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Commit b7cf4208 authored by Achraf Achkari's avatar Achraf Achkari
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Merge branch 'develop' into 'master' 

Fix SEQUOIA Confs

See merge request !17
parents 4638f8e4 5612c4ec
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2 merge requests!18Update version,!17Fix SEQUOIA Confs
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docs/installation-guide.md
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− 19
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...@@ -11,15 +11,15 @@ date: 19/10/2021 ...@@ -11,15 +11,15 @@ date: 19/10/2021
1. ##### [Introduction](#introduction) 1. ##### [Introduction](#introduction)
2. ##### [Clone Project](#cloneProject) 2. ##### [Clone Project](#cloneProject)
3. ##### [Run Tests (Optional)](#runTests) 3. ##### [Run Tests (Optional)](#runTests)
4. ##### [Generate Artifact](#generateArtifact) 4. ##### [Prepare BBR](#prepareBBR)
5. ##### [Prepare BBR](#prepareBBR) 5. ##### [Generate Artifact](#generateArtifact)
6. ##### [Generate Validator](#generateValidator) 6. ##### [Generate Validator](#generateValidator)
7. ##### [Generation Validator form UML (Alternative)](#generateValidatorFromUML) 7. ##### [Generation Validator form UML (Alternative)](#generateValidatorFromUML)
8. ##### [Validate CDA](#validateCDA) 8. ##### [Validate CDA](#validateCDA)
9. ##### [Utility Scripts](#utilityScripts) 9. ##### [Utility Scripts](#utilityScripts)
10. ##### [Extras](#extras) 10. ##### [Extras](#extras)
<div id='introduction'/> <div id='introduction'></div>
## 1. Introduction ## 1. Introduction
In this guide, we will show how to retrieve the new version of **Gazelle Objects Cheker**, In this guide, we will show how to retrieve the new version of **Gazelle Objects Cheker**,
...@@ -31,7 +31,7 @@ build it and generate a CDA Validator in a generic case, and client specific cas ...@@ -31,7 +31,7 @@ build it and generate a CDA Validator in a generic case, and client specific cas
- Thanks to maven wrapper, this version is packaged now with GOC, you can find it in `gazelle-objects-checker/hl7templates/hl7templates-packager-jar/src/main/resources/maven-wrapper` - Thanks to maven wrapper, this version is packaged now with GOC, you can find it in `gazelle-objects-checker/hl7templates/hl7templates-packager-jar/src/main/resources/maven-wrapper`
- Git - Git
<div id='cloneProject'/> <div id='cloneProject'></div>
## 2. Clone Project ## 2. Clone Project
the project is not maintained by the _forge_ anymore.<br> the project is not maintained by the _forge_ anymore.<br>
...@@ -92,7 +92,7 @@ You can skip tests if you want, but it's not recommend. ...@@ -92,7 +92,7 @@ You can skip tests if you want, but it's not recommend.
<div id='runTests'/> <div id='runTests'></div>
## 3. Run Tests (Optional) ## 3. Run Tests (Optional)
...@@ -123,7 +123,7 @@ If Something went wrong, make sure you have mentioned in maven logs: ...@@ -123,7 +123,7 @@ If Something went wrong, make sure you have mentioned in maven logs:
If not, try to run the creation resources script `CreateResourcesForTest.java` in: If not, try to run the creation resources script `CreateResourcesForTest.java` in:
- _gazelle-objects-checker/gocmodel-jar/src/main/java/net.ihe.gazelle.goc.script_ - _gazelle-objects-checker/gocmodel-jar/src/main/java/net.ihe.gazelle.goc.script_
<div id='prepareBBR'/> <div id='prepareBBR'></div>
## 4. Prepare BBR ## 4. Prepare BBR
BBR is an abbreviation of Building Block Repository, a large XML file containing all the functional specifications, BBR is an abbreviation of Building Block Repository, a large XML file containing all the functional specifications,
...@@ -149,7 +149,7 @@ then change **ccda-** by **ccda(version)-** for example for version 2.1: ...@@ -149,7 +149,7 @@ then change **ccda-** by **ccda(version)-** for example for version 2.1:
NOTICE: A script could be released for this, due to performance issues NOTICE: A script could be released for this, due to performance issues
<div id='generateArtifacts'/> <div id='generateArtifact'></div>
## 5. Generate Artifact ## 5. Generate Artifact
...@@ -183,7 +183,7 @@ The Artifact is generated at _**gazelle-objects-checker/hl7templates-packager-ja ...@@ -183,7 +183,7 @@ The Artifact is generated at _**gazelle-objects-checker/hl7templates-packager-ja
> here: [GOC Artifact Nexus](https://gazelle.ihe.net/nexus/#nexus-search;quick~hl7templates-packager) > here: [GOC Artifact Nexus](https://gazelle.ihe.net/nexus/#nexus-search;quick~hl7templates-packager)
> Choose the latest version, and download the: **hl7templates-packager-jar-X.X.X-jar-with-dependencies.jar** artifact > Choose the latest version, and download the: **hl7templates-packager-jar-X.X.X-jar-with-dependencies.jar** artifact
<div id='generateValidator'/> <div id='generateValidator'></div>
## 6. Generate Validator ## 6. Generate Validator
This section remains to **run** Gazelle Objects Checker and generate the CDA MBVal validator. This section remains to **run** Gazelle Objects Checker and generate the CDA MBVal validator.
