Implémentation des sections CDA de la partie corps (#117)

* MAJ-sections-CDA (#113)

* Sections cda (#116)

* MAJ des profils fsh des sections

* Renommage du profil FRActProcedureDocument (#112)

* MAJ des ids des profils sections CDA

* MAJ ressources CDA section

* MAJ sections FR-Resultats

* Correction suite à workflow failed

* Correction suite à workflow failed

* Mise à jour des sections (#118)

* MAJ des profils fsh des sections

* MAJ des ids des profils sections CDA

* MAJ ressources CDA section

* MAJ sections FR-Resultats

* Mise à jour des ids des sections + cardinalités des attributs du code

* Mise à jour des sections CDA (#119)

---------

Co-authored-by: Haoura <121106042+Haoura@users.noreply.github.com>

Author: souadbenmustapha

_build.bat

@@ -25,22 +25,34 @@ IF EXIST "%input_cache_path%%publisher_jar%" (
     ) ELSE (
         SET "jar_location=not_found"
         SET "default_choice=1"
+        SET "default_reason=publisher not found"
         ECHO publisher.jar not found in input-cache or parent folder
     )
 )
 
 
 :: Handle command-line argument to bypass the menu
-IF NOT "%~1"=="" (
-    IF /I "%~1"=="update" SET "userChoice=1"
-    IF /I "%~1"=="build" SET "userChoice=2"
-    IF /I "%~1"=="nosushi" SET "userChoice=3"
-    IF /I "%~1"=="notx" SET "userChoice=4"
-    IF /I "%~1"=="jekyll" SET "userChoice=5"
-    IF /I "%~1"=="clean" SET "userChoice=6"
-    IF /I "%~1"=="exit" SET "userChoice=0"
-    GOTO executeChoice
-)
+:: Known first arguments select a menu option; anything else is passed through to the publisher
+SET "extraArgs="
+IF "%~1"=="" GOTO showMenu
+IF /I "%~1"=="update" SET "userChoice=1" & GOTO parseExtra
+IF /I "%~1"=="build" SET "userChoice=2" & GOTO parseExtra
+IF /I "%~1"=="nosushi" SET "userChoice=3" & GOTO parseExtra
+IF /I "%~1"=="notx" SET "userChoice=4" & GOTO parseExtra
+IF /I "%~1"=="jekyll" SET "userChoice=5" & GOTO parseExtra
+IF /I "%~1"=="clean" SET "userChoice=6" & GOTO parseExtra
+IF /I "%~1"=="exit" SET "userChoice=0" & GOTO parseExtra
+:: Unknown first arg - default to build, pass all args through
+SET "userChoice=2"
+GOTO collectArgs
+:parseExtra
+SHIFT
+:collectArgs
+IF "%~1"=="" GOTO executeChoice
+SET "extraArgs=!extraArgs! %1"
+SHIFT
+GOTO collectArgs
+:showMenu
 
 echo ---------------------------------------------------------------
 ECHO Checking internet connection...
@@ -53,10 +65,14 @@ IF "%online_status%"=="true" (
     SET "latest_version=!latest_version: =!"
     SET "latest_version=!latest_version:~0,-1!"
 ) ELSE (
-    ECHO We're offline or tx.fhir.org is not available, can only run the publisher without TX...
+    ECHO.
+    ECHO *** WARNING: Working offline - this is not the normal mode.
+    ECHO     Some features (e.g. terminology rendering) will not work.
+    ECHO.
     SET "txoption=-tx n/a"
     SET "latest_version=unknown"
     SET "default_choice=4"
+    SET "default_reason=working offline"
 )
 
 echo ---------------------------------------------------------------
@@ -79,9 +95,11 @@ IF NOT "%online_status%"=="true" (
     IF NOT "!publisher_version!"=="!latest_version!" (
         ECHO An update is recommended.
         SET "default_choice=1"
+        SET "default_reason=newer version available"
     ) ELSE (
         ECHO Publisher is up to date.
         SET "default_choice=2"
+        SET "default_reason=publisher is up to date"
     )
 )
 
@@ -96,12 +114,9 @@ echo 4. Build IG - force no TX server
 echo 5. Jekyll build
 echo 6. Clean up temp directories
 echo 0. Exit
-:: echo [Press Enter for default (%default_choice%) or type an option number:]
 echo.
 
