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PEDSnet_DQA_Documentation.md

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Instructions for Executing the DQA Workflow

Prerequisites

Required Downloads

Create RxNorm Reference Tables

Execute DDL_RxNorm_Tables.sql

Note: If using a custom schema for DQA tables, please change all references to schema "dqa" in the above script into the custom schema.

(Oracle-only) Create Views

Create views in database by running Library/Oracle_LowerCaseViews.sql

  • Replace "CDM_VIEW", "DQA_VIEW", and "VOCABULARY_VIEW" with appropriate schemas before running

Apply Data Quality Checks

Create Configuration Files

Create a DQA configuration file named PEDSnet_config.yml using the template specified in PEDSnet_config_sample.yml of the same folder and an Argos configuration file named argos_config.json using the template specified in Argos Configuration File Structure.

Example

db:
 driver             : PostgreSQL (PostgreSQL, Oracle, MySQL, SQLite, or SQL Server)
 dbname	            : TestDb (Name of Database)
 dbuser	            : TestUser
 dbpass	            : TestUserPassword123
 dbhost             : http://testdbhost.com/
 dbport	            : 5432
 schema	            : pedsnet_domain_schema (Name of schema that holds PEDSnet domain tables)
 vocab_schema       : vocabulary (Name of schema that holds OMOP vocab tables)
 dqa_schema         : dqa (Name of schema that holds intermediate tables created for DQA purposes)
 argos_config_file_path : ~/Documents/.argos/argos_config.json (User-created location of ohdsi_argos configuration JSON file)
reporting:
 site_directory     : ~/Documents/test_directory (User-created temporary location for output of DQA reports)
 etl_script_version : v10
 dqa_script_version : 2.5.0_1 (See note)
 site               : SiteName 
 cdm                : PEDSnet
 conventions_version : 2.5.0 (the PEDSnet CDM ETL conventions version)

Notes:

  • User created directories can be replaced with other locations, so long as the settings indicate them appropriately
  • See release for dqa_script_verison. This corresponds to the latest release version of the DQA Scripts.
  • See ohdsi-argos for installation and configuration instructions.
    • For Oracle users, Argos src_name should be "oracle", and Argos dbname should be a connection string formatted as "(DESCRIPTION=(ADDRESS=(PROTOCOL=tcp)(HOST=your_host)(PORT=1521))(CONNECT_DATA=(SID=your_sid)))".

Setup

setwd("/path/to/repo/")
source("Run_DQA.R")

Level 1

All Tables

runDQA(level=1)

Single Table

generateReportDependencies()

generateSingleReport(level=1, report="table_name")

"table_name" examples include: "person", "fact_relationship", "visit_occurrence", etc

** Note: generateReportDependencies() only needs to be run once, before generating any number of single reports. It is included in the beginning of runDQA(level=1), and does not need to be run if runDQA(level=1) was used.

Level 2

All Tables:

runDQA(level=2)
  • After Level 1, the database connection may occasionally close. To re-establish it, run source("Run_DQA.R") again before starting Level 2

Single Table:

generateSingleReport(level=2, report="table_name")

"table_name" examples include: "procedure", "drug", "measurement", etc

Generate feedback (GitHub) (DCC-Only)

To investigate differences between the previous data version and the current and generate feedback, follow the instructions here.