...@@ -304,9 +304,9 @@ Example with SEQUOIA: ...@@ -304,9 +304,9 @@ Example with SEQUOIA:
- **cmdOutput.log:** contains the Standard Output of executed commands during generation (maven command to init project with archetype, generate code from OLC, packaging...) - **cmdOutput.log:** contains the Standard Output of executed commands during generation (maven command to init project with archetype, generate code from OLC, packaging...)
- **cdeModelsErrors.txt:** contains all detected inconsistencies between the provided BBR and pre-defined models used by GOC - **cdeModelsErrors.txt:** contains all detected inconsistencies between the provided BBR and pre-defined models used by GOC
![Logs Conception](media/Improved_Logging_Conception_v2.jpg "LogsConception") ![Logs Conception](Improved_Logging_Conception_v2.jpg "LogsConception")
<div id='generateValidatorFromUML' /> <div id='generateValidatorFromUML'></div>
## 7. Generate Validator from UML (Alternative) ## 7. Generate Validator from UML (Alternative)
...@@ -314,12 +314,12 @@ This section is just an alternative way to regenerate the validator when the fun ...@@ -314,12 +314,12 @@ This section is just an alternative way to regenerate the validator when the fun
without re-running GOC, but just from the generated ```model.uml``` file. without re-running GOC, but just from the generated ```model.uml``` file.
```bash ```bash
> cd /home/mylap/Documents/GOC-OUTPUT/[validator-name]-validator-jar/model/[validator-name].uml > cd /home/mylap/Documents/GOC-OUTPUT/validator/[validator-name]-validator-jar/model/[validator-name].uml
``` ```
for example for epsos5 for example for epsos5
```bash ```bash
> cd /home/mylap/Documents/GOC-OUTPUT/epsos5-validator-jar/model/epsos5.uml > cd /home/mylap/Documents/GOC-OUTPUT/validator/epsos5-validator-jar/model/epsos5.uml
``` ```
Then you can edit it with a Text Editor, or a dedicated modeling tool (ex: TopCased). Then you can edit it with a Text Editor, or a dedicated modeling tool (ex: TopCased).
...@@ -328,7 +328,7 @@ Then you can edit it with a Text Editor, or a dedicated modeling tool (ex: TopCa ...@@ -328,7 +328,7 @@ Then you can edit it with a Text Editor, or a dedicated modeling tool (ex: TopCa
Go to GOC-OUTPUT/epsos5-validator-jar and do the following: Go to GOC-OUTPUT/epsos5-validator-jar and do the following:
```bash ```bash
> cd /home/mylap/Documents/GOC-OUTPUT/epsos5-validator-jar > cd /home/mylap/Documents/GOC-OUTPUT/validator/epsos5-validator-jar
> mvn exec:exec@generateValidator -DmvnPath="/opt/apache-maven-3.5.4/bin/mvn" -DcdaProps="cdaepsos" -DprojectName="epsos5" > mvn exec:exec@generateValidator -DmvnPath="/opt/apache-maven-3.5.4/bin/mvn" -DcdaProps="cdaepsos" -DprojectName="epsos5"
> mvn clean package > mvn clean package
``` ```
...@@ -352,14 +352,13 @@ Now you can refer to [Section 8](#validateCDA) to Validate a CDA document with y ...@@ -352,14 +352,13 @@ Now you can refer to [Section 8](#validateCDA) to Validate a CDA document with y
<div id='validateCDA'/> <div id='validateCDA'></div>
## 8. Validate CDA ## 8. Validate CDA
Now we are going to use the generated validator.<br> Now we are going to use the generated validator.<br>
We will suppose we generated a validator with a BBR containing the following version: epsos5-.<br> We will suppose we generated a validator with a BBR containing the following version: epsos5-.<br>
_We didn't use the SEQUOIA's BBR because the validator needs a hack (access to SVS) before it could be used_
Open the following directory: Open the following directory:
```bash ```bash
...@@ -370,6 +369,23 @@ Open the following directory: ...@@ -370,6 +369,23 @@ Open the following directory:
