Merge pull request #29 from CEOsys/feat/action-combination-method

Feat/action-combination-method

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.7.1
+current_version = 0.8.0-snapshot
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>\S+))?
 serialize =
 	{major}.{minor}.{patch}-{release}

create-intros.py

@@ -72,28 +72,31 @@
     ig = yaml.safe_load(f)
 
 linklist = {}
-linklist_vs = {}
 
 for resource in ig["definition"]["resource"]:
     ref = resource["reference"]["reference"]
+
+    type_ = ref.split('/')[0]
+
+    link_name = ''.join(filter(str.isupper, type_)) + ':' + resource["name"]
 
     if ref.startswith('ValueSet/'):
-        linklist_vs[resource["name"]] = ref.replace('/', '-') + '.html'
+        linklist[link_name] = ref.replace('/', '-') + '.html'
 
     if ref.startswith('CodeSystem/'):
-        linklist[resource["name"]] = ref.replace('/', '-') + '.html'
+        linklist[link_name] = ref.replace('/', '-') + '.html'
 
     if not ref.startswith('StructureDefinition/') and not ref.startswith('Questionnaire/'):
       continue
 
     fname = output_path / (ref.replace('/', '-') + '-intro.md')
 
     if not fname.exists():
-        print(resource["name"])
+        print(link_name)
         with open(fname, 'w') as f:
             f.write(template_md)
 
-    linklist[resource["name"]] = ref.replace('/', '-') + '.html'
+    linklist[link_name] = ref.replace('/', '-') + '.html'
 
 
 if not linklist_fname.parent.exists():
@@ -107,8 +110,8 @@ def write_links(ll, prefix="", newline=True):
         if newline:
             f.write("\n")
 
-    write_links(linklist)
-    write_links(linklist_vs, prefix="VS ")
+    for prefix in ['VS:', 'CS:', 'SD:', 'QU:']:
+        write_links({k: v for k, v in linklist.items() if k.startswith(prefix)}, newline=True)
     write_links(linklist_general, newline=False)
 
 print(profiles_fname.name)
@@ -125,7 +128,9 @@ def write_links(ll, prefix="", newline=True):
 print(valuesets_fname.name)
 with open(valuesets_fname, "w") as f:
     f.write('### Value Sets\n\n')
-    for name in linklist_vs:
+    for name in linklist:
+        if not name.startswith('VS:'):
+            continue
         f.write(f"{{% include valueset-reference.md name='{name}' %}}\n")
 
 print("Done")

input/data/ig.yml

@@ -108,6 +108,22 @@ definition:
       system: http://hl7.org/fhir/tools/CodeSystem/ig-parameters
     value: https://simplifier.net
   resource:
+  - description: Extension used on PlanDefinition.action to specify a method for combining
+      the actions.
+    isExample: false
+    name: Action Combination Method
+    reference:
+      reference: StructureDefinition/ext-action-combination-method
+  - description: Value set for the method used to combine actions in a PlanDefinition.
+    isExample: false
+    name: Action Combination Method
+    reference:
+      reference: ValueSet/vs-action-combination-method
+  - description: Code system for the combination of actions in a PlanDefinition.
+    isExample: false
+    name: Action Combination Method
+    reference:
+      reference: CodeSystem/cs-action-combination-method
   - description: Action selection behavior with only codes that require at least one
       action to be performed.
     isExample: false
@@ -899,4 +915,4 @@ resourceType: ImplementationGuide
 status: draft
 title: Clinical Practice Guidelines (CPG) on EBMonFHIR
 url: https://www.netzwerk-universitaetsmedizin.de/fhir/cpg-on-ebm-on-fhir/ImplementationGuide/de.netzwerk-universitaetsmedizin.ebm-cpg
-version: 0.7.1
+version: 0.8.0-snapshot

input/fsh/examples/covid-dexamethason/recommendations/recommendation_05_intervention.fsh

