hiplab/parser
hiplab
/
parser
1
0
Fork 0
Code Issues 4 Pull Requests Packages Projects 1 Releases 1 Wiki Activity

documentation

This commit is contained in:
Steve Nyemba 2022-02-10 13:13:26 -06:00
parent d8f6b84951
commit a2f163c0f6
1 changed files with 48 additions and 24 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

72
README.md
View File

@ -8,27 +8,42 @@ We wrote this frame to be used in both command line or as a library within in yo
## Features ## Features
| Features | | | Features | Description|
| -------- | --- | | -------- | --- |
|X12 claims/remits| parsing of {x12} claims/remittances into JSON format with human readible attributes| |X12 claims/remits| parsing of {x12} claims/remittances into JSON format with human readible attributes|
|Multi Processing| capable of processing multiple files simultaneously to speed up processing| |Multi Processing| capable of processing multiple files simultaneously to speed up processing|
|Analytics support| descriptive statistical analytics : distribution, various counts| |Analytics support| descriptive statistical analytics : distribution, various counts|
|Process Recovery| capable of recovering interrupted runs| |Process Recovery| capable of recovering interrupted runs|
|Export to RDBMS| exports data to relational format (NoSQL -> SQL) 7 supported databases <br> * PostgreSQL,<br> * Redshift, <br>* Neteeza, <br>* Mysql, <br>* Mariadb, <br>* bigquery, <br>* sqlite3 |
|**Issues and Bug reports**| info@the-phi.com
For advanced features visit [Healthcare/IO::Parser](https://healthcareio.the-phi.com/parser) homepage
## Installation ## Installation
**System requirements**
- git (latest cli)
- python3+ (with virtualenv)
- mongodb (optional)
**Installation command**
pip install --upgrade git+https://hiplab.mc.vanderbilt.edu/git/lab/parse-edi.git pip install --upgrade git+https://hiplab.mc.vanderbilt.edu/git/lab/parse-edi.git
## Usage ## Usage
**cli :** Healthcare/IO is primarily intended to be used as a command line parser (for now). It is fully written in python 3+
**CLI :**
1. signup to get parsing configuration 1. signup to get parsing configuration
The parser is driven by a configuration file that specifies fields to parse and how to parse them. You need by signing up, to get a copy of the configuration file. The parser is driven by a configuration file that specifies fields to parse and how to parse them. You need by signing up, to get a copy of the configuration file.
#
# Use sqlite as data-store
healthcare-io.py --signup <email> [--store <mongo|sqlite>] healthcare-io.py --signup <email> [--store <mongo|sqlite>]
2. check version 2. check version
@ -37,7 +52,7 @@ We wrote this frame to be used in both command line or as a library within in yo
healthcare-io.py --check-update healthcare-io.py --check-update
3. parsing data in a folder 3. parsing data stored in a folder
The parser will recursively traverse a directory with claims and or remittances The parser will recursively traverse a directory with claims and or remittances
@ -54,11 +69,15 @@ We wrote this frame to be used in both command line or as a library within in yo
The parser will export data into other data-stores as a relational tables allowing users to construct views to support a variety of studies. The parser will export data into other data-stores as a relational tables allowing users to construct views to support a variety of studies.
healthcare-io.py --export <835|837> --config <path-export.json> healthcare-io.py --export <835|837> --export-config <path-export.json>
with: with:
--config configuration to support data-store --export-config configuration to support data-store
**example**
1. Exporting to PostgreSQL
{"provider":"postgresql","database":"healthcareio","schema":"foo"}
**NOTE** **NOTE**
@ -69,41 +88,46 @@ We wrote this frame to be used in both command line or as a library within in yo
{ {
"provider":"<postgresql|redshift|mysql|mariadb>", "provider":"<postgresql|redshift|mysql|mariadb>",
"db":"mydatabase", "database":"<name>",["host":"server-name"],["port":5432],
[ ["user":"me"],["password":"!@#z4qm"],["schema":"target-schema"]
"host":"server-name","port":5432,
"user":"me","password":"!@#z4qm",
"schema":"target-schema"
]
} }
**parameters:** **parameters:**
provider postgresql,redshift,mysql or mariadb (supported providers) provider postgresql,redshift,mysql or mariadb (supported providers)
db name of the database database name of the database
**optional:** **optional:**
schema name of the target schema. If not provided we will assume the default schema name of the target schema. If not provided we will assume the default
host host of the database. If not provided assuming localhost host host of the database. If not provided assuming localhost
port port value of the database if not provided the default will be used port port value of the database if not provided the default will be used
user database user name. If not provided we assume security settings to trust user database user name. If not provided we assume security settings to trust
password password of database user. If not set we assume security settings to trust password password of database user. If not set we assume security settings to trust
**Embedded in Code :** **Known Limitations**
The Healthcare/IO **parser** can be used within your code base as a library and handle storing data in a data store of choice 1. By default it does NOT come with all {X12} Segments.
2. Does not support an easy way to rename attributes it parses
3. For now can only read {x12} from disk
import healthcareio There is support for additional features and attributes available at [Healthcare/IO::Parser](https://healthcareio.the-phi.com/parser).
**In development**
1. Wizard/UI to enable attribute renaming
2. Dashboard for quick overview
3. Reading {x12} from s3 and other cloud buckets
4. Docker Image
## Credits ## Credits
This project was realized thanks largely to the effort of Vanderbilt University Medical Center and
* [Khanhly Nguyen] (<khanhly.t.nguyen@gmail.com>) | | | |
* [Gaylon Stanley] (<gaylon.stanley@vumc.org>) |--|--|--|
* [Cheng Gao] (<cheng.gao@vanderbilt.edu>) |- Khanhly Nguyen<br>- Heather Dunn<br>- Nina Thousand|- Byun Kang<br>- Gaylon Stanley<br>- Cheng Gao|- Thomas Brown<br>- Brad Malin<br>- Steve Nyemba
* [Brad Malin] (brad.malin@vanderbilt.edu)
* [Steve L. Nyemba] (<steve.l.nyemba@vumc.org>)