> ./validator.sh -path <Path_to_CDA.xml> -out <Path_To_output_result.xml> > ./validator.sh -path <Path_to_CDA.xml> -out <Path_To_output_result.xml>
``` ```
For SEQUOIA with version ccda21, you need to adapt it to SVS first, and for that we have a generation script that handle all of that automatically:
```bash
> cd gazelle-objects-checker/hl7templates/hl7templates-packager-jar/target
> ./SEQUOIAGeneration.sh
# or just for adapting SVS you can use the SEQUOIASVSAdaptation.sh
```
Then:
```bash
> cd <Path_To_Output>/ccda21-validator-jar/target/appassembler/bin
> chmod +x validator.sh #if on linux
> ./validator.sh -path <Path_to_CDA.xml> -out <Path_To_output_result.xml>
```
Here is a summary of possible parameters for the validator: Here is a summary of possible parameters for the validator:
<table> <table>
<thead> <thead>
...@@ -437,7 +453,7 @@ Just import it to SoapUI and run the test cases. ...@@ -437,7 +453,7 @@ Just import it to SoapUI and run the test cases.
<div id='utilityScripts'/> <div id='utilityScripts'></div>
## 9. Utility Scripts ## 9. Utility Scripts
...@@ -470,7 +486,7 @@ For SEQUOIA: ...@@ -470,7 +486,7 @@ For SEQUOIA:
``` ```
<div id='extras'/> <div id='extras'></div>
## 10. Extras ## 10. Extras
...@@ -482,6 +498,5 @@ You can find some previous made documentation here _(belong the old GOC, and cou ...@@ -482,6 +498,5 @@ You can find some previous made documentation here _(belong the old GOC, and cou
#### Next released documentation #### Next released documentation
- Functional description of GOC - Functional description of GOC
- Prepare validator for SEQUOIA
- Use interactive scripts for generation
hl7templates/hl7templates-model-jar/src/main/java/net/ihe/gazelle/tempmodel/decor/dt/utils/DTUtils.java
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...@@ -109,7 +109,7 @@ public final class DTUtils { ...@@ -109,7 +109,7 @@ public final class DTUtils {
else { else {
return false; return false;
} }
return !realDTConstrained.equals(typeRD) && UMLLoader.verifyTheParentOfType1IsType2(realDTConstrained, typeRD); return !realDTConstrained.equals(typeRD) && (UMLLoader.verifyTheParentOfType1IsType2(typeRD, realDTConstrained) || UMLLoader.verifyTheParentOfType1IsType2(realDTConstrained, typeRD));
} }
public static String cleanDTforIPS(String datatype){ public static String cleanDTforIPS(String datatype){
......
hl7templates/hl7templates-packager-jar/src/main/resources/assemble-scripts/SEQUOIAGeneration.sh
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...@@ -206,25 +206,28 @@ if [ ! -f ./SEQUOIASVSAdaptation.sh ]; then ...@@ -206,25 +206,28 @@ if [ ! -f ./SEQUOIASVSAdaptation.sh ]; then
exit 1; exit 1;
fi; fi;
pathToResources='' # adapt only if version is higher than 1.1
if [ "$versionLabel" != "1.1" ]; then
pathToResources=''
if [ ! -d ./classes/sequoia-db-hack ]; then if [ ! -d ./classes/sequoia-db-hack ]; then
echo -e "${RED}Resources for adaptations not found, please provide a path manually" echo -e "${RED}Resources for adaptations not found, please provide a path manually"
read -r $pathToResources read -r $pathToResources
else else
pathToResources=$(realpath ./classes/sequoia-db-hack) pathToResources=$(realpath ./classes/sequoia-db-hack)
fi fi
if [ ! -x ./SEQUOIASVSAdaptation.sh ]; then if [ ! -x ./SEQUOIASVSAdaptation.sh ]; then
chmod +x SEQUOIASVSAdaptation.sh chmod +x SEQUOIASVSAdaptation.sh
fi; fi;
env JAVA_HOME=$JAVA_HOME M2_BIN=$mavenPath ./SEQUOIASVSAdaptation.sh "$workspaceDir/$folderName" $pathToResources env JAVA_HOME=$JAVA_HOME M2_BIN=$mavenPath ./SEQUOIASVSAdaptation.sh "$workspaceDir/$folderName" $pathToResources
if [ $? != 0 ]; then if [ $? != 0 ]; then
echo "${RED}Adaptations failed" echo "${RED}Adaptations failed"
exit 1 exit 1
fi fi
fi;
#Zip validator #Zip validator
#move to bin path #move to bin path
......
