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Merge pull request #16 from hl7au/integration-test
Integration test
2 parents 33b279c + 0c87851 commit f16e698

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‎.github/workflows/dotnet.yml

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@@ -52,10 +52,33 @@ jobs:
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name: ${{ matrix.program }}-${{ matrix.os }}-${{ matrix.arch }}-binaries
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path: |
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Sparked.${{ matrix.program }}-${{ matrix.os }}-${{ matrix.arch }}Output
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Test-Dot-Net:
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needs:
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- Build-Dot-Net
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Download artifact
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uses: actions/download-artifact@v4
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with:
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name: Csv2FhirMapping-linux-x64-binaries
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path: /tmp
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- name: Prepare to run
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run: chmod +x /tmp/Csv2Fhir
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- name: Run converter
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run: |
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cd Sparked.Csv2FhirMapping/test &&
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/tmp/Csv2Fhir Medication ./medication.csv ./output/
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- name: Check output
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id: git-diff-action
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run: echo "changed=$(git status --porcelain=v1 2>/dev/null | wc -l | tr -d '[:space:]')" >> "$GITHUB_OUTPUT"
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- if: steps.git-diff-action.outputs.changed != '0'
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name: Fail
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run: git diff | cat && exit -1
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Release:
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if: contains(github.ref, 'tags/v')
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needs:
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- Build-Dot-Net
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- Test-Dot-Net
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- Build-Python
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runs-on: ubuntu-latest
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steps:

‎.gitignore

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/*.log
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*/dist/*
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/xls-converter/xls_converter/__pycache__/
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Sparked.Csv2FhirMapping/test/Csv2FhirMapping-linux-arm64-binaries/*
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Sparked.Csv2FhirMapping/test/Csv2FhirMapping-linux-arm64.zip

