Conversion to fsh

.gitignore

@@ -0,0 +1,15 @@
+input-cache/
+.vscode
+output/
+input/tests/results/*.txt
+temp/
+template/
+*.jar
+.DS_Store
+.DS_Store
+/fsh-generated
+/fsh-generated/resources
+package-list.json
+package-lock.json
+/node_modules
+/fsh-generated

FHIR-us-cancer-reporting.xml

@@ -1,76 +1,78 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <specification xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ballotUrl="http://hl7.org/fhir/us/cancer-reporting/2021Sep" ciUrl="http://build.fhir.org/ig/HL7/cancer-reporting" defaultVersion="1.0.1" defaultWorkgroup="oo" gitUrl="https://github.com/HL7/cancer-reporting" url="http://hl7.org/fhir/us/cancer-reporting">
 <version code="current" url="http://build.fhir.org/ig/HL7/cancer-reporting"/>
-<version code="1.0.1" url="http://hl7.org/fhir/us/cancer-reporting/STU101"/>
+<version code="1.0.1" url="http://hl7.org/fhir/us/cancer-reporting/STU1.0.1"/>
 <version code="1.0.0" url="http://hl7.org/fhir/us/cancer-reporting/STU1"/>
 <version code="0.1.0" deprecated="true" url="http://hl7.org/fhir/us/cancer-reporting/2021Sep"/>
 <artifactPageExtension value="-definitions"/>
 <artifactPageExtension value="-examples"/>
 <artifactPageExtension value="-mappings"/>
 <artifact deprecated="true" id="Observation/2118.100004300-us" key="Observation-2118.100004300-us" name="Adrenal Gland (example)"/>
 <artifact id="Specimen/adrenal-example" key="Specimen-adrenal-example" name="Adrenal Specimen example"/>
-<artifact id="Observation/observation-procedure-adrenalectomy" key="Observation-observation-procedure-adrenalectomy" name="Adrenalectomy Procedure Observation example"/>
+<artifact deprecated="true" id="Observation/observation-procedure-adrenalectomy" key="Observation-observation-procedure-adrenalectomy" name="Adrenalectomy Procedure Observation example"/>
 <artifact id="CapabilityStatement/central-cancer-registry-reporting-ehr-pathology" key="CapabilityStatement-central-cancer-registry-reporting-ehr-pathology" name="Central Cancer Registry Reporting Pathology EHR Capability Statement"/>
 <artifact deprecated="true" id="Observation/2149.100004300-us" key="Observation-2149.100004300-us" name="Distant Metastasis (pM): Not applicable- pM cannot be determined from the submitted specimen(s) (example)"/>
-<artifact id="Observation/observation-distant-metastasis" key="Observation-observation-distant-metastasis" name="Distant Metastasis Observation example"/>
+<artifact deprecated="true" id="Observation/observation-distant-metastasis" key="Observation-observation-distant-metastasis" name="Distant Metastasis Observation example"/>
 <artifact deprecated="true" id="Encounter/pathology-encounter" key="Encounter-pathology-encounter" name="Encounter (example)"/>
-<artifact id="Observation/observation-histologic-grade" key="Observation-observation-histologic-grade" name="Hisotologic Grade Observation example"/>
+<artifact deprecated="true" id="Observation/observation-histologic-grade" key="Observation-observation-histologic-grade" name="Hisotologic Grade Observation example"/>
 <artifact deprecated="true" id="Observation/49275.100004300-us" key="Observation-49275.100004300-us" name="Histologic Grade: High grade (example)"/>
-<artifact id="Observation/observation-histologic-type" key="Observation-observation-histologic-type" name="Histologic Type Observation example"/>
+<artifact deprecated="true" id="Observation/observation-histologic-type" key="Observation-observation-histologic-type" name="Histologic Type Observation example"/>
 <artifact deprecated="true" id="Observation/59852.100004300-us" key="Observation-59852.100004300-us" name="Histologic Type: Adrenal cortical carcinoma (example)"/>
-<artifact id="MessageHeader/pathology-message-header" key="MessageHeader-pathology-message-header" name="MessageHeader example"/>
