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Ktokunaga/30/add marketingyears to distribs #60

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Ktokunaga/30/add marketingyears to distribs #60

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Commits on May 16, 2021

  1. Initial mdt package structure

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  2. Initial database module within mdt package

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  3. Initial synthea module

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  4. Moved mdt_functions methods into rxclass.py

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  5. Moved mdt_functions into database.py

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  6. Moved mdt_functions into synthea.py

    @yevgenybulochnik
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  7. Moved mdt_functions into utils.py

    @yevgenybulochnik
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  8. Initial setup.py

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  9. Comment out entrypoint setup in setup.py for now

    @yevgenybulochnik
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  10. Initial run_mdt.py main script/module

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  11. added function to download RxNorm,

    @Bridg109 @yevgenybulochnik
    Bridg109 authored and yevgenybulochnik committed May 16, 2021
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  12. adds to download and load RxNorm, Pathlib use

    @Bridg109 @yevgenybulochnik
    Bridg109 authored and yevgenybulochnik committed May 16, 2021
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  13. ignore .vim, .ds_store and python egg-info

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  14. Meps utils module with get_dataset function

    @yevgenybulochnik
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  15. Move meps_lists vars into new meps module columns.py

    @yevgenybulochnik
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  16. Change meps get_dataset to get response.content vs response

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  17. Allow modules to be imported from package namespace

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  18. Add load_meps function to database.py

    @yevgenybulochnik
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  19. Add load_meps to main function of run_mdt module

    @yevgenybulochnik
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  20. Require requests and pandas to install if mdt is installed

    @yevgenybulochnik
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  21. Change package install name to mdt, include .sql files in packages

    @yevgenybulochnik
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  22. Add sql packages to rxnorm & meps, include sql files

    @yevgenybulochnik
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  23. Initial get_sql function to get meps package sql files

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  24. Import lib requires python >3.7

    @yevgenybulochnik
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  25. Missing comma in setup.py

    @yevgenybulochnik
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  26. Use meps utils function to get reference sql

    @yevgenybulochnik
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  27. Add get_sql function to rxnorm utils

    @yevgenybulochnik
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  28. Rename synthea.py to utils.py

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  29. Basic mdt config.py, will need future refactor

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  30. Add missing payload constructor import

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  31. Add missing urllib import

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  32. Add missing imports, re, pandas, meps, database functions

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  33. Move rx_api script into run_mdt.py, fix imports, currently broken

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  34. Use meps get_sql function

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  35. Use meps get_sql function in mdt.utils

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  36. Monkey patch to read age and age values from python config.py

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  37. Skip loading rxnorm and meps if MDT.db exists

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  38. Uses system args to pass rxclass_id and rxclass_rela to run_mdt.py

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  39. Add rxnorm dosage form sql

    @yevgenybulochnik
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  40. Load dfg table with load_rxnorm

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  41. Add filter_by_df function to mdt.utils, missing path.exists added

    @yevgenybulochnik
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  42. Initial FDA subpackage setup

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  43. fda utils module setup, get_dataset function

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  44. load_fda function setup

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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  45. Dev setup in readme

    @yevgenybulochnik
    yevgenybulochnik committed May 16, 2021
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Commits on May 17, 2021

  1. #30 adding marketyears to the generate_module function 

    Taking Eugene's restructure branch (from PR #59), this updates the following:
1. Added cleaned version of Rob's code to database.by --> creates an ingredient_rxcui_year table & a product_rxcui_year table, for their respective distributions in generate_module
2. added 'year' column to the generate_module dataframes/CSV files.
3. fixed default_probability typo in utils.py (if idx == 1 --> changed to if idx == 0)
    @kristentaytok
    kristentaytok committed May 17, 2021
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