diff --git a/.devcontainer/scripts/init-container.sh b/.devcontainer/scripts/init-container.sh index a958a85..8e72752 100644 --- a/.devcontainer/scripts/init-container.sh +++ b/.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 diff --git a/.vscode/launch.json b/.vscode/launch.json new file mode 100644 index 0000000..d2cf68a --- /dev/null +++ b/.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": [] + } + ] +} diff --git a/README.md b/README.md index 01cd8c5..62d7815 100644 --- a/README.md +++ b/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 diff --git a/spec/R4/auto_versioning_spec.lua b/spec/R4/auto_versioning_spec.lua new file mode 100644 index 0000000..07e9eaf --- /dev/null +++ b/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) diff --git a/spec/R4/deviceusestatement-example.json b/spec/R4/deviceusestatement-example.json new file mode 100644 index 0000000..edcd841 --- /dev/null +++ b/spec/R4/deviceusestatement-example.json @@ -0,0 +1,27 @@ +{ + "resourceType": "DeviceUseStatement", + "id": "example", + "text": { + "status": "generated", + "div": "

Generated Narrative with Details

id: example

identifier: 51ebb7a9-4e3a-4360-9a05-0cc2d869086f

status: active

subject: Patient/example

device: Device/example

reasonReference: Appendectomy (surgery)

" + }, + "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)" + } + ] +} \ No newline at end of file diff --git a/spec/R4/deviceusestatement-example.xml b/spec/R4/deviceusestatement-example.xml new file mode 100644 index 0000000..37d99e3 --- /dev/null +++ b/spec/R4/deviceusestatement-example.xml @@ -0,0 +1,18 @@ + + +

Generated Narrative with Details

id: example

identifier: 51ebb7a9-4e3a-4360-9a05-0cc2d869086f

status: active

subject: Patient/example

device: Device/example

reasonReference: Appendectomy (surgery)

 + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/spec/R4/deviceusestatement_spec.lua b/spec/R4/deviceusestatement_spec.lua new file mode 100644 index 0000000..ff28d32 --- /dev/null +++ b/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) diff --git a/spec/R4/immunization-example.json b/spec/R4/immunization-example.json new file mode 100644 index 0000000..b469a22 --- /dev/null +++ b/spec/R4/immunization-example.json @@ -0,0 +1,132 @@ +{ + "resourceType": "Immunization", + "id": "example", + "text": { + "status": "generated", + "div": "

Generated Narrative with Details

id: example

identifier: urn:oid:1.3.6.1.4.1.21367.2005.3.7.1234

status: completed

vaccineCode: Fluvax (Influenza) (Details : {urn:oid:1.2.36.1.2001.1005.17 code 'FLUVAX' = 'Fluvax)

patient: Patient/example

encounter: Encounter/example

occurrence: 10/01/2013

primarySource: true

location: Location/1

manufacturer: Organization/hl7

lotNumber: AAJN11K

expirationDate: 15/02/2015

site: left arm (Details : {http://terminology.hl7.org/CodeSystem/v3-ActSite code 'LA' = 'left arm', given as 'left arm'})

route: Injection, intramuscular (Details : {http://terminology.hl7.org/CodeSystem/v3-RouteOfAdministration code 'IM' = 'Injection, intramuscular', given as 'Injection, intramuscular'})

doseQuantity: 5 mg (Details: UCUM code mg = 'mg')

performer

function: Ordering Provider (Details : {http://terminology.hl7.org/CodeSystem/v2-0443 code 'OP' = 'Ordering Provider)

actor: Practitioner/example

performer

function: Administering Provider (Details : {http://terminology.hl7.org/CodeSystem/v2-0443 code 'AP' = 'Administering Provider)

actor: Practitioner/example

note: Notes on adminstration of vaccine

reasonCode: Procedure to meet occupational requirement (Details : {SNOMED CT code '429060002' = 'Procedure to meet occupational requirement)

isSubpotent: true

Educations

-DocumentTypePublicationDatePresentationDate
*25308869830001031112070202/07/201210/01/2013

programEligibility: Not Eligible (Details : {http://terminology.hl7.org/CodeSystem/immunization-program-eligibility code 'ineligible' = 'Not Eligible)

fundingSource: Private (Details : {http://terminology.hl7.org/CodeSystem/immunization-funding-source code 'private' = 'Private)

" + }, + "identifier": [ + { + "system": "urn:ietf:rfc:3986", + "value": "urn:oid:1.3.6.1.4.1.21367.2005.3.7.1234" + } + ], + "status": "completed", + "vaccineCode": { + "coding": [ + { + "system": "urn:oid:1.2.36.1.2001.1005.17", + "code": "FLUVAX" + } + ], + "text": "Fluvax (Influenza)" + }, + "patient": { + "reference": "Patient/example" + }, + "encounter": { + "reference": "Encounter/example" + }, + "occurrenceDateTime": "2013-01-10", + "primarySource": true, + "location": { + "reference": "Location/1" + }, + "manufacturer": { + "reference": "Organization/hl7" + }, + "lotNumber": "AAJN11K", + "expirationDate": "2015-02-15", + "site": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-ActSite", + "code": "LA", + "display": "left arm" + } + ] + }, + "route": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RouteOfAdministration", + "code": "IM", + "display": "Injection, intramuscular" + } + ] + }, + "doseQuantity": { + "value": 5, + "system": "http://unitsofmeasure.org", + "code": "mg" + }, + "performer": [ + { + "function": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0443", + "code": "OP" + } + ] + }, + "actor": { + "reference": "Practitioner/example" + } + }, + { + "function": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0443", + "code": "AP" + } + ] + }, + "actor": { + "reference": "Practitioner/example" + } + } + ], + "note": [ + { + "text": "Notes on adminstration of vaccine" + } + ], + "reasonCode": [ + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "429060002" + } + ] + } + ], + "isSubpotent": true, + "education": [ + { + "documentType": "253088698300010311120702", + "publicationDate": "2012-07-02", + "presentationDate": "2013-01-10" + } + ], + "programEligibility": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/immunization-program-eligibility", + "code": "ineligible" + } + ] + } + ], + "fundingSource": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/immunization-funding-source", + "code": "private" + } + ] + } +} \ No newline at end of file diff --git a/spec/R4/immunization-example.xml b/spec/R4/immunization-example.xml new file mode 100644 index 0000000..18ec551 --- /dev/null +++ b/spec/R4/immunization-example.xml @@ -0,0 +1,99 @@ + + +