+<artifact deprecated="true" id="MessageHeader/pathology-message-header" key="MessageHeader-pathology-message-header" name="MessageHeader example"/>
 <artifact id="RelatedPerson/pathology-next-of-kin" key="RelatedPerson-pathology-next-of-kin" name="Next-of-Kin RelatedPerson example"/>
-<artifact id="Practitioner/oncologist-example" key="Practitioner-oncologist-example" name="Oncologist Practitioner example"/>
+<artifact deprecated="true" id="Practitioner/oncologist-example" key="Practitioner-oncologist-example" name="Oncologist Practitioner example"/>
 <artifact id="PractitionerRole/practitionerrole-uspath-oncologist-example" key="PractitionerRole-oncologist-example" name="Oncologist PractitionerRole example"/>
-<artifact id="Practitioner/pathologist-example" key="Practitioner-pathologist-example" name="Pathologist Practitioner example"/>
+<artifact deprecated="true" id="Practitioner/pathologist-example" key="Practitioner-pathologist-example" name="Pathologist Practitioner example"/>
 <artifact deprecated="true" id="PractitionerRole/pathologist-example" key="PractitionerRole-pathologist-example" name="Pathologist PractitionerRole (example)"/>
 <artifact deprecated="true" id="Bundle/cancer-us-pathology-message-bundle" key="Bundle-cancer-us-pathology-message-bundle" name="Pathology Bundle (example)"/>
 <artifact id="CapabilityStatement/pathology-lab-information-system" key="CapabilityStatement-pathology-lab-information-system" name="Pathology Laboratory Information System"/>
 <artifact id="Procedure/path-specimen" key="Procedure-path-specimen" name="Pathology specimen collection procedure example"/>
 <artifact id="Patient/JoelAlexPatient" key="Patient-JoelAlexPatient" name="Patient example"/>
 <artifact deprecated="true" id="Observation/2137.100004300-us" key="Observation-2137.100004300-us" name="Primary Tumor (pT): pTX: primary tumor cannot be assessed (example)"/>
-<artifact id="Observation/observation-primary-tumor" key="Observation-observation-primary-tumor" name="Primary Tumor Observation example"/>
+<artifact deprecated="true" id="Observation/observation-primary-tumor" key="Observation-observation-primary-tumor" name="Primary Tumor Observation example"/>
 <artifact id="Organization/principal-pathology-lab" key="Organization-principal-pathology-lab" name="Principal Pathology Lab example"/>
 <artifact deprecated="true" id="Observation/42554.100004300-us" key="Observation-42554.100004300-us" name="Procedure: Adrenalectomy, total (example)"/>
 <artifact id="Organization/Redwood-Womens-Center-PC" key="Organization-Redwood-Womens-Center-PC" name="Redwood Women's Center, P.C. example"/>
 <artifact deprecated="true" id="Observation/2143.100004300-us" key="Observation-2143.100004300-us" name="Regional Lymph Nodes (pN): pN0: No regional lymph node metastasis (example)"/>
-<artifact id="Observation/observation-regional-lymph-nodes" key="Observation-observation-regional-lymph-nodes" name="Regional Lymph Nodes Observation example"/>
+<artifact deprecated="true" id="Observation/observation-regional-lymph-nodes" key="Observation-observation-regional-lymph-nodes" name="Regional Lymph Nodes Observation example"/>
 <artifact deprecated="true" id="Observation/1867.100004300-us" key="Observation-1867.100004300-us" name="Regional Lymph Nodes: None Submitted (example)"/>
 <artifact id="ServiceRequest/cancer-path-example" key="ServiceRequest-cancer-path-example" name="Service Request - Cancer Pathology example"/>
-<artifact id="Observation/observation-specimen-laterality" key="Observation-observation-specimen-laterality" name="Specimen Laterality Observation example"/>
+<artifact deprecated="true" id="Observation/observation-specimen-laterality" key="Observation-observation-specimen-laterality" name="Specimen Laterality Observation example"/>
 <artifact deprecated="true" id="Observation/52756.100004300-us" key="Observation-52756.100004300-us" name="Specimen Laterality: Bilateral (example)"/>