hl7templates/hl7templates-packager-jar/src/main/resources/sequoia-db-hack/xsd/POCD_MT000040_SDTC.xsd
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<?xml version="1.0" encoding="UTF-8" standalone="no"?> <?xml version="1.0" encoding="UTF-8" standalone="no"?>
<xs:schema targetNamespace="urn:hl7-org:v3" xmlns:mif="urn:hl7-org:v3/mif" xmlns="urn:hl7-org:v3" <xs:schema targetNamespace="urn:hl7-org:v3" xmlns:mif="urn:hl7-org:v3/mif" xmlns="urn:hl7-org:v3"
xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified"
xmlns:sdtc="urn:hl7-org:sdtc"> xmlns:sdtc="urn:hl7-org:sdtc">
<!-- <!--
***************************************************************************************************************** *****************************************************************************************************************
* XML schema for message type POCD_MT000040. * XML schema for message type POCD_MT000040.
...@@ -35,16 +35,16 @@ ...@@ -35,16 +35,16 @@
--> -->
<xs:annotation> <xs:annotation>
<xs:documentation>Manually edited to add SDTC Schema Extension (authenticator/signatureText, legalAuthenticator/signatureText), 14 July 2013</xs:documentation> <xs:documentation>Manually edited to add SDTC Schema Extension (authenticator/signatureText, legalAuthenticator/signatureText), 14 July 2013</xs:documentation>
<xs:documentation>Manually edited to add SDTC Schema Extensions, July 2012</xs:documentation> <xs:documentation>Manually edited to add SDTC Schema Extensions, July 2012</xs:documentation>
<xs:documentation>Generated using schema builder version 2.0. Stylesheets: <xs:documentation>Generated using schema builder version 2.0. Stylesheets:
RoseTreeToMIFStaticModel.xsl version: 1.1 RoseTreeToMIFStaticModel.xsl version: 1.1
StaticMifToXsd.xsl version 2.0</xs:documentation> StaticMifToXsd.xsl version 2.0</xs:documentation>
</xs:annotation> </xs:annotation>
<xs:include schemaLocation="processable/coreschemas/datatypes.xsd"/> <xs:include schemaLocation="processable/coreschemas/datatypes.xsd"/>
<xs:include schemaLocation="processable/coreschemas/voc.xsd"/> <xs:include schemaLocation="processable/coreschemas/voc.xsd"/>
<xs:include schemaLocation="processable/coreschemas/NarrativeBlock.xsd"/> <xs:include schemaLocation="processable/coreschemas/NarrativeBlock.xsd"/>
<xs:import namespace="urn:hl7-org:sdtc" schemaLocation="SDTC.xsd" /> <xs:import namespace="urn:hl7-org:sdtc" schemaLocation="SDTC.xsd" />
<xs:complexType name="POCD_MT000040.InfrastructureRoot.typeId"> <xs:complexType name="POCD_MT000040.InfrastructureRoot.typeId">
<xs:complexContent> <xs:complexContent>
<xs:restriction base="II"> <xs:restriction base="II">
<xs:attribute name="root" type="uid" use="required" fixed="2.16.840.1.113883.1.3"/> <xs:attribute name="root" type="uid" use="required" fixed="2.16.840.1.113883.1.3"/>
...@@ -916,6 +916,9 @@ StaticMifToXsd.xsl version 2.0</xs:documentation> ...@@ -916,6 +916,9 @@ StaticMifToXsd.xsl version 2.0</xs:documentation>
<xs:element name="realmCode" type="CS" minOccurs="0" maxOccurs="unbounded"/> <xs:element name="realmCode" type="CS" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="typeId" type="POCD_MT000040.InfrastructureRoot.typeId" minOccurs="0"/> <xs:element name="typeId" type="POCD_MT000040.InfrastructureRoot.typeId" minOccurs="0"/>
<xs:element name="templateId" type="II" minOccurs="0" maxOccurs="unbounded"/> <xs:element name="templateId" type="II" minOccurs="0" maxOccurs="unbounded"/>