‎Sparked.Csv2FhirMapping/test/Maps/CSV2Medication.map

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map "http://example.org/StructureMap/CSV2Medication" = "CSV2Medication"
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uses "http://example.org/StructureDefinition/MedicationCSV" as source
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uses "http://hl7.org/fhir/StructureDefinition/Medication" as target
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group ToMedication(source src : MedicationCSV, target tgt : Medication) {
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// id
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src.id as s_id where length() > 0 -> tgt.id = s_id;
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// meta.profile
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src -> tgt.meta = create('Meta') as meta then {
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src -> meta.profile = 'http://hl7.org.au/fhir/core/StructureDefinition/au-core-medication';
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};
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// code 1..1 MS
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src.code_coding1_code as s_coding1 where length() > 0 -> tgt.code as t_code then {
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s_coding1 where length() > 0 -> t_code then {
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src.code_coding1_system as coding1_system -> t_code.coding = c(coding1_system, s_coding1) as t_coding first then {
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src.code_coding1_display as s_display where length() > 0 -> t_coding.display = s_display;
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src.code_coding1_medicationType_code as s_medicationType_code where length() > 0 -> t_coding.extension as t_medication_type first then {
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s_medicationType_code -> t_medication_type.url = "http://hl7.org.au/fhir/StructureDefinition/medication-type";
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s_medicationType_code -> t_medication_type.value = c("http://terminology.hl7.org.au/CodeSystem/medication-type", s_medicationType_code) as t_coding then {
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src.code_coding1_medicationType_display as s_medicationType_display where length() > 0 -> t_coding.display = s_medicationType_display;
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};
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};
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};
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src.code_coding2_code as s_coding2 where length() > 0 -> t_code then {
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src.code_coding2_system as coding2_system -> t_code.coding = c(coding2_system, s_coding2) as t_coding first then {
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src.code_coding2_display as s_display where length() > 0 -> t_coding.display = s_display;
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};
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};
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src.code_coding3_code as s_code where length() > 0 -> t_code then {
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src.code_coding3_system as s_system -> t_code.coding = c(s_system, s_code) as t_coding first then {
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src.code_coding3_display as s_display where length() > 0 -> t_coding.display = s_display;
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};
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};
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};
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src.code_text as s_text where length() > 0 -> t_code.text = s_text;
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};
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// code coding missing
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src.code_coding1_code as s_coding1 where length() = 0 -> tgt.code as t_code then {
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// text only
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src.code_text as s_text where length() > 0 -> t_code.text = s_text;
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// code missing
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src.code_text as s_text where length() = 0 -> t_code.coding = c('http://terminology.hl7.org/CodeSystem/data-absent-reason', 'unknown');
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};
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// form 0..1
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src.form_coding1_code as s_coding1 where length() > 0 -> tgt.form as t_form then {
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s_coding1 -> t_form then {
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src.form_coding1_system as coding1_system -> t_form.coding = c(coding1_system, s_coding1) as t_coding first then {
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src.form_coding1_display as s_display where length() > 0 -> t_coding.display = s_display;
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};
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src.form_coding2_code as s_coding2 where length() > 0 -> t_form then {
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src.form_coding2_system as coding2_system -> t_form.coding = c(coding2_system, s_coding2) as t_coding first then {
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src.form_coding2_display as s_display where length() > 0 -> t_coding.display = s_display;
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};
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};
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src.form_coding3_code as s_code where length() > 0 -> t_form then {
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src.form_coding3_system as s_system -> t_form.coding = c(s_system, s_code) as t_coding first then {
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src.form_coding3_display as s_display where length() > 0 -> t_coding.display = s_display;
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};
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};
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};
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src.form_text as s_text where length() > 0 -> t_form.text = s_text;
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};
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// ingredient 0..*
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// ingredient.itemCodeableConcept 1..1
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src.ingredient_itemCodeableConcept_coding1_code as s_itemCoding1_code where length() > 0 -> tgt.ingredient as t_ingredient first then {
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src.ingredient_itemCodeableConcept_coding1_system as s_itemCoding1_system -> t_ingredient then {
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src.ingredient_itemCodeableConcept_coding1_display as s_itemCoding1_display -> t_ingredient.item = cc(s_itemCoding1_system, s_itemCoding1_code, s_itemCoding1_display) as t_item then {
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src.ingredient_itemCodeableConcept_coding2_code as s_coding_code where length() > 0 -> t_item then {
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src.ingredient_itemCodeableConcept_coding2_system as s_coding_system -> t_item.coding = c(s_coding_system, s_coding_code) as t_coding then {
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src.ingredient_itemCodeableConcept_coding2_display as s_coding_display where length() > 0 -> t_coding.display = s_coding_display;
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};
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};
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src.ingredient_itemCodeableConcept_text as s_text where length() > 0 -> t_item.text = s_text;
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};
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};
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// ingredient.strength 0..1 Ratio
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src.ingredient_strength_numerator_value as s_value where length() > 0 -> t_ingredient.strength as t_strength then {
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s_value -> t_strength.numerator as t_numerator then {
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s_value -> t_numerator.value = s_value;
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src.ingredient_strength_numerator_unit as s_unit where length() > 0 -> t_numerator.unit = s_unit;
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src.ingredient_strength_numerator_code as s_code where length() > 0 -> t_numerator.code = s_code;
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src.ingredient_strength_numerator_system as s_system where length() > 0 -> t_numerator.system = s_system;
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};
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src.ingredient_strength_denominator_value as s_value where length() > 0 -> t_strength then {
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s_value -> t_strength.denominator as t_denominator then {
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s_value -> t_denominator.value = s_value;
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src.ingredient_strength_denominator_unit as s_unit where length() > 0 -> t_denominator.unit = s_unit;
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src.ingredient_strength_denominator_code as s_code where length() > 0 -> t_denominator.code = s_code;
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src.ingredient_strength_denominator_system as s_system where length() > 0 -> t_denominator.system = s_system;
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};
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};
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};
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};
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}