@@ -16,18 +16,17 @@ Description: "Application of Dexamethasone for ventilated patients only"
 * experimental = true
 * publisher = "CPGonEBMonFHIR"
 * subjectCanonical = Canonical(PopulationCOVID19Ventilated)
+* insert rs-combination-one-or-more
 * action[+]
   * title = "Dexamethasone Application"
   * code = $cs-common-process#guideline-based-care
   * description = "Application of Dexamethasone: 6 mg once per day for 10 days p.o. or i.v. for ventilated COVID-19 patients"
   * definitionCanonical = Canonical(COVID19VentilatedPatientsDexamethasoneApplicationPlan)
-  * selectionBehavior = #exactly-one
 * action[+]
   * title = "No Dexamethasone Application"
   * code = $cs-common-process#guideline-based-care
   * description = "No Dexamethasone Application for non-ventilated COVID-19 patients"
   * definitionCanonical = Canonical(COVID19NonVentilatedPatientsDexamethasoneApplicationPlan)
-  * selectionBehavior = #exactly-one
 * relatedArtifact[recommendationJustification].resourceReference = Reference(DexamethasoneRecommendationJustification)
 * relatedArtifact[recommendationCitation].resourceReference = Reference(DexamethasoneRecommendationCitation)
 * relatedArtifact[guidelineCitation].resourceReference = Reference(COVID19IntensiveCareTreatmentGuidelineCitation)
@@ -48,12 +47,11 @@ Description: "Application of Dexamethasone: 6 mg once per day for 10 days p.o. o
 * publisher = "CPGonEBMonFHIR"
 * subjectCanonical = Canonical(PopulationCOVID19Ventilated)
 * extension[partOf].valueCanonical = Canonical(COVID19DexamethasoneApplication)
+* insert rs-combination-exactly(1)
 * action[drugAdministration][+]
   * definitionCanonical = Canonical(DexamethasoneApplicationActionOral)
-  * selectionBehavior = #exactly-one
 * action[drugAdministration][+]
   * definitionCanonical = Canonical(DexamethasoneApplicationActionIntravenous)
-  * selectionBehavior = #exactly-one
 
 Instance: COVID19NonVentilatedPatientsDexamethasoneApplicationPlan
 InstanceOf: recommendation-plan
@@ -71,9 +69,9 @@ Description: "No application of Dexamethasone for non-ventilated COVID-19 patien
 * publisher = "CPGonEBMonFHIR"
 * subjectCanonical = Canonical(PopulationCOVID19NonVentilated)
 * extension[partOf].valueCanonical = Canonical(COVID19DexamethasoneApplication)
+* insert rs-combination-exactly(1)
 * action[drugAdministration][+]
   * definitionCanonical = Canonical(NoDexamethasoneApplication)
-  * selectionBehavior = #exactly-one
 
 Instance: DexamethasoneRecommendationCitation
 InstanceOf: recommendation-citation

input/fsh/guideline-recommendation/p-recommendation.fsh

@@ -12,14 +12,17 @@ Description: "A recommendation as part of a clinical practice guideline."
 * extension[knowledgeRepresentationLevel] 1..1
   * valueCode 1..1
   * valueCode = $cs-cpg-knowledgeRepresentationLevel#structured "Structured"
+* insert rs-action-combination-method
 * action
   * definitionCanonical 1..1
   * definition[x] only canonical
   * definitionCanonical only Canonical(RecommendationPlan)
   * selectionBehavior 1..1 MS
+  * selectionBehavior = $cs-action-selection-behavior#one-or-more
   * code 1..1 MS
 * insert recommendation-related-artifacts
 
+
 Instance: ExampleRecommendation
 InstanceOf: recommendation
 Usage: #example
@@ -34,18 +37,17 @@ Description: "Recommendation"
 * insert canonical-url(example/recommendation-plan/example-recommendation)
 * experimental = true
 * publisher = "CPGonEBMonFHIR"
+* insert rs-combination-at-least(2)
 * action[+]
   * title = "example recommendation"
   * code = $cs-common-process#guideline-based-care
   * description = "Example recommendation"
   * definitionCanonical = Canonical(ExampleRecommendationPlan)
-  * selectionBehavior = #all
 * action[+]
   * title = "example recommendation"
   * code = $cs-common-process#guideline-based-care
   * description = "Example recommendation"
   * definitionCanonical = Canonical(ExampleRecommendationPlan)
-  * selectionBehavior = #all
 * relatedArtifact[recommendationJustification].resourceReference = Reference(ExampleRecommendationJustification)
 * relatedArtifact[recommendationCitation].resourceReference = Reference(ExampleRecommendationCitation)
 * relatedArtifact[guidelineCitation].resourceReference = Reference(ExampleGuidelineCitation)

input/fsh/intervention/cs-action-combination-method.fsh

@@ -0,0 +1,17 @@
+// Author: Gregor Lichtner @glichtner
+
+Alias: $cs-action-combination-method = https://www.netzwerk-universitaetsmedizin.de/fhir/cpg-on-ebm-on-fhir/CodeSystem/cs-action-combination-method
+
+CodeSystem: ActionCombinationMethod
+Id: cs-action-combination-method
+Title: "Action Combination Method"
+Description: "Code system for the combination of actions in a PlanDefinition."
+* ^url = $cs-action-combination-method
+* insert metadata(2024-02-16, #draft, 0.1.0)
+* insert cpg-computable-codesystem
+* #all "All" "All actions must be performed."
+* #any "Any" "Any action must be performed."
+* #at-least "At Least" "At least the specified number of actions must be performed."
+* #exactly "Exactly" "Exactly the specified number of actions must be performed."
+* #at-most "At Most" "At most the specified number of actions must be performed."
+* #one-or-more "One or More" "One or more actions must be performed."