-:: Using CHOICE to handle input with timeout
-:: ECHO [Enter=Continue, 1-7=Option, 0=Exit]
-choice /C 12345670 /N /CS /D %default_choice% /T 5 /M "Choose an option number or wait 5 seconds for default (%default_choice%):"
+choice /C 12345670 /N /CS /D %default_choice% /T 5 /M "Choose an option number or wait 5 seconds for default (%default_choice% - %default_reason%):"
 SET "userChoice=%ERRORLEVEL%"
 
 
@@ -115,15 +130,12 @@ IF "%userChoice%"=="4" GOTO publish_notx
 IF "%userChoice%"=="5" GOTO debugjekyll
 IF "%userChoice%"=="6" GOTO clean
 IF "%userChoice%"=="0" EXIT /B
-
-:end
-
-
+GOTO endscript
 
 :debugjekyll
     echo Running Jekyll build...
     jekyll build -s temp/pages -d output
-GOTO end
+GOTO endscript
 
 
 :clean
@@ -152,10 +164,7 @@ GOTO end
         echo Removed: .\template
     )
 
-GOTO end
-
-
-
+GOTO endscript
 
 
 :downloadpublisher
@@ -198,7 +207,7 @@ IF DEFINED FORCE (
 	GOTO download
 )
 
-IF "%skipPrompts%"=="y" (
+IF "%skipPrompts%"=="true" (
 	SET create=Y
 ) ELSE (
 	SET /p create="Download? (Y/N) "
@@ -211,7 +220,7 @@ IF /I "%create%"=="Y" (
 GOTO done
 
 :upgrade
-IF "%skipPrompts%"=="y" (
+IF "%skipPrompts%"=="true" (
 	SET overwrite=Y
 ) ELSE (
 	SET /p overwrite="Overwrite %jarlocation%? (Y/N) "
@@ -265,15 +274,15 @@ GOTO done
 
 ECHO.
 ECHO Updating scripts
-IF "%skipPrompts%"=="y" (
+IF "%skipPrompts%"=="true" (
 	SET updateScripts=Y
 ) ELSE (
 	SET /p updateScripts="Update scripts? (Y/N) "
 )
 IF /I "%updateScripts%"=="Y" (
 	GOTO scripts
 )
-GOTO end
+GOTO endscript
 
 
 :scripts
@@ -299,27 +308,28 @@ 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 "%build_bat_url%" -Outfile "_build.new.bat" }
 if %ERRORLEVEL% == 0 goto upd_script_2
 echo "Errors encountered during download: %errorlevel%"
-goto end
+goto endscript
 :upd_script_2
 start copy /y "_build.new.bat" "_build.bat" ^&^& del "_build.new.bat" ^&^& exit
 
 
-GOTO end
+GOTO endscript
 
 
 :publish_once
 
 SET JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF-8
 
 :: Debugging statements before running publisher
-ECHO 1jar_location is: %jar_location%
+ECHO jar_location is: %jar_location%
 IF NOT "%jar_location%"=="not_found" (
-	java %JAVA_OPTS% -jar "%jar_location%" -ig . %txoption% %*
+	ECHO IG Publisher FOUND, Publishing...
+	java %JAVA_OPTS% -jar "%jar_location%" -ig . %txoption% %extraArgs%
 ) ELSE (
 	ECHO IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
 )
 
-GOTO end
+GOTO endscript
 
 
 
@@ -328,14 +338,14 @@ GOTO end
 SET JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF-8
 
 :: Debugging statements before running publisher
-ECHO 3jar_location is: %jar_location%
+ECHO jar_location is: %jar_location%
 IF NOT "%jar_location%"=="not_found" (
-	java %JAVA_OPTS% -jar "%jar_location%" -ig . %txoption% -no-sushi %*
+	java %JAVA_OPTS% -jar "%jar_location%" -ig . %txoption% -no-sushi %extraArgs%
 ) ELSE (
 	ECHO IG Publisher NOT FOUND in input-cache or parent folder. Please run _updatePublisher.  Aborting...
 )
 
-GOTO end
+GOTO endscript
 
 
 :publish_notx
@@ -344,43 +354,33 @@ SET txoption=-tx n/a
 SET JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF-8
 
 :: Debugging statements before running publisher
-ECHO 2jar_location is: %jar_location%
+ECHO jar_location is: %jar_location%
 IF NOT "%jar_location%"=="not_found" (
-	java %JAVA_OPTS% -jar "%jar_location%" -ig . %txoption% %*
+	java %JAVA_OPTS% -jar "%jar_location%" -ig . %txoption% %extraArgs%
 ) ELSE (
 	ECHO IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
 )
 