Generated Narrative with Details

id: example

identifier: urn:oid:1.3.6.1.4.1.21367.2005.3.7.1234

status: completed

vaccineCode: Fluvax (Influenza) (Details : {urn:oid:1.2.36.1.2001.1005.17 code 'FLUVAX' = 'Fluvax)

patient: Patient/example

encounter: Encounter/example

occurrence: 10/01/2013

primarySource: true

location: Location/1

manufacturer: Organization/hl7

lotNumber: AAJN11K

expirationDate: 15/02/2015

site: left arm (Details : {http://terminology.hl7.org/CodeSystem/v3-ActSite code 'LA' = 'left arm', given as 'left arm'})

route: Injection, intramuscular (Details : {http://terminology.hl7.org/CodeSystem/v3-RouteOfAdministration code 'IM' = 'Injection, intramuscular', given as 'Injection, intramuscular'})

doseQuantity: 5 mg (Details: UCUM code mg = 'mg')

performer

function: Ordering Provider (Details : {http://terminology.hl7.org/CodeSystem/v2-0443 code 'OP' = 'Ordering Provider)

actor: Practitioner/example

performer

function: Administering Provider (Details : {http://terminology.hl7.org/CodeSystem/v2-0443 code 'AP' = 'Administering Provider)

actor: Practitioner/example

note: Notes on adminstration of vaccine

reasonCode: Procedure to meet occupational requirement (Details : {SNOMED CT code '429060002' = 'Procedure to meet occupational requirement)

isSubpotent: true

Educations

-DocumentTypePublicationDatePresentationDate
*25308869830001031112070202/07/201210/01/2013

programEligibility: Not Eligible (Details : {http://terminology.hl7.org/CodeSystem/immunization-program-eligibility code 'ineligible' = 'Not Eligible)

fundingSource: Private (Details : {http://terminology.hl7.org/CodeSystem/immunization-funding-source code 'private' = 'Private)

