Merge pull request #10 from vadi2/add-r4-support

Add R4 support

.devcontainer/scripts/init-container.sh

@@ -2,6 +2,7 @@
 
 set -e
 
+sudo luarocks install argparse
 sudo luarocks install lua-cjson
 sudo luarocks install rapidjson
 sudo luarocks install lunajson

.vscode/launch.json

@@ -0,0 +1,26 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Debug Lua Interpreter",
+            "type": "lua-local",
+            "request": "launch",
+            "program": {
+                "lua": "lua",
+                "file": "${file}"
+            }
+        },
+        {
+            "name": "Debug Custom Lua Environment",
+            "type": "lua-local",
+            "request": "launch",
+            "program": {
+                "command": "command"
+            },
+            "args": []
+        }
+    ]
+}

README.md

@@ -22,13 +22,27 @@ to_json("/path/to/file", {file = true})
 to_json("xml content", {pretty = true})
 -- convert an XML file given as a location to JSON and prettyprint it
 to_json("/path/to/file", {file = true, pretty = true})
+-- supported versions are 'R4', 'STU3', and 'auto' (default)
+-- 'auto' will try all FHIR versions starting from R4 and going down
+to_json("xml content", {fhirversion = "R4"})
+to_json("xml content", {fhirversion = "STU3"})
+to_json("xml content", {fhirversion = "auto"})
 
