Feature/add condition (#1)

* Updated fsh, updated add guidance * Download fonts in pipeline * removed duplicate instance definitions from fsh * fix example link * fix some validation errors * fix jekll plantuml install * Generate query output in pipeline, change use case structure * Add server examples and data model. * Fix filename of query output in pipeline * Serpate load and query in pipeline. * fix alert icons * Added guidance how to access swagger in docker instance of HAPI server. * change initial interaction to be more generic, i.e. not just condition. * link to server examples * changed cardinatlity as per comments from Marcus, include (same) contained provenance in all RA record resources. --------- Co-authored-by: Declan Kieran <[email protected]>
NHSDigital · Jan 30, 2024 · 86fcb6d · 86fcb6d
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diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -10,7 +10,7 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
-  
+
       - name: Install Node
         uses: actions/setup-node@v3
         with:
@@ -34,9 +34,33 @@ jobs:
       - name: Install Jekyll
         run: sudo gem install jekyll jekyll-plantuml
 
+      - name: Run FHIR server (TODO - load package from vars and validate - maybe just let the publisher handle that...)
+        run: docker run -d -p 8080:8080 -e hapi.fhir.daoconfig_client_id_strategy=UUID -e hapi.fhir.client_id_strategy=ANY hapiproject/hapi:latest
+
+      - name: Convert FSH to JSON and set up resources folder in input
+        run: sushi .; mkdir -p input/resources
+
+      - name: Sleep to give server time to start
+        run: sleep 90
+
+      - name: Load add-condition-transaction-example-1
+        run: curl -X POST -H "Content-type:application/fhir+json;fhirVersion=4.0" -d @fsh-generated/resources/Bundle-add-condition-transaction-example-1.json http://localhost:8080/fhir; 
+
+      - name: Query add-condition-transaction-example-1
+        run: sleep 10; curl $(cat input/queries/get-flags-associated-with-patient.md) | jq '.id = "QUERY-OUTPUT--add-condition-transaction-example-1"' > input/resources/QUERY-OUTPUT--add-condition-transaction-example-1.json
+
+      - name: Load add-condition-transaction-example-2
+        run: curl -X POST -H "Content-type:application/fhir+json;fhirVersion=4.0" -d @fsh-generated/resources/Bundle-add-condition-transaction-example-2.json http://localhost:8080/fhir; \
+
+      - name: Query add-condition-transaction-example-2
+        run: sleep 10; curl $(cat input/queries/get-flags-associated-with-patient.md) | jq '.id = "QUERY-OUTPUT--add-condition-transaction-example-2"' > input/resources/QUERY-OUTPUT--add-condition-transaction-example-2.json
+
       - name: Build IG
         run: ./_genonce.sh
 
+      - name: Download and unpack font-awesome
+        run: wget https://fontawesome.com/v4/assets/font-awesome-4.7.0.zip; unzip font-awesome-4.7.0.zip -d output
+
       - name: Publish IG Artefact
         uses: actions/upload-artifact@v3
         with:

diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,11 @@ _site/
 # Ignore folders generated by Bundler
 .bundle/
 vendor/
+input-cache
+node_modules
+output
+temp
+template
+font-awesome*
+fsh-generated
