Ti doc migration

.gitignore

@@ -9,4 +9,8 @@
 /_gencontinuous.sh
 /_genonce.bat
 /_genonce.sh
+/_updatePublisher.bat
+/_updatePublisher.sh
 .DS_Store
+/_build.bat
+/_build.sh

README.md

@@ -1,5 +1,9 @@
 # Status
-This is the supplement template for IHE-Profiles using the IG publisher. repository is under-construction. Please try using it. If you have questions, contact John Moehrke. 
+This is the IHE Imaging Diagnostic Report (IDR) Profile in FHIR IG format. 
 
-Instructions [are found here](https://github.com/IHE/supplement-template/wiki/Getting-Started)
+As of 2025 Feb, resolution of the 2024 Public Comments has been completed and the resulting Volume 1 content has been migrated into the TIDocMigration branch.
+The intention is to complete migration including the FSH content in March.
 
+For questions about the content, contact Kevin O'Donnell or Kinson Ho. 
+
+This repository is based on the [FHIR IG template for IHE Profiles](https://github.com/IHE/supplement-template/wiki/Getting-Started)

Requirements-fromNarrative.json

@@ -0,0 +1,10 @@
+{
+  "resourceType" : "Requirements",
+  "id" : "fromNarrative",
+  "url" : "https://profiles.ihe.net/RAD/IDR/Requirements/fromNarrative",
+  "name" : "FromNarrative",
+  "title" : "Narrative Conformance Statements",
+  "status" : "active",
+  "experimental" : false,
+  "description" : "Conformance statements found throughout the narrative of the IG consolidated into this computable resource for traceability purposes"
+}

_updatePublisher.bat

@@ -8,6 +8,8 @@ SET input_cache_path=%CD%\input-cache\
 SET skipPrompts=false
 
 SET scriptdlroot=https://raw.githubusercontent.com/HL7/ig-publisher-scripts/main
+SET build_bat_url=%scriptdlroot%/_build.bat
+SET build_sh_url=%scriptdlroot%/_build.sh
 SET update_bat_url=%scriptdlroot%/_updatePublisher.bat
 SET gen_bat_url=%scriptdlroot%/_genonce.bat
 SET gencont_bat_url=%scriptdlroot%/_gencontinuous.bat
@@ -20,7 +22,8 @@ IF "%~1"=="/f" SET skipPrompts=y
 
 ECHO.
 ECHO Checking internet connection...
-PING tx.fhir.org -4 -n 1 -w 1000 | FINDSTR TTL && GOTO isonline
+powershell -Command "try { $r=[System.Net.WebRequest]::Create('https://tx.fhir.org/r4/metadata'); $r.Timeout=4000; $r.GetResponse().Close(); exit 0 } catch { exit 1 }"
+IF %ERRORLEVEL% EQU 0 GOTO isonline
 ECHO We're offline, nothing to do...
 GOTO end
 
@@ -69,6 +72,7 @@ IF DEFINED FORCE (
 IF "%skipPrompts%"=="y" (
 	SET create=Y
 ) ELSE (
+	ECHO Will place publisher jar here: %input_cache_path%%publisher_jar%
 	SET /p create="Ok? (Y/N) "
 )
 IF /I "%create%"=="Y" (
@@ -211,6 +215,16 @@ goto end
 start copy /y "_updatePublisher.new.bat" "_updatePublisher.bat" ^&^& del "_updatePublisher.new.bat" ^&^& exit
 
 
+:dl_script_7
+ECHO Updating _build.bat
+call POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%build_bat_url%\",\"_build.new.bat\") } else { Invoke-WebRequest -Uri "%update_bat_url%" -Outfile "_build.new.bat" }
+if %ERRORLEVEL% == 0 goto upd_script_6
+echo "Errors encountered during download: %errorlevel%"
+goto end
+:upd_script_6
+start copy /y "_build.new.bat" "_build.bat" ^&^& del "_build.new.bat" ^&^& exit
+
+
 :end
 
 