 -- convert given JSON content as a string to XML
 to_xml("json content")
 -- convert an JSON file given as a location to XML
 to_xml("/path/to/file", {file = true})
-
--- get the FHIR definition of an element
+-- convert JSON content as a string to XML and prettyprint it
+to_xml("json content", {pretty = true})
+-- convert an JSON file given as a location to XML and prettyprint it
+to_xml("/path/to/file", {file = true, pretty = true})
+-- supported versions are 'R4', 'STU3', and 'auto' (default)
+-- 'auto' will try all FHIR versions starting from R4 and going down
+to_xml("json content", {fhirversion = "R4"})
+to_xml("json content", {fhirversion = "STU3"})
+to_xml("json content", {fhirversion = "auto"})
+
+-- get the FHIR definition of an element. Defaults to STU3
 get_fhir_definition('Patient', 'animal', 'species')
 -- returns a table with metadata about the element. Do not modify this table. Keys are:
 -- _min (int): minimum cardinality
@@ -39,6 +53,10 @@ get_fhir_definition('Patient', 'animal', 'species')
 -- _type (string): FHIR element type. Possible values are: Address, Age, Annotation, Attachment, BackboneElement, CodeableConcept, Coding, ContactDetail, ContactPoint, Contributor, Count, DataRequirement, Distance, DomainResource, Duration, Element, ElementDefinition, Extension, HumanName, Identifier, Meta, Money, Narrative, ParameterDefinition, Period, Quantity, Range, Ratio, Reference, RelatedResource, Resource, SampledData, Signature, Timing, TriggerDefinition, UsageContext, base64Binary, boolean, code, date, dateTime, decimal, id, instant, integer, markdown, oid, positiveInt, string, time, unsignedInt, uri, xhtml
 -- [1]: if present, this is a link to the base type of the resource
 -- _derivations: if present, this is a map of resources that extend on this resource
+
+-- last argument can be either 'R4' or 'STU3' to specify version. Defaults to STU3
+get_fhir_definition('Patient', 'contact', 'relationship', 'R4')
+get_fhir_definition('Patient', 'animal', 'species', 'STU3')
 ```
 
 ### Examples

spec/R4/auto_versioning_spec.lua

@@ -0,0 +1,65 @@
+--[[
+  FHIR Formats
+
+  Copyright (C) 2016 Vadim Peretokin
+
+  Licensed under the Apache License, Version 2.0 (the "License");
+  you may not use this file except in compliance with the License.
+  You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+]]
+
+package.path = "src/?.lua;"..package.path
+local in_fhir_json = require("fhirformats").to_json
+local in_fhir_xml = require("fhirformats").to_xml
+local cjson = require("cjson")
+local xml = require("xml")
+local inspect = require("inspect")
+
+describe("auto-version xml to json", function()
+    local positive_example, negative_example, immunization_example,
+    positive_example_data, immunization_example_data
+
+    setup(function()
+        io.input("spec/R4/stu3-immunization.json")
+        positive_example_data = io.read("*a")
+        immunization_example_data = in_fhir_json("spec/R4/stu3-immunization.xml", {file = true, fhirversion = "auto"})
+
+        -- for same div data test
+        assert:set_parameter("TableFormatLevel", -1)
+      end)
+
+    before_each(function()
+        positive_example = cjson.decode(positive_example_data)
+        immunization_example = cjson.decode(immunization_example_data)
+      end)
+
+    it("should have the same non-div data", function()
+        assert.same(positive_example, immunization_example)
+      end)
+  end)
+
+describe("auto-version json to xml", function()
+    local positive_example, negative_example, immunization_example,
+    positive_example_data, immunization_example_data
+
+    setup(function()
+        io.input("spec/R4/stu3-immunization.xml")
+        positive_example_data = io.read("*a")
+        immunization_example_data = in_fhir_xml("spec/R4/stu3-immunization.json", {file = true, fhirversion = "auto"})
+
+        -- for same div data test
+        assert:set_parameter("TableFormatLevel", -1)
+      end)
+
+    it("should have the same data, order included", function()
+        assert.same(positive_example_data, immunization_example_data)
+      end)
+  end)

spec/R4/deviceusestatement-example.json

@@ -0,0 +1,27 @@
+{
+  "resourceType": "DeviceUseStatement",
+  "id": "example",
+  "text": {
+    "status": "generated",
+    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: example</p><p><b>identifier</b>: 51ebb7a9-4e3a-4360-9a05-0cc2d869086f</p><p><b>status</b>: active</p><p><b>subject</b>: <a>Patient/example</a></p><p><b>device</b>: <a>Device/example</a></p><p><b>reasonReference</b>: <a>Appendectomy (surgery)</a></p></div>"
+  },
+  "identifier": [
+    {
+      "system": "http:goodhealth.org/identifiers",
+      "value": "51ebb7a9-4e3a-4360-9a05-0cc2d869086f"
+    }
+  ],
+  "status": "active",
+  "subject": {
+    "reference": "Patient/example"
+  },
+  "device": {
+    "reference": "Device/example"
+  },
+  "reasonReference": [
+    {
+      "reference": "Procedure/example",
+      "display": "Appendectomy (surgery)"
+    }
+  ]
+}

spec/R4/deviceusestatement-example.xml

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?><DeviceUseStatement xmlns="http://hl7.org/fhir">
+	<id value="example"/>
+	<text><status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: example</p><p><b>identifier</b>: 51ebb7a9-4e3a-4360-9a05-0cc2d869086f</p><p><b>status</b>: active</p><p><b>subject</b>: <a>Patient/example</a></p><p><b>device</b>: <a>Device/example</a></p><p><b>reasonReference</b>: <a>Appendectomy (surgery)</a></p></div></text><identifier>
+		<system value="http:goodhealth.org/identifiers"/>
+		<value value="51ebb7a9-4e3a-4360-9a05-0cc2d869086f"/>
+	</identifier>
+	<status value="active"/>
+	<subject>
+		<reference value="Patient/example"/>
+	</subject>
+	<device>
+		<reference value="Device/example"/>
+	</device>
+	<reasonReference>
+		<reference value="Procedure/example"/>
+		<display value="Appendectomy (surgery)"/>
+	</reasonReference>
+</DeviceUseStatement>

spec/R4/deviceusestatement_spec.lua

@@ -0,0 +1,81 @@
+--[[
+  FHIR Formats
+
+  Copyright (C) 2022 Vadim Peretokin
+
+  Licensed under the Apache License, Version 2.0 (the "License");
+  you may not use this file except in compliance with the License.
+  You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+]]
+
+package.path = "src/?.lua;"..package.path
+local in_fhir_json = require("fhirformats").to_json
+local in_fhir_xml = require("fhirformats").to_xml
+local cjson = require("cjson")
+local xml = require("xml")
+local inspect = require("inspect")
+
+describe("xml to json", function()
+    local positive_example, negative_example, deviceusestatement_example,
+    positive_example_data, deviceusestatement_example_data
+
+    setup(function()
+        io.input("spec/R4/deviceusestatement-example.json")
+        positive_example_data = io.read("*a")
+        deviceusestatement_example_data = in_fhir_json("spec/R4/deviceusestatement-example.xml",
+          {file = true, fhirversion = "R4"})
+
+        -- for same div data test
+        assert:set_parameter("TableFormatLevel", -1)
+      end)
+
+    before_each(function()
+        positive_example = cjson.decode(positive_example_data)
+        deviceusestatement_example = cjson.decode(deviceusestatement_example_data)
+      end)
+
+    it("should have the same non-div data", function()
+        -- cut out the div's, since the whitespace doesn't matter as much in xml
+        positive_example.text.div = nil
+        deviceusestatement_example.text.div = nil
+        assert.same(positive_example, deviceusestatement_example)
+      end)
+
+    it("should have xml-comparable div data", function()
+        local positive_example_div = xml.load(positive_example.text.div)
+        local deviceusestatement_example_div = xml.load(deviceusestatement_example.text.div)
+        --print(inspect(positive_example_div))
+        --print(inspect(deviceusestatement_example_div))
+        assert.same(positive_example_div, deviceusestatement_example_div)
+      end)
+  end)
+
+describe("json to xml", function()
+    local positive_example, negative_example, deviceusestatement_example,
+    positive_example_data, deviceusestatement_example_data
+
+    setup(function()
+        io.input("spec/R4/deviceusestatement-example.xml")
+        positive_example_data = io.read("*a")
+        deviceusestatement_example_data = in_fhir_xml("spec/R4/deviceusestatement-example.json",
+          {file = true, fhirversion = "R4"})
+
+        -- for same div data test
+        assert:set_parameter("TableFormatLevel", -1)
+      end)
+
+    it("should have the same data", function()
+        -- convert it down to JSON since order of elements doesn't matter in JSON, while it does in XML
+        assert.same(
+          cjson.decode(in_fhir_json(positive_example_data, {fhirversion = "R4"})),
+          cjson.decode(in_fhir_json(deviceusestatement_example_data, {fhirversion = "R4"})))
+      end)
+  end)