-<artifact id="Practitioner/surgeon-example" key="Practitioner-surgeon-example" name="Surgeon Practitioner example"/>
+<artifact deprecated="true" id="Practitioner/surgeon-example" key="Practitioner-surgeon-example" name="Surgeon Practitioner example"/>
 <artifact id="PractitionerRole/practitionerrole-uspath-surgeon-example" key="PractitionerRole-practitionerrole-uspath-surgeon-example" name="Surgeon PractitionerRole example"/>
-<artifact id="Observation/observation-TNM-descriptors" key="Observation-observation-TNM-descriptors" name="TNM Descriptors Observation example"/>
+<artifact deprecated="true" id="Observation/observation-TNM-descriptors" key="Observation-observation-TNM-descriptors" name="TNM Descriptors Observation example"/>
 <artifact deprecated="true" id="Observation/20880.100004300-us" key="Observation-20880.100004300-us" name="TNM Descriptors: m (multiple primary tumors) (example)"/>
-<artifact id="Observation/observation-tumor-extension" key="Observation-observation-tumor-extension" name="Tumor Extension Observation example"/>
+<artifact deprecated="true" id="Observation/observation-tumor-extension" key="Observation-observation-tumor-extension" name="Tumor Extension Observation example"/>
 <artifact deprecated="true" id="Observation/53526.100004300-us" key="Observation-53526.100004300-us" name="Tumor Extension-2: Tumor invasion-2 (example)"/>
 <artifact deprecated="true" id="Observation/51265.100004300-us" key="Observation-51265.100004300-us" name="Tumor Extension: Tumor invasion (example)"/>
-<artifact id="Observation/observation-tumor-invasion" key="Observation-observation-tumor-invasion" name="Tumor Invasion Observation example"/>
-<artifact id="Observation/observation-tumor-site" key="Observation-observation-tumor-site" name="Tumor Site Observation example"/>
-<artifact id="Observation/observation-tumor-size" key="Observation-observation-tumor-size" name="Tumor Size Observation example"/>
+<artifact deprecated="true" id="Observation/observation-tumor-invasion" key="Observation-observation-tumor-invasion" name="Tumor Invasion Observation example"/>
+<artifact deprecated="true" id="Observation/observation-tumor-site" key="Observation-observation-tumor-site" name="Tumor Site Observation example"/>
+<artifact deprecated="true" id="Observation/observation-tumor-size" key="Observation-observation-tumor-size" name="Tumor Size Observation example"/>
 <artifact deprecated="true" id="Observation/2129.100004300-us" key="Observation-2129.100004300-us" name="Tumor Size: Greatest dimension in Centimeters (cm) (example)"/>
-<artifact id="Observation/observation-tumor-weight" key="Observation-observation-tumor-weight" name="Tumor Weight Observation example"/>
+<artifact deprecated="true" id="Observation/observation-tumor-weight" key="Observation-observation-tumor-weight" name="Tumor Weight Observation example"/>
 <artifact deprecated="true" id="Observation/40496.100004300-us" key="Observation-40496.100004300-us" name="Tumor Weight: Specify Weight (g) (example)"/>
+<artifact id="StructureDefinition/us-composition-lab" key="StructureDefinition-us-composition-lab" name="US Composition Laboratory Report"/>
 <artifact id="PractitionerRole/practitionerrole-uspath-pathologist-example" key="PractitionerRole-practitionerrole-uspath-pathologist-example" name="US Pathologist PractitionerRole example"/>
 <artifact id="DiagnosticReport/pathology-diagnostic-report" key="DiagnosticReport-pathology-diagnostic-report" name="US Pathology Adrenal DiagnosticReport example"/>
 <artifact deprecated="true" id="StructureDefinition/us-pathology-bundle" key="StructureDefinition-us-pathology-bundle" name="US Pathology Bundle"/>
-<artifact id="StructureDefinition/us-pathology-content-bundle" key="StructureDefinition-us-pathology-content-bundle" name="US Pathology Cancer Registry Content Bundle"/>
