The EMR Exporter is a component of the Health Data Coalition technology suite. It is used to extract the data necessary to populate the Universal Schema from an Electronic Medical Record (EMR) relational database and transfer that data to an Endpoint. It is vendor agnostic and should work with all EMRs that are backed by a relational SQL database.
The following requirements must be met to run the EMR Exporter:
- The source EMR Database must be MySQL or Postgres. Support for further DBMS will be added as necessary.
- A role/user must be created in the EMR Database with read-only access to the database. A database role that has write-access is not recommended as it breaks the principle of least privilege.
The EMR Exporter must be executed on the same server that is running the EMR Database.See Version 1.10 notes below.- A private/public key pair must be generated on the EMR Database server. The public key must be installed onto the target server (eg Endpoint).
- The target server must have a user that can connect over ssh via public key authentication.
For production usage, it is recommended to use one of the pre-compiled releases. These releases are distributed as a single executable file that have no dependencies.
On the EMR Server:
- Download the executable from the Release page and save to an appropriate location. Releases are created for Windows, Linux and Mac OS.
- Open a command prompt and browse to the executable file. Run the executable with --init flag (eg ./emr-exporter-win.exe --init)
- Wait for the initialization to complete. It may take a minute to generate secure keys.
- Email the output of the initialization script to the HDC. (TBD)
- Edit the generated .env file. Specifically, update the source and target sections.
Add the Postgres service user (eg NETWORK SERVICE on Windows) to have read/write access to the generated working dir.See Version 1.10 notes below.- Run the application manually to ensure it works (eg ./emr-exporter-win.exe)
- Schedule an automated tasks to run daily. This application should not require administrative access to run.
| Command | Description |
|---|---|
npm install |
Install package dependencies. Must be run before npm start. |
npm start |
Run the exporter. |
npm test |
Run the automated test: which don't exist. Anyone with free time? |
npm outdated |
Check for outdated packages. |
npm run build |
Compile the packaged executables. |
npm run lint |
Check the coding style using eslint and the Airbnb styleguide. |
npm run depcheck |
Check the project for dependency issues. |
npm run seccheck |
Check the project for known security vulnerabilities. |
Additionally, a secret.js file needs to be added the the src folder that contains a 32 character string
module.exports = '12345678123456781234567812345678';The EMR Exporter is no longer required to run on the same server that is running the Postgres database. The application no longer uses the Postgres COPY feature to export files directly from the Postgres Database to the Postgres Database File System. Results are now streamed from the Postgres Database to the EMR Exporter File System.
If the EMR Exporter failed to finish running, it would leave behind the working directory files. Unless an external process was monitoring these, they would exist forever. The application now deletes these orphan work directories when the application starts.
Directories that match the following rules will be deleted when the application starts:
-
The directory must be generated as a direct child of the workingDir configuration value specified in the .env file.
-
The directory must be a directory (not a file, etc).
-
The directory must be in the format as specified in the dateFormat configuration value. So if the format is YYYY_MM_DD_HH_mm_ss then we will compare the working directory against a regex \d\d\d\d_\d\d_\d\d_\d\d_\d\d_\d\d
-
The directory must directly contain a file named Clinic.0.csv . This is the first file generated by the Exporter, so if there was any successful data generated, then this file will exist. Note that this will exclude working directories that were not able to export any data. This will leave empty directories on the disk.
It should be noted that if the application fails to be able to run the rules above then the application will exit. For instance, if the working directory is the root drive, and the root drive contains files/directories (eg pagefile.sys) that the application cannot run lstat on, then the application will fail.
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