 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/spec/R4/immunization_spec.lua b/spec/R4/immunization_spec.lua new file mode 100644 index 0000000..5c4e3c7 --- /dev/null +++ b/spec/R4/immunization_spec.lua @@ -0,0 +1,77 @@ +--[[ + 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, immunization_example, + positive_example_data, immunization_example_data + + setup(function() + io.input("spec/R4/immunization-example.json") + positive_example_data = io.read("*a") + immunization_example_data = in_fhir_json("spec/R4/immunization-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) + immunization_example = cjson.decode(immunization_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 + immunization_example.text.div = nil + assert.same(positive_example, immunization_example) + end) + + it("should have xml-comparable div data", function() + local positive_example_div = xml.load(positive_example.text.div) + local immunization_example_div = xml.load(immunization_example.text.div) + --print(inspect(positive_example_div)) + --print(inspect(immunization_example_div)) + assert.same(positive_example_div, immunization_example_div) + end) + end) + +describe("json to xml", function() + local positive_example, negative_example, immunization_example, + positive_example_data, immunization_example_data + + setup(function() + io.input("spec/R4/immunization-example.xml") + positive_example_data = io.read("*a") + immunization_example_data = in_fhir_xml("spec/R4/immunization-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(immunization_example_data, {fhirversion = "R4"}))) + end) + end) diff --git a/spec/R4/stu3-immunization.json b/spec/R4/stu3-immunization.json new file mode 100644 index 0000000..20cf2af --- /dev/null +++ b/spec/R4/stu3-immunization.json @@ -0,0 +1,153 @@ +{ + "resourceType": "Immunization", + "id": "example", + "identifier": [ + { + "system": "urn:ietf:rfc:3986", + "value": "urn:oid:1.3.6.1.4.1.21367.2005.3.7.1234" + } + ], + "status": "completed", + "notGiven": false, + "vaccineCode": { + "coding": [ + { + "system": "urn:oid:1.2.36.1.2001.1005.17", + "code": "FLUVAX" + } + ], + "text": "Fluvax (Influenza)" + }, + "patient": { + "reference": "Patient/example" + }, + "encounter": { + "reference": "Encounter/example" + }, + "date": "2013-01-10", + "primarySource": true, + "location": { + "reference": "Location/1" + }, + "manufacturer": { + "reference": "Organization/hl7" + }, + "lotNumber": "AAJN11K", + "expirationDate": "2015-02-15", + "site": { + "coding": [ + { + "system": "http://hl7.org/fhir/v3/ActSite", + "code": "LA", + "display": "left arm" + } + ] + }, + "route": { + "coding": [ + { + "system": "http://hl7.org/fhir/v3/RouteOfAdministration", + "code": "IM", + "display": "Injection, intramuscular" + } + ] + }, + "doseQuantity": { + "value": 5, + "system": "http://unitsofmeasure.org", + "code": "mg" + }, + "practitioner": [ + { + "role": { + "coding": [ + { + "system": "http://hl7.org/fhir/v2/0443", + "code": "OP" + } + ] + }, + "actor": { + "reference": "Practitioner/example" + } + }, + { + "role": { + "coding": [ + { + "system": "http://hl7.org/fhir/v2/0443", + "code": "AP" + } + ] + }, + "actor": { + "reference": "Practitioner/example" + } + } + ], + "note": [ + { + "text": "Notes on adminstration of vaccine" + } + ], + "explanation": { + "reason": [ + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "429060002" + } + ] + } + ] + }, + "reaction": [ + { + "date": "2013-01-10", + "detail": { + "reference": "Observation/example" + }, + "reported": true + } + ], + "vaccinationProtocol": [ + { + "doseSequence": 1, + "description": "Vaccination Protocol Sequence 1", + "authority": { + "reference": "Organization/hl7" + }, + "series": "Vaccination Series 1", + "seriesDoses": 2, + "targetDisease": [ + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1857005" + } + ] + } + ], + "doseStatus": { + "coding": [ + { + "system": "http://hl7.org/fhir/vaccination-protocol-dose-status", + "code": "count", + "display": "Counts" + } + ] + }, + "doseStatusReason": { + "coding": [ + { + "system": "http://hl7.org/fhir/vaccination-protocol-dose-status-reason", + "code": "coldchbrk", + "display": "Cold chain break" + } + ] + } + } + ] +} diff --git a/spec/R4/stu3-immunization.xml b/spec/R4/stu3-immunization.xml new file mode 100644 index 0000000..d0c92d4 --- /dev/null +++ b/spec/R4/stu3-immunization.xml @@ -0,0 +1,120 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/spec/bundle-response.json b/spec/STU3/bundle-response.json similarity index 100% rename from spec/bundle-response.json rename to spec/STU3/bundle-response.json diff --git a/spec/bundle-response.xml b/spec/STU3/bundle-response.xml similarity index 100% rename from spec/bundle-response.xml rename to spec/STU3/bundle-response.xml diff --git a/spec/complex-type-with-extension.json b/spec/STU3/complex-type-with-extension.json similarity index 100% rename from spec/complex-type-with-extension.json rename to spec/STU3/complex-type-with-extension.json diff --git a/spec/complex-type-with-extension.xml b/spec/STU3/complex-type-with-extension.xml similarity index 100% rename from spec/complex-type-with-extension.xml rename to spec/STU3/complex-type-with-extension.xml diff --git a/spec/STU3/convert-json-edge-cases.lua b/spec/STU3/convert-json-edge-cases.lua new file mode 100644 index 0000000..c0350a1 --- /dev/null +++ b/spec/STU3/convert-json-edge-cases.lua @@ -0,0 +1,10 @@ +package.path = "src/?.lua;"..package.path +local to_json = require("fhirformats").to_json +local to_xml = require("fhirformats").to_xml +local inspect = require("inspect") + +io.output("spec/STU3/json-edge-cases (fhir-formats).xml") +io.write(to_xml("spec/STU3/json-edge-cases.json", {file = true, fhirversion = "STU3"})) +io.output("spec/STU3/json-edge-cases (fhir-formats).json") +io.write(to_json("spec/STU3/json-edge-cases.xml", {file=true, pretty = true}, "STU3")) +io.output():close() diff --git a/spec/dynamic_spec.lua b/spec/STU3/dynamic_spec.lua similarity index 93% rename from spec/dynamic_spec.lua rename to spec/STU3/dynamic_spec.lua index 325a4f6..f2865ed 100644 --- a/spec/dynamic_spec.lua +++ b/spec/STU3/dynamic_spec.lua @@ -40,9 +40,9 @@ for _, testcase in ipairs(data) do describe(case_name.." xml to json", function() -- do the setup outside of setup(), as setup() can't handle creating it()'s within it local t = {} - io.input("spec/"..json_file) + io.input("spec/STU3/"..json_file) t.json_data = io.read("*a") - t.xml_data = in_fhir_json("spec/"..xml_file, {file = true}) + t.xml_data = in_fhir_json("spec/STU3/"..xml_file, {file = true, fhirversion = "STU3"}) t.json_example = cjson.decode(t.json_data) t.xml_example = cjson.decode(t.xml_data) @@ -78,9 +78,9 @@ for _, testcase in ipairs(data) do describe(case_name.. " json to xml", function() -- do the setup outside of setup(), as setup() can't handle creating it()'s within it local t = {} - io.input("spec/"..xml_file) + io.input("spec/STU3/"..xml_file) t.xml_data = io.read("*a") - t.json_data = in_fhir_xml("spec/"..json_file, {file = true}) + t.json_data = in_fhir_xml("spec/STU3/"..json_file, {file = true, fhirversion = "STU3"}) t.json_example = xml.load(t.json_data) t.xml_example = xml.load(t.xml_data) diff --git a/spec/handle_previously_problematic_cases_spec.lua b/spec/STU3/handle_previously_problematic_cases_spec.lua similarity index 98% rename from spec/handle_previously_problematic_cases_spec.lua rename to spec/STU3/handle_previously_problematic_cases_spec.lua index 68b00d8..a8e8a61 100644 --- a/spec/handle_previously_problematic_cases_spec.lua +++ b/spec/STU3/handle_previously_problematic_cases_spec.lua @@ -68,7 +68,7 @@ describe("previously failing conversions", function() -]]) +]], {fhirversion = "STU3"}) end) describe("should handle ValueSet.url correctly", function() @@ -132,7 +132,8 @@ describe("previously failing conversions", function() ], "date": "2015-06-22", "description": "This is an example value set that includes all the LOINC codes for serum/plasma cholesterol from v2.36.", - "copyright": "This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at http://loinc.org/terms-of-use."}]]) + "copyright": "This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at http://loinc.org/terms-of-use."}]], + {fhirversion = "STU3"}) end) -end) \ No newline at end of file +end) diff --git a/spec/json-edge-cases (fhir-formats).json b/spec/STU3/json-edge-cases (fhir-formats).json similarity index 100% rename from spec/json-edge-cases (fhir-formats).json rename to spec/STU3/json-edge-cases (fhir-formats).json diff --git a/spec/json-edge-cases (fhir-formats).xml b/spec/STU3/json-edge-cases (fhir-formats).xml similarity index 100% rename from spec/json-edge-cases (fhir-formats).xml rename to spec/STU3/json-edge-cases (fhir-formats).xml diff --git a/spec/json-edge-cases.json b/spec/STU3/json-edge-cases.json similarity index 100% rename from spec/json-edge-cases.json rename to spec/STU3/json-edge-cases.json diff --git a/spec/json-edge-cases.xml b/spec/STU3/json-edge-cases.xml similarity index 100% rename from spec/json-edge-cases.xml rename to spec/STU3/json-edge-cases.xml diff --git a/spec/misc_functions_spec.lua b/spec/STU3/misc_functions_spec.lua similarity index 100% rename from spec/misc_functions_spec.lua rename to spec/STU3/misc_functions_spec.lua diff --git a/spec/patient-example-good.json b/spec/STU3/patient-example-good.json similarity index 100% rename from spec/patient-example-good.json rename to spec/STU3/patient-example-good.json diff --git a/spec/patient-example.xml b/spec/STU3/patient-example.xml similarity index 100% rename from spec/patient-example.xml rename to spec/STU3/patient-example.xml diff --git a/spec/patient_example_spec.lua b/spec/STU3/patient_example_spec.lua similarity index 84% rename from spec/patient_example_spec.lua rename to spec/STU3/patient_example_spec.lua index 755a3a5..3a68f06 100644 --- a/spec/patient_example_spec.lua +++ b/spec/STU3/patient_example_spec.lua @@ -28,9 +28,9 @@ describe("xml to json", function() positive_example_data, patient_example_data setup(function() - io.input("spec/patient-example-good.json") + io.input("spec/STU3/patient-example-good.json") positive_example_data = io.read("*a") - patient_example_data = in_fhir_json("spec/patient-example.xml", {file = true}) + patient_example_data = in_fhir_json("spec/STU3/patient-example.xml", {file = true, fhirversion = "STU3"}) -- for same div data test assert:set_parameter("TableFormatLevel", -1) @@ -62,9 +62,9 @@ describe("json to xml", function() positive_example_data, patient_example_data setup(function() - io.input("spec/patient-example.xml") + io.input("spec/STU3/patient-example.xml") positive_example_data = io.read("*a") - patient_example_data = in_fhir_xml("spec/patient-example-good.json", {file = true}) + patient_example_data = in_fhir_xml("spec/STU3/patient-example-good.json", {file = true, fhirversion = "STU3"}) -- for same div data test assert:set_parameter("TableFormatLevel", -1) @@ -72,6 +72,6 @@ describe("json to xml", function() 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)), cjson.decode(in_fhir_json(patient_example_data))) + assert.same(cjson.decode(in_fhir_json(positive_example_data, {fhirversion = "STU3"})), cjson.decode(in_fhir_json(patient_example_data, {fhirversion = "STU3"}))) end) - end) \ No newline at end of file + end) diff --git a/spec/convert-json-edge-cases.lua b/spec/convert-json-edge-cases.lua deleted file mode 100644 index f2555a8..0000000 --- a/spec/convert-json-edge-cases.lua +++ /dev/null @@ -1,10 +0,0 @@ -package.path = "src/?.lua;"..package.path -local to_json = require("fhirformats").to_json -local to_xml = require("fhirformats").to_xml -local inspect = require("inspect") - -io.output("spec/json-edge-cases (fhir-formats).xml") -io.write(to_xml("spec/json-edge-cases.json", {file = true})) -io.output("spec/json-edge-cases (fhir-formats).json") -io.write(to_json("spec/json-edge-cases.xml", {file=true, pretty = true})) -io.output():close() \ No newline at end of file diff --git a/src/fhir-data/R4/fhir-elements.json b/src/fhir-data/R4/fhir-elements.json new file mode 100644 index 0000000..44f7fb9 --- /dev/null +++ b/src/fhir-data/R4/fhir-elements.json @@ -0,0 +1,59858 @@ +[ + { + "min": 0, + "path": "Element", + "weight": 1, + "max": "*", + "kind": "complex-type", + "derivations": [ + "Address", + "Annotation", + "Attachment", + "BackboneElement", + "CodeableConcept", + "Coding", + "ContactDetail", + "ContactPoint", + "Contributor", + "DataRequirement", + "Expression", + "Extension", + "HumanName", + "Identifier", + "Meta", + "Money", + "Narrative", + "ParameterDefinition", + "Period", + "Quantity", + "Range", + "Ratio", + "Reference", + "RelatedArtifact", + "SampledData", + "Signature", + "TriggerDefinition", + "UsageContext", + "base64Binary", + "boolean", + "date", + "dateTime", + "decimal", + "instant", + "integer", + "string", + "time", + "uri", + "xhtml" + ] + }, + { + "min": 0, + "path": "Element.id", + "weight": 2, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "Element.extension", + "weight": 3, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "BackboneElement", + "weight": 4, + "max": "*", + "kind": "complex-type", + "derivations": [ + "Dosage", + "ElementDefinition", + "MarketingStatus", + "Population", + "ProdCharacteristic", + "ProductShelfLife", + "SubstanceAmount", + "Timing" + ], + "type": "Element" + }, + { + "min": 0, + "path": "BackboneElement.id", + "weight": 5, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "BackboneElement.extension", + "weight": 6, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "BackboneElement.modifierExtension", + "weight": 7, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "base64Binary", + "weight": 8, + "max": "*", + "kind": "primitive-type", + "type": "Element" + }, + { + "min": 0, + "path": "base64Binary.id", + "weight": 9, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "base64Binary.extension", + "weight": 10, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "base64Binary.value", + "weight": 11, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "boolean", + "weight": 12, + "max": "*", + "kind": "primitive-type", + "type": "Element" + }, + { + "min": 0, + "path": "boolean.id", + "weight": 13, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "boolean.extension", + "weight": 14, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "boolean.value", + "weight": 15, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.Boolean" + }, + { + "min": 0, + "path": "canonical", + "weight": 16, + "max": "*", + "kind": "primitive-type", + "type": "uri" + }, + { + "min": 0, + "path": "canonical.id", + "weight": 17, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "canonical.extension", + "weight": 18, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "canonical.value", + "weight": 19, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "code", + "weight": 20, + "max": "*", + "kind": "primitive-type", + "type": "string" + }, + { + "min": 0, + "path": "code.id", + "weight": 21, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "code.extension", + "weight": 22, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "code.value", + "weight": 23, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "date", + "weight": 24, + "max": "*", + "kind": "primitive-type", + "type": "Element" + }, + { + "min": 0, + "path": "date.id", + "weight": 25, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "date.extension", + "weight": 26, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "date.value", + "weight": 27, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.Date" + }, + { + "min": 0, + "path": "dateTime", + "weight": 28, + "max": "*", + "kind": "primitive-type", + "type": "Element" + }, + { + "min": 0, + "path": "dateTime.id", + "weight": 29, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "dateTime.extension", + "weight": 30, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "dateTime.value", + "weight": 31, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.DateTime" + }, + { + "min": 0, + "path": "decimal", + "weight": 32, + "max": "*", + "kind": "primitive-type", + "type": "Element" + }, + { + "min": 0, + "path": "decimal.id", + "weight": 33, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "decimal.extension", + "weight": 34, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "decimal.value", + "weight": 35, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.Decimal" + }, + { + "min": 0, + "path": "id", + "weight": 36, + "max": "*", + "kind": "primitive-type", + "type": "string" + }, + { + "min": 0, + "path": "id.id", + "weight": 37, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "id.extension", + "weight": 38, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "id.value", + "weight": 39, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "instant", + "weight": 40, + "max": "*", + "kind": "primitive-type", + "type": "Element" + }, + { + "min": 0, + "path": "instant.id", + "weight": 41, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "instant.extension", + "weight": 42, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "instant.value", + "weight": 43, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.DateTime" + }, + { + "min": 0, + "path": "integer", + "weight": 44, + "max": "*", + "kind": "primitive-type", + "derivations": [ + "positiveInt", + "unsignedInt" + ], + "type": "Element" + }, + { + "min": 0, + "path": "integer.id", + "weight": 45, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "integer.extension", + "weight": 46, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "integer.value", + "weight": 47, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.Integer" + }, + { + "min": 0, + "path": "markdown", + "weight": 48, + "max": "*", + "kind": "primitive-type", + "type": "string" + }, + { + "min": 0, + "path": "markdown.id", + "weight": 49, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "markdown.extension", + "weight": 50, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "markdown.value", + "weight": 51, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "oid", + "weight": 52, + "max": "*", + "kind": "primitive-type", + "type": "uri" + }, + { + "min": 0, + "path": "oid.id", + "weight": 53, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "oid.extension", + "weight": 54, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "oid.value", + "weight": 55, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "positiveInt", + "weight": 56, + "max": "*", + "kind": "primitive-type", + "type": "integer" + }, + { + "min": 0, + "path": "positiveInt.id", + "weight": 57, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "positiveInt.extension", + "weight": 58, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "positiveInt.value", + "weight": 59, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "string", + "weight": 60, + "max": "*", + "kind": "primitive-type", + "derivations": [ + "code", + "id", + "markdown" + ], + "type": "Element" + }, + { + "min": 0, + "path": "string.id", + "weight": 61, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "string.extension", + "weight": 62, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "string.value", + "weight": 63, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "time", + "weight": 64, + "max": "*", + "kind": "primitive-type", + "type": "Element" + }, + { + "min": 0, + "path": "time.id", + "weight": 65, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "time.extension", + "weight": 66, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "time.value", + "weight": 67, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.Time" + }, + { + "min": 0, + "path": "unsignedInt", + "weight": 68, + "max": "*", + "kind": "primitive-type", + "type": "integer" + }, + { + "min": 0, + "path": "unsignedInt.id", + "weight": 69, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "unsignedInt.extension", + "weight": 70, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "unsignedInt.value", + "weight": 71, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "uri", + "weight": 72, + "max": "*", + "kind": "primitive-type", + "derivations": [ + "canonical", + "oid", + "url", + "uuid" + ], + "type": "Element" + }, + { + "min": 0, + "path": "uri.id", + "weight": 73, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "uri.extension", + "weight": 74, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "uri.value", + "weight": 75, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "url", + "weight": 76, + "max": "*", + "kind": "primitive-type", + "type": "uri" + }, + { + "min": 0, + "path": "url.id", + "weight": 77, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "url.extension", + "weight": 78, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "url.value", + "weight": 79, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "uuid", + "weight": 80, + "max": "*", + "kind": "primitive-type", + "type": "uri" + }, + { + "min": 0, + "path": "uuid.id", + "weight": 81, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "uuid.extension", + "weight": 82, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "uuid.value", + "weight": 83, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "xhtml", + "weight": 84, + "max": "*", + "kind": "primitive-type", + "type": "Element" + }, + { + "min": 0, + "path": "xhtml.id", + "weight": 85, + "max": "1", + "type": 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"max": "1", + "type": "code" + }, + { + "min": 1, + "path": "VisionPrescription.created", + "weight": 7648, + "max": "1", + "type": "dateTime" + }, + { + "min": 1, + "path": "VisionPrescription.patient", + "weight": 7649, + "max": "1", + "type": "Reference" + }, + { + "min": 0, + "path": "VisionPrescription.encounter", + "weight": 7650, + "max": "1", + "type": "Reference" + }, + { + "min": 1, + "path": "VisionPrescription.dateWritten", + "weight": 7651, + "max": "1", + "type": "dateTime" + }, + { + "min": 1, + "path": "VisionPrescription.prescriber", + "weight": 7652, + "max": "1", + "type": "Reference" + }, + { + "min": 1, + "path": "VisionPrescription.lensSpecification", + "weight": 7653, + "max": "*", + "type": "BackboneElement" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.id", + "weight": 7654, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.extension", + "weight": 7655, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.modifierExtension", + "weight": 7656, + "max": "*", + "type": "Extension" + }, + { + "min": 1, + "path": "VisionPrescription.lensSpecification.product", + "weight": 7657, + "max": "1", + "type": "CodeableConcept" + }, + { + "min": 1, + "path": "VisionPrescription.lensSpecification.eye", + "weight": 7658, + "max": "1", + "type": "code" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.sphere", + "weight": 7659, + "max": "1", + "type": "decimal" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.cylinder", + "weight": 7660, + "max": "1", + "type": "decimal" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.axis", + "weight": 7661, + "max": "1", + "type": "integer" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.prism", + "weight": 7662, + "max": "*", + "type": "BackboneElement" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.prism.id", + "weight": 7663, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.prism.extension", + "weight": 7664, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.prism.modifierExtension", + "weight": 7665, + "max": "*", + "type": "Extension" + }, + { + "min": 1, + "path": "VisionPrescription.lensSpecification.prism.amount", + "weight": 7666, + "max": "1", + "type": "decimal" + }, + { + "min": 1, + "path": "VisionPrescription.lensSpecification.prism.base", + "weight": 7667, + "max": "1", + "type": "code" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.add", + "weight": 7668, + "max": "1", + "type": "decimal" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.power", + "weight": 7669, + "max": "1", + "type": "decimal" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.backCurve", + "weight": 7670, + "max": "1", + "type": "decimal" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.diameter", + "weight": 7671, + "max": "1", + "type": "decimal" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.duration", + "weight": 7672, + "max": "1", + "type": "Quantity" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.color", + "weight": 7673, + "max": "1", + "type": "string" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.brand", + "weight": 7674, + "max": "1", + "type": "string" + }, + { + "min": 0, + "path": "VisionPrescription.lensSpecification.note", + "weight": 7675, + "max": "*", + "type": "Annotation" + }, + { + "min": 1, + "path": "MetadataResource", + "weight": 7676, + "max": "1", + "kind": "logical", + "type": "DomainResource" + }, + { + "min": 0, + "path": "MetadataResource.id", + "weight": 7677, + "max": "1", + "type": "http:\/\/hl7.org\/fhirpath\/System.String" + }, + { + "min": 0, + "path": "MetadataResource.meta", + "weight": 7678, + "max": "1", + "type": "Meta" + }, + { + "min": 0, + "path": "MetadataResource.implicitRules", + "weight": 7679, + "max": "1", + "type": "uri" + }, + { + "min": 0, + "path": "MetadataResource.language", + "weight": 7680, + "max": "1", + "type": "code" + }, + { + "min": 0, + "path": "MetadataResource.text", + "weight": 7681, + "max": "1", + "type": "Narrative" + }, + { + "min": 0, + "path": "MetadataResource.contained", + "weight": 7682, + "max": "*", + "type": "Resource" + }, + { + "min": 0, + "path": "MetadataResource.extension", + "weight": 7683, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "MetadataResource.modifierExtension", + "weight": 7684, + "max": "*", + "type": "Extension" + }, + { + "min": 0, + "path": "MetadataResource.url", + "weight": 7685, + "max": "1", + "type": "uri" + }, + { + "min": 0, + "path": "MetadataResource.version", + "weight": 7686, + "max": "1", + "type": "string" + }, + { + "min": 0, + "path": "MetadataResource.name", + "weight": 7687, + "max": "1", + "type": "string" + }, + { + "min": 0, + "path": "MetadataResource.title", + "weight": 7688, + "max": "1", + "type": "string" + }, + { + "min": 1, + "path": "MetadataResource.status", + "weight": 7689, + "max": "1", + "type": "code" + }, + { + "min": 0, + "path": "MetadataResource.experimental", + "weight": 7690, + "max": "1", + "type": "boolean" + }, + { + "min": 0, + "path": "MetadataResource.date", + "weight": 7691, + "max": "1", + "type": "dateTime" + }, + { + "min": 0, + "path": "MetadataResource.publisher", + "weight": 7692, + "max": "1", + "type": "string" + }, + { + "min": 0, + "path": "MetadataResource.contact", + "weight": 7693, + "max": "*", + "type": "ContactDetail" + }, + { + "min": 0, + "path": "MetadataResource.description", + "weight": 7694, + "max": "1", + "type": "markdown" + }, + { + "min": 0, + "path": "MetadataResource.useContext", + "weight": 7695, + "max": "*", + "type": "UsageContext" + }, + { + "min": 0, + "path": "MetadataResource.jurisdiction", + "weight": 7696, + "max": "*", + "type": "CodeableConcept" + } +] \ No newline at end of file diff --git a/src/fhir-data/fhir-elements.json b/src/fhir-data/STU3/fhir-elements.json similarity index 100% rename from src/fhir-data/fhir-elements.json rename to src/fhir-data/STU3/fhir-elements.json diff --git a/src/fhir-data/download-fhir.sh b/src/fhir-data/download-fhir.sh index 0ecbedd..1e915b5 100755 --- a/src/fhir-data/download-fhir.sh +++ b/src/fhir-data/download-fhir.sh @@ -1,3 +1,5 @@ +#!