGE_PATTERN, first_table_on_page - ): # Check if the page matches the continuation pattern - if current_group: - current_group.append(page_num) - else: # If the first page we're processing is a continuation page, we start a new group (edge case) - current_group = [page_num] - group_metadata = get_page_metadata(page_content) - else: # If the page doesn't match any pattern - if current_group: # if we're in the middle of a group, close it - group_start_page = current_group[0] - groups[group_start_page] = { - "metadata": group_metadata, - "group": current_group, - } - current_group = [] # reset the current group - group_metadata = None - if current_group: # save off the current group if we're at the end of the text - group_start_page = current_group[0] - groups[group_start_page] = {"metadata": group_metadata, "group": current_group} - return groups - - -def insert_metadata(metadata: str, table_content: str) -> str: - """ - Inserts metadata at the beginning of the table content. - - Args: - metadata (str): The metadata to be inserted. - table_content (str): The content of the table. - - Returns: - str: The combined string with metadata followed by the table content. - """ - return f"{metadata}\n{table_content}" - - -def insert_column_headers( - data_dict: dict[str, list[str]], columns: list -) -> dict[str, list[str]]: - """ - Inserts column headers into a dictionary of data. It takes the existing column headers and inserts them as the first row of the data. - - Args: - data_dict (dict): The dictionary containing the data to be modified. - columns (list): A list of column headers to be inserted. - - Returns: - dict: A new dictionary with the column headers inserted. If the input dictionary is empty, returns an empty dictionary. - """ - if not data_dict: - print("Dictionary not found in the text.") - return {} - record = list(data_dict.items()) - modified_dict = { - col_name: [col_items[0]] + col_items[1] - for col_name, col_items in zip(columns, record) - } - - return modified_dict - - -def correct_column_headers_and_merge( - text_dict: dict[str, str], groups: dict[str, dict[str, Any]] -) -> dict[str, List[pd.DataFrame]]: - """ - Corrects column headers and merges tables from multiple pages. - - Args: - text_dict (dict[str, str]): A dictionary where keys are page numbers and values are the text content of those pages. - groups (dict): A dictionary where keys are the starting page numbers of groups and values are dictionaries containing group data. - - Returns: - dict: A dictionary where keys are the starting page numbers of groups and values are lists of DataFrames representing the merged tables. - """ - - page_tables_map = {} - - columns_to_use: List[str] = [] # for mypy - - for group_start_page, group_data in groups.items(): # Loop through groups - dfs_list = [] - columns = None - - for page in group_data["group"]: # Loop through pages in the group - page_content = text_dict[page] - - str_dicts = get_str_dictionaries_from_text(page_content, only_first=False) - for str_dict in str_dicts: - data_dict = convert_str_to_dict(str_dict) - # if the page contains multiple tables, rewrite the latest column headers each time - # Otherwise, use the column headers from the first table in the group - columns_to_use = ( - data_dict.keys() if page == group_start_page else columns_to_use - ) - - col_corrected_dict = insert_column_headers(data_dict, columns_to_use) - - if ( - page == group_start_page - ): # on the first table, we've already changed the keys to be the first row, so we need to drop that row - df = pd.DataFrame(col_corrected_dict).drop(index=0) - else: - df = pd.DataFrame(col_corrected_dict) - - df["page_num"] = page - - dfs_list.append(df) - - tables = dfs_list - page_tables_map[group_start_page] = ( - tables # List of dataframes corresponding to the tables in the group - ) - return page_tables_map - - -def group_and_merge_tables(text_dict: dict[str, str]) -> tuple[dict, dict]: - """ - Groups pages containing tables and merges the tables after correcting column headers. - - Args: - text_dict (dict[str, str]): A dictionary where keys are page identifiers and values are the text content of the pages. - - Returns: - tuple[dict, dict]: A tuple containing: - - groups (dict): A dictionary where keys are group identifiers and values are lists of page identifiers that belong to each group. - - page_tables_map (dict): A dictionary where keys are page identifiers and values are the merged tables after correcting column headers. - """ - groups = group_pages_containing_tables(text_dict) - - page_tables_map = correct_column_headers_and_merge( - text_dict, groups - ) # extract the tables from all pages, correct the col headers, put the individual tables in the df, then merge those dfs - - return groups, page_tables_map - - -def split_table_to_pages(groups: dict, page_tables_map: dict, row_limit: int) -> dict: - """ - Splits tables into pages based on the provided groups and page tables map. - Args: - groups (dict): A dictionary where keys are the starting page numbers of groups and values are dictionaries containing group data. - page_tables_map (dict): A dictionary mapping page numbers to lists of DataFrames representing tables on those pages. - row_limit (int, optional): The number of rows per table split. Defaults to 5. - Returns: - dict: A dictionary where keys are the starting page numbers of groups and values are dictionaries mapping page numbers to lists of related tables. - """ - group_table_split_info = {} - - for group_start_page, group_data in groups.items(): # Loop through groups - dfs_list = page_tables_map[group_start_page] # get list of tables for the group - metadata_list = group_data["metadata"] - - if all( - [isinstance(metadata, tuple) for metadata in metadata_list] - ): # if the metadata is a list of tuples, this page has multiple tables - metadata_list = [ - metadata[0] for metadata in metadata_list - ] # Just extract the metadata strings (the second element of the tuple in the metadata is a text dictionary snippet) - - # if the group contains multiple pages with common metadata, duplicate the metadata for each page - # This handles