<!-- Begin Extension: (SDTC) -->
<xs:element ref="sdtc:functionCode" minOccurs="0" />
<!-- End Extension: (SDTC) -->
<xs:element name="time" type="IVL_TS" minOccurs="0"/> <xs:element name="time" type="IVL_TS" minOccurs="0"/>
<xs:element name="awarenessCode" type="CE" minOccurs="0"/> <xs:element name="awarenessCode" type="CE" minOccurs="0"/>
<xs:element name="participantRole" type="POCD_MT000040.ParticipantRole"/> <xs:element name="participantRole" type="POCD_MT000040.ParticipantRole"/>
...@@ -957,9 +960,9 @@ StaticMifToXsd.xsl version 2.0</xs:documentation> ...@@ -957,9 +960,9 @@ StaticMifToXsd.xsl version 2.0</xs:documentation>
<xs:element name="raceCode" type="CE" minOccurs="0"/> <xs:element name="raceCode" type="CE" minOccurs="0"/>
<!-- Begin Extension: (SDTC) --> <!-- Begin Extension: (SDTC) -->
<xs:element ref="sdtc:raceCode" minOccurs="0" maxOccurs="unbounded"/> <xs:element ref="sdtc:raceCode" minOccurs="0" maxOccurs="unbounded"/>
<xs:element ref="sdtc:ethnicGroupCode" minOccurs="0" maxOccurs="unbounded"/>
<!-- End Extension: (SDTC) --> <!-- End Extension: (SDTC) -->
<xs:element name="ethnicGroupCode" type="CE" minOccurs="0"/> <xs:element name="ethnicGroupCode" type="CE" minOccurs="0"/>
<xs:element ref="sdtc:ethnicGroupCode" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="guardian" type="POCD_MT000040.Guardian" minOccurs="0" maxOccurs="unbounded"/> <xs:element name="guardian" type="POCD_MT000040.Guardian" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="birthplace" type="POCD_MT000040.Birthplace" minOccurs="0"/> <xs:element name="birthplace" type="POCD_MT000040.Birthplace" minOccurs="0"/>
<xs:element name="languageCommunication" type="POCD_MT000040.LanguageCommunication" minOccurs="0" maxOccurs="unbounded"/> <xs:element name="languageCommunication" type="POCD_MT000040.LanguageCommunication" minOccurs="0" maxOccurs="unbounded"/>
...@@ -999,6 +1002,9 @@ StaticMifToXsd.xsl version 2.0</xs:documentation> ...@@ -999,6 +1002,9 @@ StaticMifToXsd.xsl version 2.0</xs:documentation>
<xs:element name="realmCode" type="CS" minOccurs="0" maxOccurs="unbounded"/> <xs:element name="realmCode" type="CS" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="typeId" type="POCD_MT000040.InfrastructureRoot.typeId" minOccurs="0"/> <xs:element name="typeId" type="POCD_MT000040.InfrastructureRoot.typeId" minOccurs="0"/>
<xs:element name="templateId" type="II" minOccurs="0" maxOccurs="unbounded"/> <xs:element name="templateId" type="II" minOccurs="0" maxOccurs="unbounded"/>
<!-- Begin Extension: (SDTC) -->
<xs:element ref="sdtc:functionCode" minOccurs="0" />
<!-- End Extension: (SDTC) -->
<xs:element name="time" type="IVL_TS" minOccurs="0"/> <xs:element name="time" type="IVL_TS" minOccurs="0"/>
<xs:element name="modeCode" type="CE" minOccurs="0"/> <xs:element name="modeCode" type="CE" minOccurs="0"/>
<xs:element name="assignedEntity" type="POCD_MT000040.AssignedEntity"/> <xs:element name="assignedEntity" type="POCD_MT000040.AssignedEntity"/>
......
hl7templates/hl7templates-packager-jar/src/main/resources/sequoia-db-hack/xsd/SDTC.xsd
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− 0
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...@@ -53,6 +53,8 @@ ...@@ -53,6 +53,8 @@
<xs:element name="signatureText" type="hl7:ED"/> <xs:element name="signatureText" type="hl7:ED"/>
<xs:element name="functionCode" type="hl7:CE" />
......
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