pyproject requirements, prep for logging fixes
* remove chroma
* update project name to "doczy-field-extraction" in pyproject.toml
* update lock file
* replace print statements with logging for better traceability in process_file function
* replace print statements with logging for improved error tracking and information logging
* replace print statements with logging for improved error handling and traceability
* replace print statements with logging for improved error handling in llm_utils and string_utils
* remove unused table_utils module; supplanted by table_funcs and unreferenced
* replace capsys with caplog in test_invalid_input_type for improved logging of invalid input
Approved-by: Katon Minhas
Refactor/one time io
* Delete client work
* Streamline imports
* Fix list class
* Update tests
* Clear code funcs test
* Fix unit tests
* Single read code funcs
* Single-read model
* Single-load embeddings
* Successful E2E test
* update unit tests
* Update importsg
* Reload poetry.lock
* remove old exhibit header function
* Remove aarete_derived generic function
* remove align and format tables
* Remove strings to dict
* references
* Clear code
* Move preprocessing_funcs
* remove keywords
* refactor postprocessing_funcs
* Pass unit test - remove qa_qc directory
* Black and isort
* remove print
Approved-by: Alex Galarce
DRAFT: Bugfix/effective date fix
* Merged in bugfix/extra-fields (pull request #500)
Do not run Exhibit level prompt if there are no exhibit level fields
* Do not run Exhibit level prompt if there are no exhibit level fields
* Update dynamic test
* Remove test from one-to-n test module
* Update test
* Fix unit test
Approved-by: Alex Galarce
* Merged in bugfix/tin-npi-prompt-fixes (pull request #499)
Bugfix/tin npi prompt fixes
* Change delimiter for other provider information from comma to pipe
* filter out invalid providers
* Update extraction and formatting instructions for provider entities in TIN_NPI_TEMPLATE
* Merged main into bugfix/tin-npi-small-bugfixes
* Refactor deduplication logic to use string_utils for checking empty provider fields
* Merge branch 'bugfix/tin-npi-small-bugfixes' of https://bitbucket.org/aarete/doczy.ai into bugfix/tin-npi-small-bugfixes
* Update deduplication logic to exclude providers with 'UNKNOWN' TIN, NPI, or NAME
* Merge remote-tracking branch 'origin/main' into bugfix/tin-npi-small-bugfixes
* Fix deduplication logic to not drop subsequent names
* Fix formatting of provider names in deduplication logic
* add payer name filtering
* reorder execution order to allow to find payer_name first
* Add handling for previously unfound group providers in identify_group_provider function
* Merge remote-trackin…
* Merged in feature/update-testbed-script (pull request #501)
Feature/update testbed script
* Update preprocessing
* Update preprocessing
* remove quit
* Update date for filename
* Merged main into feature/update-testbed-script
Approved-by: Alex Galarce
* Merged in bugfix/smart-chunks (pull request #503)
missing of text in chunks fixed
* missing of text in chunks fixed
Approved-by: Katon Minhas
* Merged in feature/rework-reimb-tin-npi (pull request #502)
Feature/rework reimb tin npi
* use LLM for reimb_[tin/npi/name]
* Merge remote-tracking branch 'origin/main' into feature/rework-reimb-tin-npi
* Merge remote-tracking branch 'origin/main' into feature/rework-reimb-tin-npi
* deduplicate tin/name/npi before adding to prompt
* Pull out prompt and llm_response in methodology_breakout_single_row for easier debugging
* Refactor reimbursement_tin_npi to handle multiple providers and update valid TIN, NPI, and NAME fields accordingly
* Reorder REIMB_PROV_NAME field in investment_prompts.json
* Update REIMB_PROV_NAME prompt to specify valid values for provider names
* Remove valid_values constraint from prov_name to raise accuracy
* Remove debugging print statements from reimbursement_tin_npi and related functions
* Remove debugging print statements from run_provider_info_fields function
* Merge remote-tracking branch 'origin/main' into feature/rework-reimb-tin-npi
* Remove debugging print statem…
* Merged in feature/preformat-single-quotes-input (pull request #506)
Replace double quotes with single quotes in context strings for parsability
* Replace double quotes with single quotes in context strings for parsability
* Merged main into feature/preformat-single-quotes-input
Approved-by: Katon Minhas
* updated sig pages fnxn
* Merge branch 'main' into bugfix/effective_date_fix