‎Sparked.Csv2FhirMapping/test/medication.csv

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id,code_coding1_medicationType_code,code_coding1_medicationType_display,code_coding1_system,code_coding1_code,code_coding1_display,code_coding2_system,code_coding2_code,code_coding2_display,code_coding3_system,code_coding3_code,code_coding3_display,code_text,form_coding1_system,form_coding1_code,form_coding1_display,form_coding2_system,form_coding2_code,form_coding2_display,form_coding3_system,form_coding3_code,form_coding3_display,ingredient_itemCodeableConcept_coding1_system,ingredient_itemCodeableConcept_coding1_code,ingredient_itemCodeableConcept_coding1_display,ingredient_itemCodeableConcept_coding2_system,ingredient_itemCodeableConcept_coding2_code,ingredient_itemCodeableConcept_coding2_display,ingredient_strength_numerator_value,ingredient_strength_numerator_unit,ingredient_strength_numerator_system,ingredient_strength_numerator_code,ingredient_strength_denominator_value,ingredient_strength_denominator_unit,ingredient_strength_denominator_system,ingredient_strength_denominator_code
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1active-ingredient,BPD,Branded product with no strengths or form,http://snomed.info/sct,4445011000036103,Chlorsig,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
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2active-ingredients,,,http://pbs.gov.au/code/item,13382H,PERINDOPRIL + AMLODIPINE,,,,,,,"perindopril arginine 10 mg + amlodipine 10 mg tablet, 30",,,,,,,,,,,,,,,,,,,,,,,
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simvastatin,,,http://snomed.info/sct,320000009,Simvastatin 40 mg oral tablet,,,,,,,simvastatin 40 MG Disintegrating Oral Tablet,http://snomed.info/sct,263011000036100,orally disintegrating tablet,,,,,,,http://snomed.info/sct,2588011000036103,simvastatin,,,,40,mg,http://unitsofmeasure.org,mg,1,tablet,http://unitsofmeasure.org,{tbl}
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metformin-mp,,,http://snomed.info/sct,21614011000036102,metformin,,,,,,,,http://snomed.info/sct,154011000036109,tablet,,,,,,,,,,,,,,,,,,,,
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metformin-mpp,,,http://snomed.info/sct,28037011000036102,"Metformin hydrochloride 500 mg tablet, 100",,,,,,,,http://snomed.info/sct,154011000036109,tablet,,,,,,,,,,,,,,,,,,,,
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metformin-tpp,,,http://snomed.info/sct,929529011000036109,"Metformin (Apo) 500 mg tablet, 100",,,,,,,,http://snomed.info/sct,154011000036109,tablet,,,,,,,,,,,,,,,,,,,,
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perindopril-amlodipine-mpp,,,http://snomed.info/sct,86430011000036105,"Perindopril arginine 10 mg + amlodipine 10 mg tablet, 30",,,,,,,,http://snomed.info/sct,154011000036109,tablet,,,,,,,,,,,,,,,,,,,,
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reaptan-tpp,,,http://snomed.info/sct,926214011000036103,"Reaptan 10 mg/10 mg (perindopril arginine/amlodipine) tablet, 30",,,,,,,,http://snomed.info/sct,154011000036109,tablet,,,,,,,,,,,,,,,,,,,,
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reaptan-missing-code,,,,,,,,,,,,,http://snomed.info/sct,154011000036109,tablet,,,,,,,,,,,,,,,,,,,,

‎Sparked.Csv2FhirMapping/test/output/Medication-1active-ingredient.json

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{
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"resourceType": "Medication",
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"id": "1active-ingredient",
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"meta": {
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"profile": [
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"http://hl7.org.au/fhir/core/StructureDefinition/au-core-medication"
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]
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},
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"code": {
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"coding": [
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{
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"extension": [
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{
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"url": "http://hl7.org.au/fhir/StructureDefinition/medication-type",
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"valueCoding": {
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"system": "http://terminology.hl7.org.au/CodeSystem/medication-type",
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"code": "BPD",
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"display": "Branded product with no strengths or form"
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}
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}
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],
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"system": "http://snomed.info/sct",
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"code": "4445011000036103",
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"display": "Chlorsig"
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}
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]
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}
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}

