Source for FHIR JSON-LD AMIA submission

Clone this repository

> git clone git@github.com:fhircat/FHIRJsonLDAmiaPaper.git

Install pipenv and packages

> cd FHIRJsonLDAmiaPaper
> pipenv install  

The main script for generation and testing is json_to_original.sh

> ./json_to_original.sh --help
Usage: json_to_original-sh [-1, -2, -3 or -a] [-v] [-java, -js or -all] [-cs contextsource] [-co compareopts] [directory]
>

Parameters:

• "-1" -- run the JSON preprocessing step, which transforms all json files found in data/<directory>/examples-json/ into their equivalents in data/<directory>/json-pre/python/
• "-2" -- run the JSON to RDF transformation, transforming all files in data/<directory>/json-pre/python/ into the RDF representation in data/<directory>/original/java --or-- data/<directory>/original/js depending on whether we are using the JAVA or Javascript JSON-LD processor.
• "-3" -- compare the contents of data/<directory>/original/java --or-- data/<directory>/original/js with the contents in data/<directory>examples-ttl/ and publish a compare report in data/$dir/compare-report/java/ or data/$dir/compare-report/js/
• "-a" -- do all three steps. Same as "-1 -2 -3"
• "-java" -- use the java JSON-LD processor
• "-js" -- use the Javascript JSON-LD processor
• "-all" -- use both processors. Same as "-java -js"
• "-cs" -- The base URL for the JSON-LD contexts.
• "-co" -- Comparison options for the
• directory

Upgrade nodejs to > 13.*

> brew update
> brew upgrade node
> npm install -g npm

Install yarn and node packages

> cd fhir_jsonld_js; yarn install 
> cd ..

Unzip appropriate FHIR examples

> ./expand.sh ['fhir-r5' or 'fhir-r4']  (default: 'fhir-r5')

fhir-r4 - Image of current HL7 R4 content

• compare-report - transformation reports on a per file basis *
• examples-json - Vanilla HL7 R4 example JSON files
• examples-ttl - HL7 R4 RDF output as transformed by current build process
  • account-example.ttl
  • ...
• jsonld-pre - example-json preprocessed by fhir_jsonld_amia/json_to_r4.py
  • account-example.json
  • ...
• jsonld-r4 - jsonld-pre files as processed by fhir_jsonld_js/yarn jsonld
  • account-example.nq
  • ...
• examples-json.zip - Downloaded from https://build.fhir.org on 8/17/2020.
• examples-ttl.zip - Downloaded from https://build.fhir.org on 8/17/2020.

fhir-r5 - Image of current HL7 R5 content

• compare-report - transformation reports on a per file basis *
• examples-json - Vanilla HL7 R4 example JSON files
• examples-ttl - HL7 R4 RDF output as transformed by current build process
  • account-example.ttl
  • ...
• jsonld-pre - example-json preprocessed by fhir_jsonld_amia/json_to_r4.py
  • account-example.json
  • ...
• jsonld-r4 - jsonld-pre files as processed by fhir_jsonld_js/yarn jsonld
  • account-example.nq
• examples-json.zip - Downloaded from https://hl7.org/fhir/ on 8/17/2020.
• examples-ttl.zip - Downloaded from https://hl7.org/fhir/ on 8/17/2020.

The three scripts that are used to convert all files and compare the results are:

1. Preprocess JSON file to insert @context, OWL header and structural changes

pipenv run python fhir_jsonld_amia/json_to_r4.py -id <input_directory> -od <output_directory> -c -fs http://hl7.org/fhir/

input_directory: Where the JSON files are stored. output_directory: Where the generated JSONLD files are stored.

2. Expand the JSONLD files

This is done by using the jsonld-js nodejs package.

cd fhir_jsonld_js; yarn jsonld -c expand -n <jsonld_pre_directory> -m <expanded_files_directory>

jsonld_pre_directory: where the preprocessed JSONLD files is stored expanded_files_directory: the directory where the expanded files are going to be stored.

3. Compare the expanded files with the FHIR examples in Turtle format.

pipenv run python fhir_jsonld_amia/compare_rdf.py -id <expanded_files> -td <fhir_examples> -od <report_directory> 

Right now this script only compare JSONLD files with Turtle.

Here are the commands to make conversions of fhir-r4 files.

pipenv run python fhir_jsonld_amia/json_to_r4.py -id data/fhir-r4/examples-json -od data/fhir-r4/jsonld-pre -c -fs http://hl7.org/fhir/
cd fhir_jsonld_js; yarn jsonld -c expand -n ../data/fhir-r4/jsonld-pre -m ../data/fhir-r4/jsonld-r4
pipenv run python fhir_jsonld_amia/compare_rdf.py -id data/fhir-r4/jsonld-r4 -od data/fhir-r4/compare-report -td data/fhir-r4/examples-ttl

Here are the commands to do tests with small set of files. Just put the files in the data/test directory and run the commands.

pipenv run python fhir_jsonld_amia/json_to_r4.py -id data/test/examples-json -od data/test/jsonld-pre -c -fs https://hl7.org/fhir/
cd fhir_jsonld_js; yarn jsonld -c expand -n ../data/test/jsonld-pre -m ../data/test/jsonld-r4
pipenv run python fhir_jsonld_amia/compare_rdf.py -id data/test/jsonld-r4 -od data/test/compare-report -td data/test/examples-ttl

Run 3/4/2020

Convert FHIR JSON to R4

Step 1: Total=3026 Successful=3024 Step 2: Total 3024 Converted 2998 Missing contexts:

'https://fhircat.org/fhir/contexts/r5/conditiondefinition.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/manufactureditemdefinition.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/administrableproductdefinition.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/packagedproductdefinition.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/permission.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/topic.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/clinicaluseissue.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/ingredient.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/medicationusage.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/medicinalproductdefinition.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/capabilitystatement2.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/substancedefinition.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/regulatedauthorization.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/nutritionintake.context.jsonld', 'https://fhircat.org/fhir/contexts/r5/nutritionproduct.context.jsonld'