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Program to manage some common clinical research tasks from the command line

Project description

Program to manage some common clinical research task from the command. Very much a work in progress line

Getting Started

This program requires python 3 and a few external packages. Strongly advise installing into a virtual environment as I’m new at this!


Requires python and above

$ python 3.5

$ pip install openpyxl
$ pip install xlrd
$ pip install pandas
$ pip install numpy
$ pip install matplotlib


$ pip install clinical_research_study_manager

Get Help

$ clinical_research_study_manager -h
optional arguments:
  -h, --help            show this help message and exit
  -create_project Project_Name
                        Creates a new project titled Project_Name in the
                        Projects directory
  -load_project Project_Name
                        Loads Project Project_Name from the Projects directory
                        for study activities
  -list_projects        List available projects to load

Create New Project

$ clinical_reseaerch_study_manager -create_project Testing
Creating new project titled Testing
Created patient_data[phi] for project Testing at /home/beliefs22/Clinical_Research_Manager_Projects/Projects/Testing
Created patient_data[de_identified] for project Testing at /home/beliefs22/Clinical_Research_Manager_Projects/Projects/Testing
Created logs for project Testing at /home/beliefs22/Clinical_Research_Manager_Projects/Projects/Testing
Created logs/logs_with_phi for project Testing at /home/beliefs22/Clinical_Research_Manager_Projects/Projects/Testing
Created data_visualization for project Testing at /home/beliefs22/Clinical_Research_Manager_Projects/Projects/Testing
Created log files for project Testing
Created Screening_Log.xlsx log for Testing at /home/beliefs22/Clinical_Research_Manager_Projects/Projects/Testing/logs/Screening_Log.xlsx
Created Master_Linking_Log.xlsx log for Testing at /home/beliefs22/Clinical_Research_Manager_Projects/Projects/Testing/logs/logs_with_phi/Master_Linking_Log.xlsx
Created Follow_Up_Log.xlsx log for Testing at /home/beliefs22/Clinical_Research_Manager_Projects/Projects/Testing/logs/Follow_Up_Log.xlsx
Created Enrollment_Log.xlsx log for Testing at /home/beliefs22/Clinical_Research_Manager_Projects/Projects/Testing/logs/Enrollment_Log.xl

Load Specific Project

$ clinical_research_study_manager -load_project Testing
Opening Testing
1. Manage Logs
2. Query Logs
Please choose what actions you would like to take, q to quit.

List Available Projects

$ clinical_research_study_manager -list_projects
Current Projects are:
1 : Testing

Running the tests

$ clinical_research_study_manager_tests
Launching unittests with arguments python -m unittest /home/beliefs22/PycharmProjects/clinical_research_study_manager/build/lib/clinical_research_study_manager/tests/ in /home/beliefs22/PycharmProjects/clinical_research_study_manager/build/lib/clinical_research_study_manager/tests
testing invalid age input
testing invalid date input
testing invalid eligibility status input
testing invalid enrollment status input
testing invalid sex input
testing invalid time input

testing valid age input
testing valid date input
testing valid eligibility status input
testing valid enrollment status input
testing valid initials input
testing valid reason ineligible input
testing valid reason not enrolled input
testing valid sex input
testing valid time input

Ran 15 tests in 0.022s


These test will check valid and invalid input expected from the user


Seth Pitts


This project is licensed under the MIT License - see the LICENSE.txt file for details

Project details

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