+input/resources/QUERY-OUTPUT*
diff --git a/ig-template/package/includes/_append.fragment-header.html b/ig-template/package/includes/_append.fragment-header.html
@@ -1,4 +1,5 @@
 <link rel="stylesheet" href="../font-awesome-4.7.0/css/font-awesome.min.css">
+<link rel="stylesheet" href="./font-awesome-4.7.0/css/font-awesome.min.css">
 
 <!-- Left logo - typically the publisher's logo - project or affiliate -->
         <div id="project-nav">

diff --git a/input/fsh/examples/add-condition-transaction-example-1.fsh b/input/fsh/examples/add-condition-transaction-example-1.fsh
@@ -0,0 +1,97 @@
+Alias: $consentscope = http://terminology.hl7.org/CodeSystem/consentscope
+Alias: $RARecord-FlagCategory-1 = https://fhir.nhs.uk/STU3/CodeSystem/RARecord-FlagCategory-1
+Alias: $sct = https://snomed.info/sct
+Alias: $condition-clinical = http://terminology.hl7.org/CodeSystem/condition-clinical
+Alias: $CareConnect-ConditionCategory-1 = https://fhir.hl7.org.uk/STU3/CodeSystem/CareConnect-ConditionCategory-1
+Alias: $RARecord-ConditionCode-1 = https://fhir.nhs.uk/STU3/CodeSystem/RARecord-ConditionCode-1
+Alias: $DataOperation = http://terminology.hl7.org/CodeSystem/v3-DataOperation
+Alias: $CareConnect-SDSJobRoleName-1 = https://fhir.hl7.org.uk/STU3/CodeSystem/CareConnect-SDSJobRoleName-1
+Alias: $RARecord-AdjustmentCategory-1 = https://fhir.nhs.uk/STU3/CodeSystem/RARecord-AdjustmentCategory-1
+
+Instance: add-condition-transaction-example-1
+InstanceOf: Bundle
+Usage: #example
+* type = #transaction
+* entry[0].fullUrl = "urn:uuid:6253c43b-5cc8-4645-93b1-38e41be82a77"
+* entry[=].resource = patient-example-1
+* entry[=].request.method = #PUT
+* entry[=].request.url = "Patient?identifier=9912003888"
+* entry[+].fullUrl = "urn:uuid:959fbc3c-0907-419e-aa3d-ab88f2d90c5e"
+* entry[=].resource = consent-example-1
+* entry[=].request.method = #PUT
+* entry[=].request.url = "Consent?patient=urn:uuid:6253c43b-5cc8-4645-93b1-38e41be82a77"
+* entry[+].fullUrl = "urn:uuid:41a84a93-1c95-4162-b13c-1c617509e6e2"
+* entry[=].resource = condition-example-1
+* entry[=].request.method = #PUT
+* entry[=].request.url = "Condition?patient=urn:uuid:6253c43b-5cc8-4645-93b1-38e41be82a77"
+* entry[+].fullUrl = "urn:uuid:fba99f70-fe1d-42e2-b77a-916e44b53c19"
+* entry[=].resource = master-flag-example-1
+* entry[=].request.method = #PUT
+* entry[=].request.url = "Flag/fba99f70-fe1d-42e2-b77a-916e44b53c19"
+* entry[+].fullUrl = "urn:uuid:04adcb5b-3de7-4f67-97f0-b2fdf941ba85"
+* entry[=].resource = condition-flag-example-1
+* entry[=].request.method = #PUT
+* entry[=].request.url = "Flag/04adcb5b-3de7-4f67-97f0-b2fdf941ba85"
+
+Instance: patient-example-1
+InstanceOf: Patient
+Usage: #inline
+* identifier.system = "https://fhir.nhs.uk/Id/nhs-number"
+* identifier.value = "9912003888"
+* active = true
+* name.use = #official
+* name.family = "Duck"
+* name.given = "Donald"
+* gender = #male
+* birthDate = "1970-01-01"
+
+Instance: consent-example-1
+InstanceOf: Consent
+Usage: #inline
+* status = #active
+* scope = $consentscope#patient-privacy
+* category = $RARecord-FlagCategory-1#NRAF "National Reasonable Adjustments Flag"
+* provision.purpose = $sct#370856009 "Limiting access to confidential patient information"