input/fsh/intervention/ext-action-combination-method.fsh

@@ -0,0 +1,22 @@
+// Author: Gregor Lichtner @glichtner
+
+// use a fixed URL to make sure it is properly referenced in the the nested-action-requires-combination-method invariant
+Alias: $ext-action-combination-method = https://www.netzwerk-universitaetsmedizin.de/fhir/cpg-on-ebm-on-fhir/StructureDefinition/ext-action-combination-method
+
+Extension: ActionCombinationMethod
+Id: ext-action-combination-method
+Title: "Action Combination Method"
+Description: "Extension used on PlanDefinition.action to specify a method for combining the actions."
+* insert metadata(2022-07-06, #draft, 0.1.0)
+* . ^short = "combinationMethod"
+* . ^definition = "Extension used on PlanDefinition.action to specify a method for combining the actions."
+* ^context.type = #fhirpath
+* ^context.expression = "PlanDefinition | PlanDefinition.action | BackboneElement"
+* ^url = $ext-action-combination-method
+* extension contains method 1..1 and threshold 0..1
+* extension[method] ^short = "Expresses the method for combining the actions"
+* extension[method].value[x] only CodeableConcept
+* extension[method].valueCodeableConcept from vs-action-combination-method (required)
+* extension[threshold] ^short = "Expresses the threshold for the method for combining the actions"
+* extension[threshold].value[x] only positiveInt
+* value[x] 0..0

input/fsh/intervention/p-recommendation-plan.fsh

@@ -25,44 +25,8 @@ Description: "Definition of an activity that is part of an intervention in the c
   * valueCanonical 1..1 MS
   * valueCanonical only Canonical(Recommendation)
 * action 1..*
-* action ^slicing.discriminator.type = #pattern
-* action ^slicing.discriminator.path = "code"
-* action ^slicing.rules = #open
-* action contains
-    drugAdministration 0..* and
-    ventilatorManagement 0..* and
-    bodyPositioning 0..* and
-    sedationManagement 0..* and
-    painManagement 0..* and
-    assessment 0..*
-  * code 1..1 MS
-    * coding 1..*
-      * system 1..
-      * code 1..
-  * goalId
-    * obeys goal-must-be-linked
-  * definition[x] 0..1 MS
-  * definition[x] only canonical
-  * definitionCanonical only Canonical(RecommendationAction)
-  * selectionBehavior from vs-action-selection-behavior-required (required)
-* action[drugAdministration]
-  * code = $sct#432102000 "Administration of substance (procedure)"
-  * definitionCanonical only Canonical(DrugAdministrationAction)
-* action[ventilatorManagement]
-  * code = $sct#410210009 "Ventilator care management (procedure)"
-  * goalId 1..* MS
-* action[bodyPositioning]
-  * code = $sct#229824005 "Positioning patient (procedure)"
-  * definitionCanonical only Canonical(BodyPositioningAction)
-* action[sedationManagement]
-  * code = $sct#406187008 "Sedation management (regime/therapy)"
-  * goalId 1..* MS
-* action[painManagement]
-  * code = $sct#278414003 "Pain management (procedure)"
-  * goalId 1..* MS
-* action[assessment]
-  * code = $sct#386053000 "Evaluation procedure (procedure)"
-  * definitionCanonical only Canonical(AssessmentAction)
+* insert rs-action-slices
+* insert rs-action-combination-slice
 * goal 0..* MS
   * category 1..1 MS
     * coding 1..*
@@ -102,6 +66,70 @@ Description: "Definition of an activity that is part of an intervention in the c
     * measure from vs-assessment-scales
     * detail[x] 1..1 MS
 