-GOTO end
-
-
+GOTO endscript
 
 
 :publish_continuous
 
 SET JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF-8
 
-:: Debugging statements before running publisher
-ECHO Checking %input_cache_path% for publisher.jar
-IF EXIST "%input_cache_path%\%publisher_jar%" (
-	java %JAVA_OPTS% -jar "%input_cache_path%\%publisher_jar%" -ig . %txoption% -watch %*
+ECHO jar_location is: %jar_location%
+IF NOT "%jar_location%"=="not_found" (
+	java %JAVA_OPTS% -jar "%jar_location%" -ig . %txoption% -watch %extraArgs%
 ) ELSE (
-    ECHO Checking %upper_path% for publisher.jar
-    IF EXIST "..\%publisher_jar%" (
-	    java %JAVA_OPTS% -jar "..\%publisher_jar%" -ig . %txoption% -watch %*
-    ) ELSE (
-	    ECHO IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
-    )
+	ECHO IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
 )
 
-GOTO end
+GOTO endscript
 
 
-:end
+:endscript
 
 :: Pausing at the end
-
-
 IF NOT "%skipPrompts%"=="true" (
   PAUSE
 )

input/fsh/MappingLM_CDA_FHIR_Corps/sections/FRSectionExposureRadiationLMCDAFHIR.fsh

@@ -39,11 +39,11 @@ Description: "Mapping des éléments du modèle métier FRLMExpositionRadiations
 * group[=].element[=].target[=].equivalence = #equivalent
 // Entrée observation de grossesse
 * group[=].element[+].code = #FRLMExpositionRadiations.entree.observationGrossesse
-* group[=].element[=].target[+].code = #FRCDADICOMExpositionAuxRadiations.entry:frDICOMObservation
+* group[=].element[=].target[+].code = #FRCDADICOMExpositionAuxRadiations.entry:frDicomObservationGrossesse
 * group[=].element[=].target[=].equivalence = #equivalent
 // Entrée observation indication
 * group[=].element[+].code = #FRLMExpositionRadiations.entree.observationIndication
-* group[=].element[=].target[+].code = #FRCDADICOMExpositionAuxRadiations.entry:frDICOMObservation
+* group[=].element[=].target[+].code = #FRCDADICOMExpositionAuxRadiations.entry:frDicomObservationIndication
 * group[=].element[=].target[=].equivalence = #equivalent
 
 // Groupe Mapping 2 : CDA → FHIR
@@ -78,10 +78,10 @@ Description: "Mapping des éléments du modèle métier FRLMExpositionRadiations
 * group[=].element[=].target[+].code = #FRCompositionDocument.section:exposureRadiation.entry:FRObservationRadiationExposureDocument.partOf:medicationAdministrationRef
 * group[=].element[=].target[=].equivalence = #equivalent
 // Entrée observation de grossesse
-* group[=].element[+].code = #FRCDADICOMExpositionAuxRadiations.entry:frDICOMObservation
+* group[=].element[+].code = #FRCDADICOMExpositionAuxRadiations.entry:frDicomObservationGrossesse
 * group[=].element[=].target[+].code = #FRCompositionDocument.section:exposureRadiation.entry:FRObservationRadiationExposureDocument.hasMember:observationGrossesse
 * group[=].element[=].target[=].equivalence = #equivalent
 // Entrée observation indication
-* group[=].element[+].code = #FRCDADICOMExpositionAuxRadiations.entry:frDICOMObservation
+* group[=].element[+].code = #FRCDADICOMExpositionAuxRadiations.entry:frDicomObservationIndication
 * group[=].element[=].target[+].code = #FRCompositionDocument.section:exposureRadiation.entry:FRObservationRadiationExposureDocument.hasMember:observationIndication
 * group[=].element[=].target[=].equivalence = #equivalent