/usr/bin/env bash + # FHIR Formats # Copyright (C) 2016-2017, 2022 Vadim Peretokin @@ -14,12 +16,44 @@ # See the License for the specific language governing permissions and # limitations under the License. -rm *.json +# Set default FHIR version to STU3 +version="STU3" + +# Parse command line argument +while getopts ":r:" opt; do + case $opt in + r) + # Set FHIR version + version=$OPTARG + ;; + \?) + echo "Invalid option: -$OPTARG" >&2 + exit 1 + ;; + :) + echo "Option -$OPTARG requires an argument." >&2 + exit 1 + ;; + esac +done -# STU 3.0.1 snapshot -wget http://hl7.org/fhir/STU3/profiles-types.json -wget http://hl7.org/fhir/STU3/profiles-resources.json +# Create folder for data +mkdir $version + +# Change to folder +cd $version + +# Remove existing JSON files +rm *.json -# Latest Continuous Build -# wget http://hl7-fhir.github.io/profiles-resources.json -# wget http://hl7-fhir.github.io/profiles-types.json +# Download FHIR profiles and types +if [ "$version" = "STU3" ]; then + wget http://hl7.org/fhir/STU3/profiles-types.json + wget http://hl7.org/fhir/STU3/profiles-resources.json +elif [ "$version" = "R4" ]; then + wget http://hl7.org/fhir/R4/profiles-types.json + wget http://hl7.org/fhir/R4/profiles-resources.json +else + echo "Error: Invalid FHIR version specified" + exit 1 +fi diff --git a/src/fhir-data/generate-fhir-data.lua b/src/fhir-data/generate-fhir-data.lua index 890997b..2b4002e 100644 --- a/src/fhir-data/generate-fhir-data.lua +++ b/src/fhir-data/generate-fhir-data.lua @@ -18,8 +18,15 @@ local from_json = require("cjson").decode local pretty = require "resty.prettycjson" +local argparse = require "argparse" -local default_file = "fhir-elements.json" + +local parser = argparse("generate-fhir-data.lua", "Generate condensed FHIR data from the FHIR specification, just elements necessary for version conversion.") +-- see https://argparse.readthedocs.io/en/stable/index.html +parser:option("-r --fhir-release", 'FHIR version to work with', "STU3"):choices({"STU3", "R4"}):count("1") +local args = parser:parse() + +local output_file = args.fhir_release.."/fhir-elements.json" local function read_json(filename) io.input(filename) @@ -130,7 +137,7 @@ local function parse_data(data, output, resources_map, weight_counter) end local function save(output) - io.output(default_file) + io.output(output_file) io.write(pretty(output)) io.close() end @@ -153,8 +160,8 @@ end -- resources_map is used to compute derivations (who extends Resource and then DomainResource) -- weight_counter is for sorting elements for the XML format local output, resources_map, weight_counter = {}, {}, 1 -output, resources_map, weight_counter = parse_data(read_json("profiles-types.json"), output, resources_map, weight_counter) -output, resources_map, weight_counter = parse_data(read_json("profiles-resources.json"), output, resources_map, weight_counter) +output, resources_map, weight_counter = parse_data(read_json(args.fhir_release.."/profiles-types.json"), output, resources_map, weight_counter) +output, resources_map, weight_counter = parse_data(read_json(args.fhir_release.."/profiles-resources.json"), output, resources_map, weight_counter) update_backlinks(resources_map) diff --git a/src/fhirformats.lua b/src/fhirformats.lua index c173899..91056c3 100755 --- a/src/fhirformats.lua +++ b/src/fhirformats.lua @@ -46,7 +46,13 @@ local convert_to_json, file_exists, read_filecontent, read_file, make_json_datat local handle_json_recursively, print_simple_datatype, convert_to_lua_from_json local convert_to_xml, print_complex_datatype, list_to_map -local fhir_data +-- global pointers to the FHIR schema to operate on, and any errors that happened during conversion. +-- These are the only such global pointers in the whole program, and the reduced complexity of the code +-- is worth it. +local fhir_data, conversion_errors + +-- individual FHIR schemas per FHIR version supported +local fhir_data_stu3, fhir_data_r4 local null_value local json_decode, json_encode @@ -63,7 +69,7 @@ elseif lunajson then return lunajson.encode(data, null_value) end else - error("neither rapidjson nor luajson libraries found to do JSON encoding/decoding with") + error("neither rapidjson nor lunajson libraries found to do JSON encoding/decoding with") end -- credit: http://stackoverflow.com/a/4991602/72944 @@ -75,9 +81,27 @@ end -- find the location of the running instance of fhirformats.lua, so the error messages can be more informative local PATH = (... and (...):match("(.+)%.[^%.]+$") or (...)) or "(path of the script unknown)" -read_fhir_data = function(filename) +function table.size(t) + if not t then + return 0 + end + local i = 0 + for k, v in pairs(t) do + i = i + 1 + end + return i +end + +read_fhir_data = function(filename, fhirversion) + assert(fhirversion == "STU3" or fhirversion == "R4", + string.format("fhirversion must be STU3 or R4. '%s' is not supported at this level", tostring(fhirversion))) + -- prefer the filename, but substitute the nil if not given - local locations = {(filename or ""), "fhir-data/fhir-elements.json", "src/fhir-data/fhir-elements.json", "../src/fhir-data/fhir-elements.json", "fhir-data/fhir-elements.json"} + local locations = { + (filename or ""), "fhir-data/"..fhirversion.."/fhir-elements.json", + "src/fhir-data/"..fhirversion.."/fhir-elements.json", + "../src/fhir-data/"..fhirversion.."/fhir-elements.json" + } local data for _, file in ipairs(locations) do @@ -114,8 +138,8 @@ getindex = function(list, value) end end --- returns a list as a key-value map, value can be a value --- to assign or a function to evaluate before assignment. +-- returns a list as a key-value map, 'value' can be a static value +-- to assign to all entries or a function to evaluate before assignment. -- Function will have the processed list value as first argument list_to_map = function(list, value) if not list then return nil end @@ -199,7 +223,7 @@ map_fhir_data = function(raw_fhir_data) parse_element(element) end - -- and lastly, to ensure all derivations are in (as the order of resources could affect it + -- and lastly, to ensure all derivations are in (as the order of resources could affect it) for i = 1, #raw_fhir_data do local element = raw_fhir_data[i] parse_element(element) @@ -229,7 +253,7 @@ fhir_typed = function(output_stack, node) local fhir_definition = get_fhir_definition(output_stack, node.xml) if not fhir_definition then - print(string.format("Warning: %s is not a known FHIR element; couldn't check its FHIR type to decide the JSON type.", tconcat(output_stack, "."))) + conversion_errors[#conversion_errors+1] = string.format("Warning: %s is not a known FHIR element; couldn't check its FHIR type to decide the JSON type.", tconcat(output_stack, ".")) return value end @@ -280,9 +304,21 @@ is_fhir_resource = function (resourcename) end -- accepts the path as a set of strings instead of a table+string, and is exposed publicly +-- last argument can be "STU3" or "R4" to pick a FHIR version. +-- Defaults to STU3 and will continue to as future FHIR versions are released to keep API compatibility. -- returns a copy of the fhir element with underscores removed get_fhir_definition_public = function(...) local output_stack = {...} + if output_stack[#output_stack] == "STU3" then + fhir_data = fhir_data_stu3 + output_stack[#output_stack] = nil + elseif output_stack[#output_stack] == "R4" then + fhir_data = fhir_data_r4 + output_stack[#output_stack] = nil + else + fhir_data = fhir_data_stu3 + end + local element_to_check = output_stack[#output_stack] output_stack[#output_stack] = nil @@ -300,7 +336,7 @@ make_json_datatype = function(output_stack, element_to_check) local fhir_definition = get_fhir_definition(output_stack, element_to_check) if not fhir_definition then - print(string.format("Warning: %s.