+* patient = Reference(urn:uuid:6253c43b-5cc8-4645-93b1-38e41be82a77)
+* policy.authority = "https://www.gov.uk/"
+* policy.uri = "https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/535024/data-security-review.pdf"
+
+Instance: master-flag-example-1
+InstanceOf: Flag
+Usage: #inline
+* status = #active
+* code = $RARecord-FlagCategory-1#NRAF "National Reasonable Adjustments Flag"
+* category = $RARecord-FlagCategory-1#NRAF "National Reasonable Adjustments Flag"
+* subject = Reference(urn:uuid:6253c43b-5cc8-4645-93b1-38e41be82a77)
+* contained.resourceType = "Provenance"
+* contained.id = "4c75ce1f-1ad7-4391-b5f6-104754c7e904"
+* contained.target.reference = "#"
+* contained.recorded = "2024-01-01T11:00:00+00:00"
+* contained.activity = $DataOperation#CREATE "create"
+* contained.agent.role = $CareConnect-SDSJobRoleName-1#R0260 "General Medical Practitioner"
+* contained.agent.who.reference = "https://sds.spineservices.nhs.uk/STU3/Practitioner/2ee4tr6a9"
+* contained.agent.onBehalfOf.reference = "https://directory.spineservices.nhs.uk/STU3/Organization/a3e5i7"
+
+Instance: condition-example-1
+InstanceOf: Condition
+Usage: #inline
+* clinicalStatus = $condition-clinical#active
+* category = $CareConnect-ConditionCategory-1#issue "Issue"
+* code = $RARecord-ConditionCode-1#5 "Learning or understanding or concentrating"
+* subject = Reference(urn:uuid:6253c43b-5cc8-4645-93b1-38e41be82a77)
+
+Instance: condition-flag-example-1
+InstanceOf: Flag
+Usage: #inline
+* status = #active
+* code = $RARecord-AdjustmentCategory-1#001 "Communication support"
+* category = $RARecord-FlagCategory-1#NRAF "National Reasonable Adjustments Flag"
+* subject = Reference(urn:uuid:6253c43b-5cc8-4645-93b1-38e41be82a77)
+* contained.resourceType = "Provenance"
+* contained.id = "ddb4df1c-d15a-4d02-9346-c034732c5a37"
+* contained.target.reference = "#"
+* contained.recorded = "2024-01-01T11:00:00+00:00"
+* contained.activity = $DataOperation#CREATE "create"
+* contained.agent.role = $CareConnect-SDSJobRoleName-1#R0260 "General Medical Practitioner"
+* contained.agent.who.reference = "https://sds.spineservices.nhs.uk/STU3/Practitioner/2ee4tr6a9"
+* contained.agent.onBehalfOf.reference = "https://directory.spineservices.nhs.uk/STU3/Organization/a3e5i7"
diff --git a/input/fsh/examples/add-condition-transaction-example-2.fsh b/input/fsh/examples/add-condition-transaction-example-2.fsh
@@ -0,0 +1,66 @@
+Alias: $consentscope = http://terminology.hl7.org/CodeSystem/consentscope
+Alias: $RARecord-FlagCategory-1 = https://fhir.nhs.uk/STU3/CodeSystem/RARecord-FlagCategory-1
+Alias: $sct = https://snomed.info/sct
+Alias: $condition-clinical = http://terminology.hl7.org/CodeSystem/condition-clinical
+Alias: $CareConnect-ConditionCategory-1 = https://fhir.hl7.org.uk/STU3/CodeSystem/CareConnect-ConditionCategory-1
+Alias: $RARecord-ConditionCode-1 = https://fhir.nhs.uk/STU3/CodeSystem/RARecord-ConditionCode-1
+Alias: $DataOperation = http://terminology.hl7.org/CodeSystem/v3-DataOperation
+Alias: $CareConnect-SDSJobRoleName-1 = https://fhir.hl7.org.uk/STU3/CodeSystem/CareConnect-SDSJobRoleName-1
+Alias: $RARecord-AdjustmentCategory-1 = https://fhir.nhs.uk/STU3/CodeSystem/RARecord-AdjustmentCategory-1
+