input/fsh/RessourcesCDACorps/profils/composantsElementaires/FRCDAResultats.fsh

@@ -0,0 +1,58 @@
+Profile: FRCDAResultats
+Parent: http://hl7.org/cda/stds/core/StructureDefinition/Organizer
+Id: fr-cda-resultats
+Title: "CDA - FR resultats"
+Description: "Entrée FR-resultats: L'entrée 'FR-Resultats' est une entrée de type 'organizer' regroupant les types des résultats classés par type d’examens (BIO, IMG, etc…)."
+* classCode MS
+* classCode = #CLUSTER
+* moodCode MS
+* id 1..1
+* id ^short = "Identifiant de l'entrée"
+* id ^definition = "Identifiant de l'entrée"
+* templateId 1..1
+* templateId ^slicing.discriminator.type = #value
+* templateId ^slicing.discriminator.path = "root"
+* templateId ^slicing.rules = #open
+* templateId contains frResultats 1..1
+* templateId[frResultats] 1..1
+* templateId[frResultats].root = "1.2.250.1.213.1.1.3.208"
+* templateId[frResultats] ^short = "Conformité FR-Resultats (CI-SIS)"
+* templateId[frResultats] ^definition = "Conformité FR-Resultats (CI-SIS)"
+* code MS
+* code 1..1
+* code ^short = "Code de l'entrée en LOINC.
+Type de résultat : 
+- 26436-6 Biologie polyvalente 
+- 18748-4 Imagerie
+- 26438-2 Cytologie
+- 27898-6 Pathologie
+- 26435-8 Génétique humaine"
+* code ^definition = "Code de l'entrée en LOINC"
+* code from https://smt.esante.gouv.fr/fhir/ValueSet/jdv-resultat-type-cisis
+* statusCode MS
+* statusCode 1..1
+* statusCode ^short = "Statut de l'entrée : completed"
+* statusCode ^definition = "Statut de l'entrée"
+* effectiveTime MS
+* effectiveTime 0..1
+* effectiveTime ^short = "Date"
+* effectiveTime ^definition = "Date"
+* performer 1..1
+* performer ^short = "Exécutant"
+* performer ^definition = "Exécutant"
+* performer only FRCDALaboratoireExecutant
+* author 1..1
+* author ^short = "Auteur"
+* author ^definition = "Auteur"
+* author only FRCDAAuthor
+* component MS
+* component 1..1
+* component ^slicing.discriminator.type = #type
+* component ^slicing.discriminator.path = "$this"
+* component ^slicing.rules = #open
+* component contains
+frResultat 1..1 
+* component[frResultat].observation 0..1 
+* component[frResultat].observation only FRCDAResultat
+* component[frResultat].observation ^short = "Entrée FR-Resultat"
+* component[frResultat].observation ^definition = "Entrée FR-Resultat"

input/fsh/RessourcesCDACorps/profils/sections/FRCDASectionAllergiesEtHypersensibilites.fsh

@@ -0,0 +1,43 @@
+Profile: FRCDASectionAllergiesEtHypersensibilites
+Parent: http://hl7.org/cda/stds/core/StructureDefinition/Section
+Id: fr-cda-allergies-et-hypersensibilites
+Title: "CDA - FR Allergies et hypersensibilites"
+Description: "IHE-PCC - Allergies-And-Other-Adverse-Reactions 
+ - La section 'Allergies et hypersensibilités' permet de décrire la liste codée des allergies et hypersensibilités (médicaments, environnements, aliments,..) précisant notamment l'agent et les réactions observées."
+* templateId 1..3
+* templateId ^slicing.discriminator.type = #value
+* templateId ^slicing.discriminator.path = "root"
+* templateId ^slicing.rules = #open
+* templateId contains iheAllergiesAndOtherAdverseReactionsSection 1..1
+and ccdAlertsSection 1..1
+and frSectionAllergiesEtHypersensibilites 1..1
+* templateId[iheAllergiesAndOtherAdverseReactionsSection].root = "1.3.6.1.4.1.19376.1.5.3.1.3.13"
+* templateId[iheAllergiesAndOtherAdverseReactionsSection] ^short = "Déclaration de conformité de la section aux spécifications IHE PCC"
+* templateId[ccdAlertsSection].root = "2.16.840.1.113883.10.20.1.2"
+* templateId[ccdAlertsSection] ^short = "Déclaration de conformité de la section aux spécifications C-CDA"
+* templateId[frSectionAllergiesEtHypersensibilites].root = "1.2.250.1.213.1.1.2.137"
+* templateId[frSectionAllergiesEtHypersensibilites] ^short = "Déclaration de conformité de la section aux spécifications CI-SIS"
+* id MS
+* id ^short = "Identifiant de la section"
+* id ^definition = "Identifiant de la section"
+* code MS
+* code 1..1
+* code ^short = "Code de la section"
+* code ^definition = "Code de la section"
+* code.code 1..1
+* code.code = #48765-2
+* code.displayName 1..1
+* code.displayName = "Allergies et hypersensibilités"
+* code.codeSystem 1..1
+* code.codeSystem = "2.16.840.1.113883.6.1"
+* code.codeSystemName = "LOINC"
+* title 1..1
+* title ^short = "Titre de la sectionFixé à 'Allergies et hypersensibilités'"
+* title ^definition = "Titre de la section"
+* text 1..1 MS
+* text ^short = "Bloc narratif"
+* text ^definition = "Bloc narratif"
+* entry MS
+* entry 1..*
+* entry.act only FRCDAListeDesAllergiesEtHypersensibilites
+* entry ^short = "Entrée Liste des allergies et hypersensibilités"