-<artifact id="StructureDefinition/us-pathology-reporting-bundle" key="StructureDefinition-us-pathology-reporting-bundle" name="US Pathology Cancer Registry Reporting Bundle"/>
-<artifact id="Bundle/us-pathology-reporting-bundle-example" key="Bundle-us-pathology-reporting-bundle-example" name="US Pathology Cancer Registry Reporting Bundle example"/>
-<artifact id="Bundle/us-pathology-content-bundle-example" key="Bundle-us-pathology-content-bundle-example" name="US Pathology Content bundle example"/>
+<artifact deprecated="true" id="StructureDefinition/us-pathology-content-bundle" key="StructureDefinition-us-pathology-content-bundle" name="US Pathology Cancer Registry Content Bundle"/>
+<artifact deprecated="true" id="StructureDefinition/us-pathology-reporting-bundle" key="StructureDefinition-us-pathology-reporting-bundle" name="US Pathology Cancer Registry Reporting Bundle"/>
+<artifact deprecated="true" id="Bundle/us-pathology-reporting-bundle-example" key="Bundle-us-pathology-reporting-bundle-example" name="US Pathology Cancer Registry Reporting Bundle example"/>
+<artifact deprecated="true" id="Bundle/us-pathology-content-bundle-example" key="Bundle-us-pathology-content-bundle-example" name="US Pathology Content bundle example"/>
 <artifact id="StructureDefinition/us-pathology-diagnostic-report" key="StructureDefinition-us-pathology-diagnostic-report" name="US Pathology Diagnostic Report"/>
 <artifact id="Encounter/uspath-specimen-collection-example" key="Encounter-uspath-specimen-collection-example" name="US Pathology Encounter Specimen Collection example"/>
+<artifact id="StructureDefinition/us-pathology-document-bundle" key="StructureDefinition-us-pathology-document-bundle" name="US Pathology Exchange Bundle"/>
 <artifact id="Bundle/us-pathology-exchange-bundle-example" key="Bundle-us-pathology-exchange-bundle-example" name="US Pathology Exchange bundle example"/>
 <artifact id="StructureDefinition/us-pathology-exchange-bundle" key="StructureDefinition-us-pathology-exchange-bundle" name="US Pathology ExchangeBundle"/>
-<artifact id="StructureDefinition/us-pathology-message-header" key="StructureDefinition-us-pathology-message-header" name="US Pathology MessageHeader"/>
+<artifact deprecated="true" id="StructureDefinition/us-pathology-message-header" key="StructureDefinition-us-pathology-message-header" name="US Pathology MessageHeader"/>
 <artifact deprecated="true" id="StructureDefinition/us-pathology-next-of-kin" key="StructureDefinition-us-pathology-next-of-kin" name="US Pathology Next of Kin"/>
 <artifact id="ValueSet/us-pathology-provider-types" key="ValueSet-us-pathology-provider-types" name="US Pathology Provider Types"/>
 <artifact deprecated="true" id="CodeSystem/us-pathology-provider-types" key="CodeSystem-us-pathology-provider-types" name="US Pathology Provider Types CodeSystem"/>
 <artifact id="StructureDefinition/us-pathology-related-practitioner-role" key="StructureDefinition-us-pathology-related-practitioner-role" name="US Pathology Related PractitionerRoles"/>
 <artifact id="StructureDefinition/us-pathology-service-request" key="StructureDefinition-us-pathology-service-request" name="US Pathology Service Request"/>
 <artifact id="StructureDefinition/us-pathology-specimen" key="StructureDefinition-us-pathology-specimen" name="US Pathology Specimen"/>
-<artifact id="Parameters/expansion-parameters-fhir-cancer-ig" key="Parameters-expansion-parameters-fhir-cancer-ig" name="expansion-parameters-fhir-cancer-ig"/>
+<artifact deprecated="true" id="Parameters/expansion-parameters-fhir-cancer-ig" key="Parameters-expansion-parameters-fhir-cancer-ig" name="expansion-parameters-fhir-cancer-ig"/>
 <page key="NA" name="(NA)"/>
 <page key="many" name="(many)"/>
 <page key="artifacts" name="Artifacts Summary"/>