_updatePublisher.sh

@@ -12,6 +12,8 @@ gencont_bat_url=$scriptdlroot/_gencontinuous.bat
 gencont_sh_url=$scriptdlroot/_gencontinuous.sh
 gen_sh_url=$scriptdlroot/_genonce.sh
 update_sh_url=$scriptdlroot/_updatePublisher.sh
+build_sh_url=$scriptdlroot/_build.sh
+build_bat_url=$scriptdlroot/_build.bat
 
 skipPrompts=false
 FORCE=false
@@ -103,6 +105,16 @@ if [[ $skipPrompts != true ]]; then
 if [[ $skipPrompts == true ]] || [[ $response =~ ^[yY].*$ ]]; then
   echo "Downloading most recent scripts "
 
+  curl -L $build_bat_url -o /tmp/_build.new
+  cp /tmp/_build.new _build.bat
+  rm /tmp/_build.new
+
+
+  curl -L $build_sh_url -o /tmp/_build.new
+  cp /tmp/_build.new _build.sh
+  chmod +x _build.sh
+  rm /tmp/_build.new
+
   curl -L $update_bat_url -o /tmp/_updatePublisher.new
   cp /tmp/_updatePublisher.new _updatePublisher.bat
   rm /tmp/_updatePublisher.new
@@ -129,4 +141,4 @@ if [[ $skipPrompts == true ]] || [[ $response =~ ^[yY].*$ ]]; then
   cp /tmp/_updatePublisher.new _updatePublisher.sh
   chmod +x _updatePublisher.sh
   rm /tmp/_updatePublisher.new
-fi
+fi

input/fsh/Aliases.fsh

@@ -1,8 +1,8 @@
 Alias: SCT = http://snomed.info/sct
 Alias: UCUM = http://unitsofmeasure.org
 Alias: LOINC = http://loinc.org
-Alias: CPT = http://terminology.hl7.org/5.0.0/CodeSystem-CPT.html
-Alias: ICD10 = http://hl7.org/fhir/sid/icd-10
+Alias: CPT = http://www.ama-assn.org/go/cpt
+Alias: ICD10 = http://hl7.org/fhir/sid/icd-10-cm
 
 Alias: HL7V2 = http://terminology.hl7.org/CodeSystem/v2-0203
 Alias: FHIRObservation = http://terminology.hl7.org/CodeSystem/observation-category
@@ -16,8 +16,10 @@ Alias: FHIREndpointStatus = http://hl7.org/fhir/endpoint-status
 Alias: FHIRDiagnosticReportStatus = http://hl7.org/fhir/diagnostic-report-status
 Alias: FHIRDiagnosticService = http://terminology.hl7.org/CodeSystem/v2-0074
 Alias: FHIRNarrativeStatus = https://hl7.org/fhir/R5/codesystem-narrative-status.html
-Alias: FHIRConditionVerificationstatus = http://terminology.hl7.org/5.1.0/CodeSystem-condition-ver-status.html
 Alias: FHIRProvenanceSignatureType = http://uri.etsi.org/01903/v1.2.2
+Alias: FHIRConditionClinical = http://terminology.hl7.org/CodeSystem/condition-clinical
+Alias: FHIRConditionVerStatus = http://terminology.hl7.org/CodeSystem/condition-ver-status
+Alias: FHIRConditionCategory = http://terminology.hl7.org/CodeSystem/condition-category
 
 Alias: DICOM = http://dicom.nema.org/resources/ontology/DCM
 Alias: DICOMUID = urn:dicom:uid

input/fsh/Attachment.fsh

@@ -1,5 +1,5 @@
 // Invariant
 Invariant:   IDRAttachmentInvariant
-Description: "Either data or url SHALL be present"
+Description: "Either data or url SHALL be present for any attachment (e.g. in DiagnosticReport)."
 Expression:  "data.exists() or url.exists()"
 Severity:    #error

input/fsh/Communication.fsh

@@ -1,29 +1,72 @@
 Profile:        IDRCommunication
 Parent:         Communication
 Id:             idr-communication
-Title:          "Communications for Imaging Diagnostic Reports"
-Description:    "Communications for Imaging Diagnostic Reports."
+Title:          "IDR Report Communication"
+Description:    "Communication of impressions, critical results and/or actionable findings in Imaging Diagnostic Reports."
 