+RuleSet: rs-action-code-required
+* code 1..1 MS
+  * coding 1..*
+    * system 1..
+    * code 1..
+* goalId
+  * obeys goal-must-be-linked
+* definition[x] 0..1 MS
+* definition[x] only canonical
+* definitionCanonical only Canonical(RecommendationAction)
+
+RuleSet: rs-action-slices
+* insert rs-action-combination-method
+* action ^slicing.discriminator.type = #pattern
+* action ^slicing.discriminator.path = "code"
+* action ^slicing.rules = #closed
+* action contains
+    combination 0..* and
+    drugAdministration 0..* and
+    ventilatorManagement 0..* and
+    bodyPositioning 0..* and
+    sedationManagement 0..* and
+    painManagement 0..* and
+    assessment 0..* and
+    other 0..*
+    //* selectionBehavior from vs-action-selection-behavior-required (required)
+* action[combination]
+  * code 0..0
+  * goalId 0..0
+  * definition[x] 0..0
+  * action 1..* MS
+* action[drugAdministration]
+  * insert rs-action-code-required
+  * code = $sct#432102000 "Administration of substance (procedure)"
+  * definitionCanonical only Canonical(DrugAdministrationAction)
+* action[ventilatorManagement]
+  * insert rs-action-code-required
+  * code = $sct#410210009 "Ventilator care management (procedure)"
+  * goalId 1..* MS
+* action[bodyPositioning]
+  * insert rs-action-code-required
+  * code = $sct#229824005 "Positioning patient (procedure)"
+  * definitionCanonical only Canonical(BodyPositioningAction)
+* action[sedationManagement]
+  * insert rs-action-code-required
+  * code = $sct#406187008 "Sedation management (regime/therapy)"
+  * goalId 1..* MS
+* action[painManagement]
+  * insert rs-action-code-required
+  * code = $sct#278414003 "Pain management (procedure)"
+  * goalId 1..* MS
+* action[assessment]
+  * insert rs-action-code-required
+  * code = $sct#386053000 "Evaluation procedure (procedure)"
+  * definitionCanonical only Canonical(AssessmentAction)
+* action[other]
+  * code = $sct#74964007 "Other (qualifier value)"
+  * insert rs-action-code-required
+
+RuleSet: rs-action-combination-slice
+// can't use this directly in rs-action-slices because sushi complains about circular references
+* action[combination]
+  * insert rs-action-slices
+
 Invariant: goal-must-be-linked
 Description: "The goal linked by goalId is not defined"
 Expression: "$this in %resource.goal.id"
@@ -123,18 +151,22 @@ Description: "An active recommendation plan."
 * publisher = "CPGonEBMonFHIR"
 * subjectCanonical = Canonical(ExampleRecommendationEligibilityCriteria)
 * extension[partOf].valueCanonical = Canonical(ExampleRecommendation)
+* insert rs-combination-exactly(1)
 * action[drugAdministration][+]
   * code = $sct#432102000 "Administration of substance (procedure)"
   * definitionCanonical = Canonical(ExampleDrugAdministrationAction)
-  * selectionBehavior = #exactly-one
 * action[bodyPositioning][+]
   * code = $sct#229824005 "Positioning patient (procedure)"
   * definitionCanonical = Canonical(ExampleBodyPositioningAction)
   * goalId[+] = "ventilator-management-goal"
-  * selectionBehavior = #exactly-one
 * action[ventilatorManagement][+]
   * code = $sct#410210009 "Ventilator care management (procedure)"
   * goalId[+] = "ventilator-management-goal"
+* action[combination][+]
+  * insert rs-combination-one-or-more
+  * action[ventilatorManagement][+]
+    * code = $sct#410210009 "Ventilator care management (procedure)"
+    * goalId[+] = "ventilator-management-goal"
 * goal[ventilatorManagement][+]
   * category = $sct#385857005 "Ventilator care and adjustment (regime/therapy)"
   * id = "ventilator-management-goal"

input/fsh/intervention/vs-action-combination-method.fsh

@@ -0,0 +1,7 @@
+ValueSet: ActionCombinationMethod
+Id: vs-action-combination-method
+Title: "Action Combination Method"
+Description: "Value set for the method used to combine actions in a PlanDefinition."
+* insert metadata(2024-02-16, #draft, 0.1.1)
+* insert cpg-computable-valueset
+* include codes from system cs-action-combination-method

input/fsh/invariants.fsh

@@ -31,3 +31,8 @@ Invariant: code-xor-repeat
 Description: "Either a code or a repeat structure should be defined, but not both"
 Expression: "code.empty() or repeat.empty()"
 Severity: #error
+
+Invariant: nested-action-requires-combination-method
+Description: "If a nested action is present, a combination method must be present."
+Expression: "action.exists() implies extension('https://www.netzwerk-universitaetsmedizin.de/fhir/cpg-on-ebm-on-fhir/StructureDefinition/ext-action-combination-method').exists()"
+Severity: #error