Webtemplate Parser for EHRBase

parse an EHRBase webtemplate and return one of:

1. All info for each leaf defined in the webtemplate (use type_of_output=all)
2. The path in FLAT format vs the original path in the webtemplate node (use type_of_output=flatpath)
3. An example composition with all the leafs instantiated (use type_of_output=composition)

1. Requirements

Any Python v3 will do.

2. Parameters

parameter	Description	values	mandatory
inputfile	path to webtemplate file (produced by EHRBase)	e.g., ~/mywebtemplate.json	yes
outputfile	path to output filename	e.g., ~/parsing_output	yes
type_of_output	output type chosen	one of [all, flatpath, composition]	no (default=all)

3. How to run

From the code directory to obtain a composition in FLAT format for EHRBase:

python3 Webtemplate_parser.py --inputfile {full_path_to_webtemplate_file} --outputfile {full_path_to_output_file} --type_of_output composition

4. Output

4.1 type_of_output=all

We obtain rows like:

1) category, category, /category, category, DV_CODED_TEXT, [{'list': [{'label': 'event', 'localizedLabels': {'en': 'event'}, 'value': '433'}], 'suffix': 'code', 'terminology': 'openehr', 'type': 'CODED_TEXT'}], []

Meaning of each leaf/row:

index	id	name	webtemplate_path	FLAT_path	rm_type	inputs	children
1)	category	category	/category	category	DV_CODED_TEXT	[{'list': [{'label': 'event', 'localizedLabels': {'en': 'event'}, 'value': '433'}], 'suffix': 'code', 'terminology': 'openehr', 'type': 'CODED_TEXT'}]	[]

4.2 type_of_output=flatpath

The result, for each leaf, is a dictionary with mapping between FLAT and webtemplate paths, which can be useful to find the webtemplate path to put in queries. A row will look like:

  "interhealth_cancer_registry/category": "/category",

  FLAT path -> webtemplate path

4.3 type_of_output=composition

A composition in FLAT format is obtained with all the leafs instantiated:

{
  "interhealth_cancer_registry/category|code": "433",
  "interhealth_cancer_registry/category|value": "event",
  "interhealth_cancer_registry/category|terminology": "openehr"
  ......

Acknowledgments

This work has been partially funded by the the following sources:

• “Total Patient Management” (ToPMa) project (grant by the Sardinian Regional Authority, grant number RC_CRP_077);
• the “Processing, Analysis, Exploration, and Sharing of Big and/or Complex Data” (XDATA) project (grant by the Sardinian Regional Authority).