-* text MS
+* text 1..1 MS
+* text ^definition = """
+A summary sentence describing the communication, as currently appears in report narratives.
+"""
+
+* basedOn ^comment = """
+This is often absent unless there was a specific request for the communication that can be referenced.  See communication.reason for communications triggered by specific impression findings.
+"""
 
 * partOf 1..1 MS
 * partOf only Reference(ImagingDiagnosticReport)
+* partOf ^comment = "The current diagnostic report, which provides the context of the communication"
+
+* status ^comment = """
+Should be COMPLETED in many cases. When documenting attempted communications, the status might have another value.
+
+Communication resources where the .status is not COMPLETED may trigger subsequent follow-up workflows, but the management of such follow-up is not reflected in the diagnostic report.
+
+In some reporting workflows, such communications may be included in an Addendum to the report (e.g. when the report is distributed prior to the communication being successfully completed).
+"""
+
+* medium MS
+* medium ^comment = """
+For imaging, the value will typically be PHONE, or in the case of leaving a voicemail message, DICTATE.
+"""
 
 * subject 1..1 MS
-* subject only Reference(IDRPatient)
+* subject only Reference(Patient)
 
 * topic MS
-
-* reason MS
-* reason only CodeableReference(IDRImpressionCondition or IDRRecommendationServiceRequest)
+* topic ^comment = """
+May contain the code for "summary-report". Sites may wish to use a code for critical findings. 
+"""
 
 * about MS
 * about only Reference(IDRImpressionCondition or IDRRecommendationServiceRequest)
+* about ^comment = """
+May reference any or all of the specific impression Conditions or recommendation ServiceRequests discussed during the communication if such information is made available to the encoding system.
+"""
 
-* medium MS
+* encounter ^comment = """
+Should either reference the encounter for the imaging procedure, or be absent.
+"""
+
+* sent 1..1 MS
+
+* received MS
+* received ^comment = """
+For phone communications, this value will typically be the same time as Communication.sent. In the case of leaving a message, this will likely be be absent since it won't be known and the resource is not expected to be updated.
+"""
 
 * sender MS
+* sender ^comment = """
+For imaging, the value should be the imaging clinician in most cases but may be their staff.
+"""
 
 * recipient MS
+* recipient ^comment = """
+For imaging, the value should be the patient or the referring clinician in most cases, but may be their staff.
+"""
 
-* sent 1..1 MS
+* reason MS
+* reason only CodeableReference(IDRImpressionCondition or IDRRecommendationServiceRequest)
+* reason ^comment = """
+May reference one or more of the specific impression Conditions or recommendation ServiceRequests that prompted the communication.
+"""

input/fsh/Condition.fsh

@@ -1,78 +1,116 @@
+//TODOQ Can drop this first one? Or are we mandating the text for assembling History text
 Profile:        IDRPatientHistoryCondition
 Parent:         Condition
 Id:             idr-patient-history-condition
-Title:          "Past diagnosis of patient in Imaging Diagnostic Report"
-Description:    "A past diagnosis of a patient in an Imaging Diagnostic Report."
+Title:          "IDR Patient History Condition"
+Description:    "A past diagnosis of a patient in an imaging report."
 
 * text MS
 
 
 Profile:        IDRImpressionCondition
 Parent:         Condition
 Id:             idr-impression-condition
-Title:          "Impression as Condition"
-Description:    "An impression as a condition in imaging report."
+Title:          "IDR Report Impression Condition"
+Description:    "A condition appearing in the impression of an imaging report."
 
 * text MS
 
 * category 1..1 MS
+// JIRA FHIR-48358 and UP-635 are adding the "diagnostic-report-impression" code to R6. WIP 2025.08.01
+// TODOQ If we want to fix it to "diagnostic-report-impression" is VS the right mechanism?
 * category from IDRImpressionConditionCategoryVS (required)
 
 * verificationStatus 1..1 MS
+* verificationStatus ^comment = """
+Typical values will be confirmed, differential, provisional, unconfirmed, and refuted. 
+
+\"confirmed\" would not be used unless the imaging report is the definitive source of such a diagnosis.
+
+\"refuted\", per <https://www.hl7.org/fhir/R5/condition.html#9.2.4.5>, is used for subsequent disproof of a previously asserted condition so it would not be used unless the condition was previously asserted and the radiology report is negative and is definitive for such an assertion. Other negative assertions are handled as observations.
+"""
 
 * code 1..1 MS
+* code ^comment = """
+Codes may be drawn from SNOMED or similar coding system.
+"""
 
 * severity MS
+* severity ^comment = """
+Note 1. Severity does not map directly to patient risk. A mild stroke might present a greater risk than a severe ingrown toenail.
+"""
 