+Instance: add-condition-transaction-example-2
+InstanceOf: Bundle
+Usage: #example
+* type = #transaction
+* entry[0].fullUrl = "urn:uuid:6253c43b-5cc8-4645-93b1-38e41be82a77"
+* entry[=].resource = patient-example-1
+* entry[=].request.method = #PUT
+* entry[=].request.url = "Patient?identifier=9912003888"
+* entry[+].fullUrl = "urn:uuid:959fbc3c-0907-419e-aa3d-ab88f2d90c5e"
+* entry[=].resource = consent-example-1
+* entry[=].request.method = #PUT
+* entry[=].request.url = "Consent?patient=urn:uuid:6253c43b-5cc8-4645-93b1-38e41be82a77"
+* entry[+].fullUrl = "urn:uuid:fba99f70-fe1d-42e2-b77a-916e44b53c19"
+* entry[=].resource = master-flag-example-1
+* entry[=].request.method = #PUT
+* entry[=].request.url = "Flag/fba99f70-fe1d-42e2-b77a-916e44b53c19"
+* entry[+].fullUrl = "urn:uuid:41a84a93-1c95-4162-b13c-1c617509e6e2"
+* entry[=].resource = condition-example-1
+* entry[=].request.method = #PUT
+* entry[=].request.url = "Condition?patient=urn:uuid:6253c43b-5cc8-4645-93b1-38e41be82a77"
+* entry[+].fullUrl = "urn:uuid:04adcb5b-3de7-4f67-97f0-b2fdf941ba85"
+* entry[=].resource = condition-flag-example-1
+* entry[=].request.method = #PUT
+* entry[=].request.url = "Flag/04adcb5b-3de7-4f67-97f0-b2fdf941ba85"
+* entry[+].fullUrl = "urn:uuid:b19124e9-f742-49b4-9247-5c2d58ac1ef4"
+* entry[=].resource = condition-example-2
+* entry[=].request.method = #PUT
+* entry[=].request.url = "Condition/b19124e9-f742-49b4-9247-5c2d58ac1ef4"
+* entry[+].fullUrl = "urn:uuid:212c1018-f52a-4db7-9bc2-59a88622eb4f"
+* entry[=].resource = condition-flag-example-2
+* entry[=].request.method = #PUT
+* entry[=].request.url = "Flag/212c1018-f52a-4db7-9bc2-59a88622eb4f"
+
+Instance: condition-example-2
+InstanceOf: Condition
+Usage: #inline
+* clinicalStatus = $condition-clinical#active
+* category = $CareConnect-ConditionCategory-1#issue "Issue"
+* code = $sct#73618009 "Autistic spectrum disorder with isolated skills"
+* subject = Reference(urn:uuid:6253c43b-5cc8-4645-93b1-38e41be82a77)
+
+Instance: condition-flag-example-2
+InstanceOf: Flag
+Usage: #inline
+* status = #active
+* code = $RARecord-AdjustmentCategory-1#001 "Communication support"
+* category = $RARecord-FlagCategory-1#NRAF "National Reasonable Adjustments Flag"
+* subject = Reference(urn:uuid:6253c43b-5cc8-4645-93b1-38e41be82a77)
+* contained.resourceType = "Provenance"
+* contained.id = "55ac7111-dbd1-42f2-906c-a167b04d47ce"
+* contained.target.reference = "#"
+* contained.recorded = "2024-01-01T11:00:00+00:00"
+* contained.activity = $DataOperation#CREATE "create"
+* contained.agent.role = $CareConnect-SDSJobRoleName-1#R0260 "General Medical Practitioner"
+* contained.agent.who.reference = "https://sds.spineservices.nhs.uk/STU3/Practitioner/2ee4tr6a9"
+* contained.agent.onBehalfOf.reference = "https://directory.spineservices.nhs.uk/STU3/Organization/a3e5i7"
diff --git a/input/fsh/extensions/Extension-England-DateTime.fsh b/input/fsh/extensions/Extension-England-DateTime.fsh
diff --git a/input/fsh/extensions/Extension-England-FlagRemovalReason.fsh b/input/fsh/extensions/Extension-England-FlagRemovalReason.fsh
diff --git a/input/fsh/extensions/Extension-England-OrganisationRole.fsh b/input/fsh/extensions/Extension-England-OrganisationRole.fsh