%s is not a known FHIR element; couldn't check max cardinality for it to decide on a JSON object or array.", tconcat(output_stack, "."), element_to_check)) + conversion_errors[#conversion_errors+1] = string.format("Warning: %s.%s is not a known FHIR element; couldn't check max cardinality for it to decide on a JSON object or array.", tconcat(output_stack, "."), element_to_check) end if fhir_definition and fhir_definition._max == "*" then @@ -319,7 +355,7 @@ get_json_datatype = function(output_stack, element_to_check) local fhir_data_pointer = get_fhir_definition(output_stack, element_to_check) if fhir_data_pointer == nil then - print(string.format("Warning: %s.%s is not a known FHIR element; couldn't check max cardinality for it to decide on a JSON object or array.", tconcat(output_stack, "."), element_to_check)) + conversion_errors[#conversion_errors+1] = string.format("Warning: %s.%s is not a known FHIR element; couldn't check max cardinality for it to decide on a JSON object or array.", tconcat(output_stack, "."), element_to_check) end if fhir_data_pointer and fhir_data_pointer._max == "*" then @@ -332,7 +368,7 @@ end get_xml_weight = function(output_stack, element_to_check) local fhir_definition = get_fhir_definition(output_stack, element_to_check) if not fhir_definition then - print(string.format("Warning: %s.%s is not a known FHIR element; won't be able to sort it properly in the XML output.", tconcat(output_stack, "."), element_to_check)) + conversion_errors[#conversion_errors+1] = string.format("Warning: %s.%s is not a known FHIR element; won't be able to sort it properly in the XML output.", tconcat(output_stack, "."), element_to_check) return 0 else return fhir_definition._weight @@ -343,7 +379,7 @@ end get_datatype_kind = function(output_stack, element_to_check) local fhir_definition = get_fhir_definition(output_stack, element_to_check) if not fhir_definition then - print(string.format("Warning: %s.%s is not a known FHIR element; might not convert it to a proper JSON 'element' or '_element' representation.", tconcat(output_stack, "."), element_to_check)) + conversion_errors[#conversion_errors+1] = string.format("Warning: %s.%s is not a known FHIR element; might not convert it to a proper JSON 'element' or '_element' representation.", tconcat(output_stack, "."), element_to_check) return 0 else local datatype_fhir_definition = get_fhir_definition({}, fhir_definition._type) @@ -559,11 +595,33 @@ function read_only( t ) end end +function load_fhir_data(fhirversion) + if fhirversion == "auto" then + fhir_data_stu3 = fhir_data_stu3 or map_fhir_data(read_fhir_data(nil, "STU3")) + fhir_data_r4 = fhir_data_r4 or map_fhir_data(read_fhir_data(nil, "R4")) + fhir_data = fhir_data_r4 + read_only(fhir_data_r4) + read_only(fhir_data_stu3) + elseif fhirversion == "STU3" then + fhir_data_stu3 = fhir_data_stu3 or map_fhir_data(read_fhir_data(nil, "STU3")) + fhir_data = fhir_data_stu3 + read_only(fhir_data_stu3) + elseif fhirversion == "R4" then + fhir_data_r4 = fhir_data_r4 or map_fhir_data(read_fhir_data(nil, "R4")) + fhir_data = fhir_data_r4 + read_only(fhir_data_r4) + end +end + +-- options.fhirversion is optional, and defaults to "auto" which is try all FHIR versions, starting from R4 +-- idea here is to make it as easy as possible to convert - it should just work convert_to_json = function(data, options) - fhir_data = fhir_data or map_fhir_data(read_fhir_data()) + local valid_versions = {["STU3"] = "STU3", ["R4"] = "R4"} + options.fhirversion = valid_versions[options.fhirversion] or "auto" + + load_fhir_data(options.fhirversion) assert(next(fhir_data), "convert_to_json: FHIR Schema could not be parsed in.") - read_only(fhir_data) local xml_data if options and options.file then @@ -576,7 +634,29 @@ convert_to_json = function(data, options) local output_levels = {[1] = {output}} local output_stack = {} + conversion_errors = {} local data_in_lua = convert_to_lua_from_xml(xml_data, nil, output, output_levels, output_stack) + -- if R4 on auto didn't work, try STU3 + if options.fhirversion == "auto" and #conversion_errors > 0 then + local amount_of_errors = #conversion_errors + + load_fhir_data("STU3") + output = {} + output_levels = {[1] = {output}} + output_stack = {} + + data_in_lua = convert_to_lua_from_xml(xml_data, nil, output, output_levels, output_stack) + if #conversion_errors > amount_of_errors then + print("Neither R4 nor STU3 conversion worked, have ".. #conversion_errors.. " errors.") + for _, error in ipairs(conversion_errors) do + print(error) + end + end + else + for _, error in ipairs(conversion_errors) do + print(error) + end + end return (options and options.pretty) and prettyjson(data_in_lua, nil, ' ', nil, json_encode) or json_encode(data_in_lua) @@ -748,11 +828,15 @@ convert_to_lua_from_json = function(json_data, output, xml_output_levels, output return handle_json_recursively(json_data, xml_output_levels, output_stack) end +-- options.fhirversion is optional, and defaults to "auto" which is try all FHIR versions, starting from R4 +-- idea here is to make it as easy as possible to convert - it should just work convert_to_xml = function(data, options) - fhir_data = fhir_data or map_fhir_data(read_fhir_data()) + local valid_versions = {["STU3"] = "STU3", ["R4"] = "R4"} + options.fhirversion = valid_versions[options.fhirversion] or "auto" + + load_fhir_data(options.fhirversion) assert(next(fhir_data), "convert_to_xml: FHIR Schema could not be parsed in.") - read_only(fhir_data) local json_data if options and options.file then @@ -761,16 +845,37 @@ convert_to_xml = function(data, options) json_data = read_filecontent(data, json_decode) end - local output, output_stack = {}, {} + local resourceType, output, output_stack = json_data.resourceType, {}, {} local xml_output_levels = {output} + conversion_errors = {} convert_to_lua_from_json(json_data, output, xml_output_levels, output_stack) + -- if R4 on auto didn't work, try STU3 + if options.fhirversion == "auto" and #conversion_errors > 0 then + local amount_of_errors = #conversion_errors + load_fhir_data("STU3") + + -- convert_to_lua_from_json strips the resourcetype, so add it back in + json_data.resourceType = resourceType + output, output_stack = {}, {} + xml_output_levels = {output} + convert_to_lua_from_json(json_data, output, xml_output_levels, output_stack) + if amount_of_errors ~= #conversion_errors then + print("Neither R4 nor STU3 conversion worked, have ".. #conversion_errors.. " errors.") + for _, error in ipairs(conversion_errors) do + print(error) + end + end + else + for _, error in ipairs(conversion_errors) do + print(error) + end + end return xml.dump(output) end -map_fhir_data(read_fhir_data()) -read_only(fhir_data) +load_fhir_data("auto") return { to_json = convert_to_json,