cases: - # - when the group contains multiple pages with common metadata, this will work - # - when the page contains multiple tables which start AND end on the single page, this will work - # An unhandled edge case, when the page contains multiple tables in this scenario: - # - when the LAST table of a page is the beginning of a table continued onto the next page, we won't get the metadata right - - # If the group has a single page with multiple tables - if len(group_data["group"]) > 1: # if the group contains multiple pages - metadata_list = [ - metadata_list[0] for _ in range(len(dfs_list)) - ] # duplicate the metadata for each page - - if ( - len(group_data["group"]) == 1 - ): # its a single page group with len(dfs_list) number of tables - eg [6]->[6,6,6,6] if the group contains just page "6" and page "6" has 4 tables - group_data["group"] = [group_data["group"][0] for _ in range(len(dfs_list))] - - chunked_tables_page_mapping = defaultdict(list) - - # loop through each page, metadata, and dataframe in the group - for page_num, metadata, df in zip(group_data["group"], metadata_list, dfs_list): - num_rows = df.shape[0] - num_tables = math.ceil(num_rows / row_limit) # number of output tables - - related_tables = [] - - for i in range(num_tables): - start_row = i * row_limit - end_row = min((i + 1) * row_limit, df.shape[0]) - table_df = df.iloc[start_row:end_row, :] - - str_df = str(table_df.drop(columns=["page_num"]).to_dict(orient="list")) - - table_dict = insert_metadata(metadata, str_df) - - assert ( # TODO: convert to `raise` instead of `assert` - table_df["page_num"].nunique() == 1 - ), "All rows in a table should belong to the same page" - - page_num = table_df["page_num"].unique()[0] - - related_tables.append( - table_dict - ) # these tables are splits of a larger table from one page - - chunked_tables_page_mapping[page_num].append(related_tables) - - group_table_split_info[group_start_page] = chunked_tables_page_mapping - - return group_table_split_info - - -def replace_tables_in_page( - page_num: int, modified_text_dict: dict, new_tables_list: list -) -> None: - """ - Replaces existing tables within pages to modified (corrected) tables. - Args: - page_num (int): The page number where the reinsertion should occur. - modified_text_dict (dict): A dictionary containing the text of each page, with page numbers as keys. - new_tables_list (list): A list of lists, where each inner list contains tables to be inserted. - Returns: - None: This function modifies the `modified_text_dict` in place. - """ - - text = modified_text_dict[page_num] - - formatted_tables = [] - - for ( - table_list - ) in new_tables_list: # Format new tables for insertion back into pages - lst = [] - - for table in table_list: - lst.append(f"{START_MARKER}\n{table}\n{END_MARKER}") - - concatenated_tables = "\n".join(lst) - - formatted_tables.append(concatenated_tables) - - detect_tables_pattern = rf"({START_MARKER}.+?{END_MARKER})" - - tables_to_replace = re.findall(detect_tables_pattern, text, re.DOTALL) - - for original_table, replacement_table in zip(tables_to_replace, formatted_tables): - text = re.sub( - re.escape(original_table), replacement_table, text, count=1, flags=re.DOTALL - ) - - modified_text_dict[page_num] = text - - -def reinsert_new_tables_to_text(group_table_split_info: dict, text_dict: dict) -> dict: - """ - Take what's in groups, apply `replace_tables_in_page` to each group, and then reinsert the tables back into the text. - This is really a wrapper function for `replace_tables_in_page` which goes through each page and applies the function. - - Args: - group_table_split_info (dict): A dictionary where the keys are the starting page numbers of groups and the values - are dictionaries mapping page numbers to lists of split tables. - - Returns: - dict: A modified version of the original text dictionary with the tables reinserted. - """ - modified_text_dict = copy.deepcopy(text_dict) - - for group_start_page, chunked_tables_page_mapping in group_table_split_info.items(): - - for page_num in chunked_tables_page_mapping.keys(): - split_tables_list = chunked_tables_page_mapping[page_num] - # perform the reinsertion (inplace) - replace_tables_in_page(page_num, modified_text_dict, split_tables_list) - - return modified_text_dict - - -def split_tables_to_separate_subpages(text_dict: dict[str, str]) -> dict[str, str]: - """ - Splits the text content of each page in the input dictionary into separate subpages based on a table end marker. - - Args: - text_dict (dict[str, str]): A dictionary where keys are page identifiers and values are the text content of those pages. - - Returns: - dict[str, str]: A new dictionary where keys are modified page identifiers (including subpage indices) and values are the split text content. Empty strings are removed from the result. - """ - new_text_dict = {} - for page in text_dict.keys(): - # split the text into separate pages based on the table end marker - if END_MARKER in text_dict[page]: - new_text_list = re.split( - rf"(?<={END_MARKER})", text_dict[page] - ) # this regex will split on the end marker, and keep the end marker in the text - for i, text in enumerate(new_text_list): - new_text_dict[f"{page}.{i}"] = text - else: - new_text_dict[page] = text_dict[page] - return {k: v for k, v in new_text_dict.items() if v.strip()} # remove empty strings diff --git a/fieldExtraction/tests/test_string_utils.py b/fieldExtraction/tests/test_string_utils.py index 03aa19f..e9af0ad 100644 --- a/fieldExtraction/tests/test_string_utils.py +++ b/fieldExtraction/tests/test_string_utils.py @@ -151,13 +151,12 @@ class TestStringUtils: result = contains_reimbursement(text, page) assert result == expected - def test_invalid_input_type(self, capsys): + def test_invalid_input_type(self, caplog): text = ["This is a list, not a dictionary or string."] page = "1" result = contains_reimbursement(text, page) assert result is False - captured = capsys.readouterr() - assert "contains_reimbursement - Invalid data type" in captured.out + assert "contains_reimbursement - Invalid data type" in caplog.text @pytest.mark.parametrize( "value, expected",