 * stage MS
-
-* bodySite 1..1 MS
-
-* participant 1..* MS
+* stage ^comment = """
+This typically depends on the condition having formal (often disease-specific) staging concepts. The imaging clinician might not always assess the stage.
+"""
+
+// JIRA FHIR-50859 for ImagingStudy positioningset up use of BodyStructure encoding not bodySite. Variability increases implementation and testing complexity
+* bodySite 0..*
+* bodySite ^comment = """
+Should not be present. R6 specifies not to use bodySite when bodyStructure is present. This IG specifies usage of bodyStructure. 
+"""
+
+* bodyStructure 0..1 MS
+/* TOAddR6toR4 
+* extension contains AddR6toR4ConditionBodyStructure named bodyStructure 0..1 MS
+*/
+* bodyStructure ^comment = """
+The BodyStructure.includedStructure.structure may contain codes drawn from SNOMED or similar coding system. BodyStructure.laterality shall record laterality if the bodyStructure is a paired structure.
+
+Note: When a condition spans multiple structures, .includedStructure may include multiple items.  
+"""
+// TODOQ TCQ should we include guidance on when to use fine grained/pre-coordinated structure codes vs the .qualifier element?
+
+/* TOAddR6toR5 Note: In R4, not R5, back in R6. Need extension for implementers? */
+* asserter 1..1 MS
+* asserter ^comment = "In an imaging report, this is the imaging clinician."
+
+* clinicalStatus ^comment = """
+This element is required to be present by the Condition resource. In diagnostic reports, the clinicalStatus will frequently be \"unknown\", but the other defined values may be used when appropriate.
+"""
 
 * evidence MS
-
-* extension contains IDRImpressionLaterality named laterality 0..1 MS
+* evidence ^comment = """
+May contain a reference to the DiagnosticReport and/or references to Observation resources in the Findings and/or Impression sections, or references to other information elsewhere that contributed to this impression item.
+"""
 
 * extension contains IDRImpressionLikelihood named likelihood 0..1 MS
 
-* extension contains IDRImpressionOrder named order 1..1 MS
-
 * extension contains IDRImpressionActionable named actionable 0..1 MS
 
-* extension contains IDRImpressionIncidental named incidental 0..1 MS
-
-Extension: IDRImpressionLaterality
-Title: "IDR BodySite Laterality in Impression."
-Id: idrImpressionLaterality
-Description: "Laterality of impression"
-Context: Condition
-* value[x] only CodeableConcept
-
 Extension: IDRImpressionLikelihood
-Title: "IDR BodySite Likelihood in Impression."
+Title: "IDR Impression Condition Likelihood."
 Id: idrImpressionLikelihood
-Description: "likelihood of impression"
+Description: "likelihood of condition assertion"
 Context: Condition
 * value[x] only CodeableConcept
 
-Extension: IDRImpressionOrder
-Title: "Impression Order."
-Id: IDRImpressionOrder
-Description: "Order in impression"
-Context: Condition
-* value[x] only positiveInt
+/* TODO
+- Condition.likelihood shall record the likelihood of the
+  condition, if expressed by the imaging clinician. (See Open Issue
+  about adoption of a coding system)
+
+Note: "Consistent with" in the narrative form of an impression typically
+implies strong imaging support for an existing (tentative) diagnosis in
+place beforehand. Most other impressions represent conditions put
+forward by the imaging clinician. If the Condition resource for the
+existing diagnosis is known, consider referencing that instance and
+adding information to Condition.evidence.
+*/
 
 Extension: IDRImpressionActionable
-Title: "Actionable indication in Impression."
+Title: "IDR Actionable Condition"
 Id: idrImpressionActionable
 Description: "Actionable indication in impression."
 Context: Condition
 * value[x] only CodeableConcept
 
-Extension: IDRImpressionIncidental
-Title: "Incidental indication of Impression."
-Id: idrImpressionIncidental
-Description: "Incidental indication of impression."
+/* TOAddR6toR4
+Extension: AddR6toR4ConditionBodyStructure
+Title: "(AddR6toR4) Condition.bodyStructure"
+Id: idrConditionBodyStructure
+Description: "Body Structure where the condition occurs."
 Context: Condition
-* value[x] only boolean
+* value[x] only Reference(BodyStructure)
+*/