UpdatesToMake.txt

@@ -0,0 +1,23 @@
+Recommendation: eliminate MedMoprh and IHE SDC on FHIR from F-CPDS
+Add Observation for handling unstructured Pathology Observations
+Change Bundle to Collection only
+DiagnosticReport in the Collection Bundle should be 1..* - is current 1..1
+Potential structure: 
+Path Report Bundle
+  DiagRep -- OBR + ORC
+    presentedForm - eCP
+  DiagRep
+    OBSx - OBX 
+  DiagRep
+    OBSx
+
+Need to include Procedure, ServiceRequest
+
+
+A consideration is to separate SDC and make IHE SDC/eCP on FHIR only for Pathology Observations 
+Or add Observations to F-CPDS
+
+Refer to https://build.fhir.org/ig/HL7/uv-lab-rep-ig/ spec as potential option to reference - is currently based on the EU
+- Have bundle structure 
+
+Write up issues we've had with Observation Grouper in representing multi specimen. Include an example from NAACCR Vol V 

_gencontinuous.bat

@@ -0,0 +1,2 @@
+@ECHO OFF
+CALL ./_genonce.bat -watch

_gencontinuous.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+./_genonce.sh -watch

_genonce.bat

@@ -0,0 +1,27 @@
+@ECHO OFF
+SET publisher_jar=publisher.jar
+SET input_cache_path=%CD%\input-cache
+
+ECHO Checking internet connection...
+PING tx.fhir.org -4 -n 1 -w 1000 | FINDSTR TTL && GOTO isonline
+ECHO We're offline...
+SET txoption=-tx n/a
+GOTO igpublish
+
+:isonline
+ECHO We're online
+SET txoption=
+
+:igpublish
+
+SET JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF-8
+
+IF EXIST "%input_cache_path%\%publisher_jar%" (
+	JAVA -jar "%input_cache_path%\%publisher_jar%" -ig . %txoption% %*
+) ELSE If exist "..\%publisher_jar%" (
+	JAVA -jar "..\%publisher_jar%" -ig . %txoption% %*
+) ELSE (
+	ECHO IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
+)
+
+PAUSE

_genonce.sh

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+#!/bin/bash
+publisher_jar=publisher.jar
+input_cache_path=./input-cache/
+echo Checking internet connection...
+curl -sSf tx.fhir.org > /dev/null
+
+if [ $? -eq 0 ]; then
+	echo "Online"
+	txoption=""
+else
+	echo "Offline"
+	txoption="-tx n/a"
+fi
+
+echo "$txoption"
+
+export JAVA_TOOL_OPTIONS="$JAVA_TOOL_OPTIONS -Dfile.encoding=UTF-8"
+
+publisher=$input_cache_path/$publisher_jar
+if test -f "$publisher"; then
+	java -jar $publisher -ig . $txoption $*
+
+else
+	publisher=../$publisher_jar
+	if test -f "$publisher"; then
+		java -jar $publisher -ig . $txoption $*
+	else
+		echo IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
+	fi
+fi