python

Introduction

The document upload example code requires Python 3.6.8+ to run.

Given a CSV file with the names of documents to upload, this program will parse each row, read in the file from disk, and upload the document to the chart specified by the patient_id column in the CSV.

Setup

# Create a virtualenv for imported 3rd party library (requests)
$ /usr/bin/python -m venv my_venv

# Activate virtualenv
$ source my_venv/bin/activate

# Bash shell indicates active virtualenv
# Type 'deactivate' when done
(my_venv) $

# Install requests and python-magic
(my_venv) $ pip install requests python-magic
Collecting requests
  Using cached https://files.pythonhosted.org/packages/2d/61/08076519c80041bc0ffa1a8af0cbd3bf3e2b62af10435d269a9d0f40564d/requests-2.27.1-py2.py3-none-any.whl
Collecting python-magic
  Using cached https://files.pythonhosted.org/packages/6c/73/9f872cb81fc5c3bb48f7227872c28975f998f3e7c2b1c16e95e6432bbb90/python_magic-0.4.27-py2.py3-none-any.whl
Collecting charset-normalizer~=2.0.0; python_version >= "3" (from requests)
  Using cached https://files.pythonhosted.org/packages/06/b3/24afc8868eba069a7f03650ac750a778862dc34941a4bebeb58706715726/charset_normalizer-2.0.12-py3-none-any.whl
Collecting idna<4,>=2.5; python_version >= "3" (from requests)
  Using cached https://files.pythonhosted.org/packages/fc/34/3030de6f1370931b9dbb4dad48f6ab1015ab1d32447850b9fc94e60097be/idna-3.4-py3-none-any.whl
Collecting urllib3<1.27,>=1.21.1 (from requests)
  Using cached https://files.pythonhosted.org/packages/fe/ca/466766e20b767ddb9b951202542310cba37ea5f2d792dae7589f1741af58/urllib3-1.26.14-py2.py3-none-any.whl
Collecting certifi>=2017.4.17 (from requests)
  Using cached https://files.pythonhosted.org/packages/71/4c/3db2b8021bd6f2f0ceb0e088d6b2d49147671f25832fb17970e9b583d742/certifi-2022.12.7-py3-none-any.whl
Installing collected packages: charset-normalizer, idna, urllib3, certifi, requests, python-magic
Successfully installed certifi-2022.12.7 charset-normalizer-2.0.12 idna-3.4 python-magic-0.4.27 requests-2.27.1 urllib3-1.26.14
WARNING: You are using pip version 20.2.3; however, version 22.3.1 is available.
You should consider upgrading via the '/home/sstuck/.pyenv/versions/3.9.2/bin/python3.9 -m pip install --upgrade pip' command.

Running

(my_venv) $ python upload.py
Usage: upload.py WebChartUrl docpath mrcsvfile wcuser

(my_venv) $ python upload.py "https://zeus.med-web.com/webchart/wctsstuck/webchart.cgi" ./ sample_data.csv dave
Please enter the webchart password for user [ dave ]: =>
Importing file [ 1 / 2 ]  ccr.xml => MIE-10019
Importing file [ 2 / 2 ]  example.pdf => MIE-10019

Document import process complete:
Uploaded: 2
Skipped: 0
Errors: 0

See import.log for details