* poetry add pymupdf
* created vision funcs
* Merged main into bugfix/effective_date_fix
* fixed pipeline issue
* updated string_utils_test
* updated test values
* updated extract signature page fxn
* updated test values
* updated test values
* Merged main into bugfix/effective_date_fix
* Prompt template in all-caps
* remove debugging prints
* Merged main into bugfix/effective_date_fix
* Change vision to False by default
* Change vision to False by default
* fix tests
* fix tests
Approved-by: Katon Minhas
DRAFT: Feature/split out error log
* Refactor result handling to separate successful and error results in processing
* Add forced exception for testing in safe_process_file function
* Merged main into feature/split-out-error-log
* main.py edited online with Bitbucket
* Add support for error output type in write_s3 function
Approved-by: Katon Minhas
Fix load_embeddings()
* move datetime_str function to string_utils module
* enhance load_embeddings to create directory structure and handle download errors
* Merged main into feature/reimbursement-primary-optimizization
Approved-by: Katon Minhas
Bugfix/proc code lists
* Add admit type code
* add proc mod description
* Add bill type pos mapping
* Merged main into feature/proc-desc
* Uncomment test code
* Bugfix
* script optimisation for codes
* modified is empty function in string utils
* Remove test.py
* bug fix to handle list of proc_codes
* Merged main into bugfix/proc-code-lists
* changed any method to all method in list handling
* code mapping moved outside to run once
* Merge branch 'feature/daip2-97' into bugfix/proc-code-lists
* merge conflict fixed
* merge conflicts fixed
* incorporated latest changes from main
* Merged main into bugfix/proc-code-lists
* Move load all dataset to io_utils
* Fix list is_empty
* Updated poetry.lock
* Docstring
* Docstrings
* Merge branch 'main' into bugfix/proc-code-lists
* bug fix
Approved-by: Mayank Aamseek
Approved-by: Alex Galarce
feature/dynamic and generalized branch
* included txt files for nltk_data
* move nltk_data to src
* Fix last upload count
* Last upload count bugfix
* Fixed B processing
* Remove client-specific postprocessing
* split consolidate_output
* Run by file
* Fix output
* Reconfigure smart_chunk fields
* Add Full Context
* Fix merge conflicts
* Regex, Smart-Chunked, and Full working - not adding smart-chunked-->full when necessary
* Modernized run_full_context_fields()
* Switched set to list in field_context
* Move fields from smart_chunked to full_context as part of 'field_context' function
* Working version with placeholders
* Update poetry and pyproject
* Update s3 output
* Remove deprecated unit test
* Updated error messages
* Updated smart chunk ac name to one to one
* Update dependencies - end-to-end test for write s3 functional
* Add basic multithreading
* Send individual output to s3/local
Approved-by: Alex Galarce
Task/unit tests investment and client
* move io_utils.py
* add __init__.py
* refactor: move string_funcs and update import paths to use utils namespace
* rename string_funcs to string_utils
* move and rename table_utils.py
* refactor: rename claude_funcs to llm_utils in multiple files
* update unit tests
* added unit tests for src/string_utils.py
* added unit tests for src/table_utils.py
* added unit tests for src/llm_utils.py
* added unit tests for src/io_utils.py
* Merge branch 'main' into task/unit-tests-investment-and-client; TODO: fix unit tests
* Unit tests to fix
* fix unit tests
* fix invalid references
Approved-by: Alex Galarce
Refactor/split investment and client
* refactor: clean up tests
* Renamed tests/qcqa to tests/qa_qc for consistency
* comment out faulty test - see docstring note at top
* split to client/investment
* add __init__.py to investment and client to avoid mypy confusion
* fix imports
* update imports for consistency across investment module
* move back to one config
* try changing import to relative
* add init.py to src
* try relative import
* try one more sys.path.append
* fix path for client main
* fix imports in file_processing
* make prompts common
* move keywords out to `src`
* move smart_chunking_funcs to `src`
* fix mypy error
* start moving to explicit imports
* remove old keywords and fix imports for keywords and prompts
* change all imports to full paths
* fix unit tests
* add readme for new way of running things
* isort after all that import work
* remove unused sys.path.append from some tests
Approved-by: Katon Minhas
Alex Galarce