https://github.com/ctsit/redi-uniq

https://github.com/ctsit/redi-uniq

redi reviewphilip

Last synced: about 1 year ago
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• Host: GitHub
• URL: https://github.com/ctsit/redi-uniq
• Owner: ctsit
• Archived: true
• Created: 2017-02-10T15:58:46.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2017-02-16T15:13:58.000Z (over 9 years ago)
• Last Synced: 2025-02-27T20:32:32.089Z (over 1 year ago)
• Topics: redi, reviewphilip
• Language: Python
• Homepage:
• Size: 27.3 KB
• Stars: 0
• Watchers: 8
• Forks: 2
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • Authors: AUTHORS.md

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README

          
# RED-I Uniq - A small version of the RED-I UniqueIds project

Designed to process RED-I data in individual files, the ability to run a single

person is operational, to run a group of people is not yet, but will be configurable

## Contents of the Repository

* The Makefile:

	* Pre RED-I Tasks

		* make - will show all available make targets

		* make emr - Get the EMR data (based on a RED-I settings.ini file)

		* make filter - Filter 'raw.txt' based on a configured rule list

		* make count - Count lines in 'raw.txt' and compare to per participant files

		* make uniq - Create the unique file based from a raw file

	* During RED-I Tasks

		* make lastlog - Get the last log for a particular subject (ID=000-0000)

	* Post RED-I Tasks

		* make watch - Watch the state of the current run for a specific site

		* make cprep - Copy reports files from complete runs

		* make merge - Merge the reports files into JSON for email report

		* make email - Send the reports to target recipient

* All scripts:

	* Shell Scripts:

		* collect_reports.sh - Used by 'make cprep', this script goes through all the user_data participant files and looks for the report file that is set in the configuration (uniq.ini). These reports are generated by RED-I if the run actually completes

		* count_lines.sh - This is used by 'make count', this script goes through the participant files in user_data and compares the total line count with the raw files line count.

		* cron.sh - This is the script that is setup in a cron entry, which triggers get_emr.sh, filter_raw.sh, get_unique.sh, run_redi.sh, and collect_reports.sh (based on configuration in uniq.ini)

		* filter_raw.sh - Used by 'make filter', this script goes through the raw file and runs the python script filter_raw.py, using a rules.json file to clean the raw file.

		* get_config.sh - Used to be the traffic cop, this will collect the path to your uniq.ini file.

		* get_emr.sh - Used by 'make emr', this script uses a RED-I settings.ini file (emr_* variables) and collets a fresh copy of the EMR data for the configured site.

		* get_last_log.sh - Used by 'make lastlog', this script collects the latest log path from a particular participant (specified by ID=000-0000).

		* get_unique.sh - Used by 'make uniq', this script is the script that started the whole idea. It parses the raw.txt data and collects all subjects based on a column given in uniq.ini.

		* merge_reports.sh - Used by 'make merge', this script collects all the designated output XML files from RED-I and merges them into a single report JSON file

		* run_redi.sh - This is the script that actually triggers the RED-I process to run

		* send_email.sh - Used by 'make email', this script collects the output from 'make merge' and sends a customized email to the configured recipients

		* watch_run.sh - Used by 'make watch', this script looks at the latest RED-I run, based on configuration from uniq.ini for a specific site.

	* Python Scripts:

		* __init__.py - Um duh!

		* filter_raw.py - Used in the execution of 'make filter', which runs filter_raw.sh.

		* get_unique.py - Used in the execution of 'make uniq', which runs get_unique.sh.

		* merge_reports.py - Used in the execution of 'make merge', which runs merge_reports.sh

		* send_email.py - Used in the execution of 'make email', which runs send_email.sh

		* myrules.py - Yes, the only one not named something_somethingelse. This script is the 'decision.py' of this process, and sets the available rule types for the filter process.

		

## Danger

Only tested with redi version 0.15.4