‎Sparked.Csv2FhirMapping/test/output/Medication-2active-ingredients.json

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{
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"resourceType": "Medication",
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"id": "2active-ingredients",
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"meta": {
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"profile": [
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"http://hl7.org.au/fhir/core/StructureDefinition/au-core-medication"
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]
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},
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"code": {
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"coding": [
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{
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"system": "http://pbs.gov.au/code/item",
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"code": "13382H",
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"display": "PERINDOPRIL + AMLODIPINE"
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}
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],
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"text": "perindopril arginine 10 mg + amlodipine 10 mg tablet, 30"
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}
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}

‎Sparked.Csv2FhirMapping/test/output/Medication-metformin-mp.json

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{
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"resourceType": "Medication",
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"id": "metformin-mp",
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"meta": {
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"profile": [
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"http://hl7.org.au/fhir/core/StructureDefinition/au-core-medication"
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]
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},
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"code": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "21614011000036102",
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"display": "metformin"
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}
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]
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},
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"form": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "154011000036109",
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"display": "tablet"
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}
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]
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}
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}

‎Sparked.Csv2FhirMapping/test/output/Medication-metformin-mpp.json

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{
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"resourceType": "Medication",
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"id": "metformin-mpp",
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"meta": {
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"profile": [
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"http://hl7.org.au/fhir/core/StructureDefinition/au-core-medication"
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]
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},
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"code": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "28037011000036102",
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"display": "Metformin hydrochloride 500 mg tablet, 100"
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}
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]
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},
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"form": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "154011000036109",
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"display": "tablet"
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}
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]
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}
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}

‎Sparked.Csv2FhirMapping/test/output/Medication-metformin-tpp.json

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{
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"resourceType": "Medication",
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"id": "metformin-tpp",
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"meta": {
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"profile": [
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"http://hl7.org.au/fhir/core/StructureDefinition/au-core-medication"
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]
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},
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"code": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "929529011000036109",
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"display": "Metformin (Apo) 500 mg tablet, 100"
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}
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]
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},
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"form": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "154011000036109",
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"display": "tablet"
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}
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]
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}
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}

‎Sparked.Csv2FhirMapping/test/output/Medication-perindopril-amlodipine-mpp.json

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{
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"resourceType": "Medication",
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"id": "perindopril-amlodipine-mpp",
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"meta": {
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"profile": [
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"http://hl7.org.au/fhir/core/StructureDefinition/au-core-medication"
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]
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},
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"code": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "86430011000036105",
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"display": "Perindopril arginine 10 mg + amlodipine 10 mg tablet, 30"
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}
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]
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},
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"form": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "154011000036109",
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"display": "tablet"
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}
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]
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}
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}

‎Sparked.Csv2FhirMapping/test/output/Medication-reaptan-missing-code.json

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{
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"resourceType": "Medication",
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"id": "reaptan-missing-code",
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"meta": {
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"profile": [
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"http://hl7.org.au/fhir/core/StructureDefinition/au-core-medication"
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]
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},
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"code": {
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"coding": [
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{
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"system": "http://terminology.hl7.org/CodeSystem/data-absent-reason",
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"code": "unknown"
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}
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]
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},
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"form": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "154011000036109",
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"display": "tablet"
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}
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]
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}
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}

‎Sparked.Csv2FhirMapping/test/output/Medication-reaptan-tpp.json

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{
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"resourceType": "Medication",
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"id": "reaptan-tpp",
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"meta": {
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"profile": [
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"http://hl7.org.au/fhir/core/StructureDefinition/au-core-medication"
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]
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},
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"code": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "926214011000036103",
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"display": "Reaptan 10 mg/10 mg (perindopril arginine/amlodipine) tablet, 30"
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}
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]
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},
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"form": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "154011000036109",
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"display": "tablet"
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}
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]
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}
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}

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