Code

Parquet input to OS#186

Code

Merged

milanmlft merged 29 commits intomainSAFEHR-data/PIXL:mainfrom rmg/parquet_inpSAFEHR-data/PIXL:rmg/parquet_inpCopy head branch name to clipboardDec 21, 2023

+595-235

Commits

Commits on Dec 14, 2023

• Add -e to pip install command in cli test

  ruaridhg

  committed
  5b60fd4

• Added flag for csv=True and ran tests for cli

  ruaridhg

  committed
  68cc3bb

Commits on Dec 15, 2023

• Added test for parquet directory and messages_from_parquet func

  ruaridhg

  committed
  91b5dfe

• Use resources fixture to find test parquest files. Make input options

  Show description for 20988f7
  jeremyestein

  committed
  20988f7

Commits on Dec 18, 2023

• Add synthetic "private" OMOP data taken from the issue

  jeremyestein

  committed
  e6bfb7d

• Add dependency for reading parquet files

  jeremyestein

  committed
  faf50dc

• Add procedure occurrence id column to message. Use pandas merge instead

  Show description for 9129be3
  jeremyestein

  committed
  9129be3

• Remove option for CSV cohort file

  jeremyestein

  committed
  273e38e

• Merge branch 'main' into rmg/parquet_inp

  jeremyestein

  committed
  bbc101b

• formatting changes

  jeremyestein

  committed
  2245c96

• Linting fixes

  jeremyestein

  committed
  48efeea

• Fix other uses of modified method

  jeremyestein

  committed
  48db87a

• ruff fix

  jeremyestein

  committed
  0915cc8

• Downstream class needs new attribute as well

  jeremyestein

  committed
  a9691a1

• Add type annotations to test_messages_from_parquet()

  milanmlft

  committed
  77da37a

• Add project name and OMOP ES timestamp to rabbitmq messages

  milanmlft

  committed
  3b37183

• Update serialise() callers with new arguments

  milanmlft

  committed
  42b1c85

Commits on Dec 19, 2023

• Add project_name and omop_es_timestamp fields to ImagingStudy class

  milanmlft

  committed
  bf39b46

Commits on Dec 20, 2023

• Refactor message serialisation and deserialisation (#197)

  Show description for 90b6672
  milanmlft

  authored
  90b6672

• Format README

  milanmlft

  committed
  a243f6f

• Update documentation with new parquet inputs

  milanmlft

  committed
  b4c7a51

• Update system test to use parquet files

  milanmlft

  committed
  10dd3e6

Commits on Dec 21, 2023

• Move extract_summary.json one level up and update docs

  milanmlft

  committed
  1192210

• Change parquet-dir to a click argument instead of option

  milanmlft

  committed
  6b4f38c

• click.argument doesn't have a help parameter

  Show description for 3a04feb
  milanmlft

  committed
  3a04feb

• Slim down parquet test files to only those needed

  milanmlft

  committed
  1a2fab4

• Raise more appropriate exceptions for missing file or directory

  milanmlft

  committed
  c4cecc9

• Print log message about messages created during regular runs

  milanmlft

  committed
  76c3897

• Update error message for parquet files

  milanmlft

  committed
  845e826