+ Healthcare/IO::Parser was developed by Khanhly Nguyen during her summer internship 2019 with Health Information Privacy Laborary(HIPLAB) at Vanderbilt University Medical Center. + +
+| Khanly Nguyen | +Heather Dunn | +Nina Thousand | +
| Byun Kang | +Gaylon Stanley | +Cheng Gao | +
| Thomas Brown | +Brad. Malin | +Steve Nyemba | +
Also our users have helped refine the parser and have been instrumental in improving the usability of {x12} parser.
++
-
+
- steve.l.nyemba@vumc.org +
- or info@the-phi.com +
- clone the source code here +
+ 0. Check that you have the installer, the command below will display all the supported actions. +
+ 1. initialize the environment (one-time run), with database parameters. By default this will be using sqlite database + +
Note : +
To use another database please visit data-transport page to learn about how to create an auth-file, it's a file with database access parameters. +
The configuration file will live on $HOME/.healthcareio/config.json + +
+ 2. Parse {x12} files stored in a folder. The output will be stored in a database specified upon initialization. +
Note : +
The data is stored in JSON format in the database specified in $HOME/.healthcareio/config.json +
Once stored, it is possible to export them to a relational database supported by data-transport. + + +
+
-
+
- Installed {x12} parser via pip (python 3+) +
- Familiarity with terminal commands +
- Have {x12} files in a folder
Samples {x12} files can be found at https://x12.org/examples
+
+
-
+
- Plugins
+ The plugins determine what elements need to be parsed for a given {x12} file, and thus determine relational structure+If no plugins are specified, the default built-in are used+It is possible to develop plugins (in python) for custom parsing or to extend the elements parsed by default.+
+
- Parser versions
+ Add data on existing database if using the same custom plugins across {x12} parser versions. As long as the custom plugins have not changed ++Do NOT add data on existing database if using default plugins & a newer version of {x12} parser. ++
+
+
+
+ + 0. clone respository +
+ 1. Edit env.sh file, use a text editor and the content of the file should look like the following
+
provide values of choice
+
# +
# Edit the env.sh file following variables, the others remain unchanged +
PG_USER= +
PG_PASSWORD= +
USER_EMAIL= +
Note : The file updates with basic information to be used to configure the {x12} parser environment +
PG_USER, PG_PASSWORD set PostgreSQL username/password +
USER_EMAIL configures {x12} parser with user's email + + + +
+ 2. Build the image with the files found in podman-parser folder +
+ 3. Build the container +
+ 4. Execute the parser (CLI), to parse the files +
+
-
+
- + Make sure to have either docker or podman installed + +
- You should be familiar with containers
+ Bind port 5000 to an available port+Mount a volume to /data that holds {x12} files+ +
+
+
-
+
- This is the best way to try the parser in a sandboxed environment +
- The image is not yet available on a public registry, thus will require building +
- Tools installed in the container:
+
+ PostgreSQL database+PGWeb interface on port 5000+ +
+
- The container has the latest copy of {x12} parser code-base +
- There is not need to initialize the {x12} parser, this will happen automatically + +
+
-
+
+
+ 0. The content of an auth-file for an sqlite3+ export, use the ETL Configurator to generate an ETL file +
Note : +
You can use the wizard in the studio menu to generate this file. + +
+ 1. Execute the export help function to display how the function is used +
+ 2. Execute the export function with the file created above +
+
+ +-
+
- Have a data-transport auth-file available
+
supported databases and vendors and listed below + +
+
+
-
+
- Export claims or remits should be specified individually
+
A function that will do both on a single call is not yet supported + +
+ - The relational data is normalized
+
Database specific referrential integrity is not set. This might need to be set manually when large volumes of data are involved +
We recommend using the exported data as staging data, and might need better typing and null/empty value handling +
+
+ Whether you prefer using it as a library within your Python projects, via a command-line interface (CLI) for quick tasks, or in a containerized environment (Podman/Docker) for scalability and portability, our parser fits seamlessly into your workflow. +
+Seamlessly export parsed data into relational databases, ensuring a normalized data representation that's ready for analysis and integration with your existing systems. +
++ Our parser is designed with extensibility in mind. You can create custom plugins for enhanced formatting, parsing, and processing tailored to your specific needs +
++ Embrace flexibility and transparency with our parser's source code, available under the permissive MIT license. Modify, customize, and contribute to the project with confidence +
++
pip install git+https://hiplab.mc.vanderbilt.edu/git/hiplab/parser.git
+ healthcare-io [init|parse|export] --help +
git clone https://healthcareio.the-phi.com/git/code/podman-parser.git
docker build -t healthcareio:0.1 .
docker container create -v
search for the database provider +
+
+
Note : +
Copy the code above to the auth-file and fill with appropriate values +
Attributes with zero i.e 0 are optional +
+
+ + +-
+
- Familiarity with JSON format +
- Understand your current database security access policy
+
The {x12} parser needs networking access to the database server +
The {x12} parser needs CREATE tables and WRITE data to the database +
+
-
+
- Values assigned to attributes
+
value of one i.e 1 suggests a value must be provided +
value of zero i.e 0 suggests the attribute is optional and can be removed +
+ - + Supported databases (or database providers) to use in search + + +