Add Installation Guide docs

docs/installation-guide.md

+# Instalation Guide of Gazelle Objects Checker
+
+### Table of Content
+1. ##### [Introduction](#introduction)
+2. ##### [Clone Project](#cloneProject)
+3. ##### [Run Tests (Optional)](#runTests)
+4. ##### [Generate Artifact](#generateArtifact)
+5. ##### [Prepare BBR](#prepareBBR)
+6. ##### [Generate Validator](#generateValidator)
+7. ##### [Validate CDA](#validateCDA)
+8. ##### [Extras](#extra)
+
+<div id='introduction'/>
+
+## 1. Introduction
+In this guide, we will show how to retrieve the new version of **Gazelle Objects Cheker**, 
+build it and generate a CDA Validator in a generic case, and client specific case 
+
+**Requirements:**
+- **JDK 11** or higher
+- maven
+- git
+<div id='cloneProject'/>
+
+## 2. Clone Project 
+the project is not maintained by the _forge_ anymore.<br>
+Gazelle Objects Checker has been migred to **[Gitlab](https://gitlab.inria.fr)** and package under one module called **gazelle-objects-checker**<br>
+If you worked already with the pervious versions of GOC, the following structure could be familiar to you:
+- Archetypes
+  - generated-validator
+- Hl7templates
+  - gocmodel-jar
+  - hl7templates-model-jar
+  - hl7templates-api-jar
+  - hl7templates-generator-jar
+  - hl7templates-packager-jar
+- Models
+  - cda-models
+  - cdaepsos-models
+  - datatypes-models
+  - common-models
+  - infr-model
+  - model-resources
+  - nblock-model
+  - voc-model
+
+In the current version `3.0.0`, the `Archtypes` and `Hl7templates` modules _(with all their sub modules)_ are packaged in one module `Gazelle Objects Checker` <br>
+The resources models are packaged in a module called `UML Models`. 
+
+<table>
+  <thead>
+    <th>Project</th>
+    <th>Link Gitlab</th>
+  </thead>
+  <tr>
+    <td>Gazelle Objects Checker</td>
+    <td><a href="https://gitlab.inria.fr/gazelle/library/gazelle-objects-checker">https://gitlab.inria.fr/gazelle/library/gazelle-objects-checker</a></td>
+  </tr>
+  <tr>
+    <td>UML Models</td>
+    <td><a href="https://gitlab.inria.fr/gazelle/library/uml-models">https://gitlab.inria.fr/gazelle/library/uml-models</a></td>
+  </tr>
+</table>
+
+<br>
+
+##### Cloning gazelle-objects-checker:
+
+you need to have `git` and `maven` installed<br><br>
+Run the following command:
+> `git clone https://gitlab.inria.fr/gazelle/library/gazelle-objects-checker.git`
+>
+> `cd gazelle-objects-checker`
+
+> Notice: the install of gazelle-objects-checker will be done in the [Generate Artifact](#generateArtifact) section.<br>
+You can skip tests if you want, but it's not recommand to do.
+> 
+> You don't have to install the `uml-models` module, it's already released
+
+
+
+
+<div id='runTests'/>
+
+## 3. Run Tests (Optional)
+
+_/!\ You can skip this section, but it's recommanded to have all tests passed before continue_
+
+GOC provide two types of tests, units tests and integration tests.<br>
+The unit tests are _environement independents_.
+The integration tests create some temporary resources (UML Models) using the `uml-modes` (no need to have it installed locally, it has been packaged in [Nexus](https://gazelle.ihe.net/nexus/#nexus-search;quick~uml-models))
+<br>
+**Run Unit tests**
+>`cd gazelle-objects-checker`
+> 
+> `mvn test`
+> 
+
+
+**Run Integration Tests**
+>`cd gazelle-objects-checker`
+>
+> `mvn verify`
+> 
+If Something went wrong, make sure you have mentioned in maven logs:
+- Resources created successfully
+- Ressources deleted successfully
+
+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_
+
+<div id='prepareBBR'/>
+
+## 4. Prepare BBR
+BBR is an abreveation of Building Block Repository, a large XML file containing all the fonctional specifications, 
+that will be used by GOC to generate OCL which is converted finally to a Java validatorrr.<br>
+So Basically, the BBR is considered as **the main input for GOC**
+
+Each client provide his own BBR, and we can retrieve it from the ART-DECOR plateform that belong to this client.<br>
+We'll take the example of a BBR in SEQUOIA's ART-DECOR.
+
+To retrieve the project follow the link:
+>[https://gazellecontent.sequoiaproject.org/apps/decor/services/RetrieveProject](https://gazellecontent.sequoiaproject.org/apps/decor/services/RetrieveProject)
+
+Choose project as _**(BBR) Consolidated CDA (en-US)**_.<br>
+Make sure to select the **_Compiled_** version. <br> 
+Then check the **_Download_** radio.<br>
+Press **_send_** button.<br>
+
+Once you download it, you need to adapt it before using it in the next section of generation.<br>
+
+You first need to open it _(as it is a very large file, I recommand you to use VSCode as it's optimized for that )_
+then change **ccda-** by **ccda(version)-** for example for version 2.1:
+**ccda21-** (without the '.')
+
+NOTICE: A script could be released for this, due to performance issues
+
+<div id='generateArtifacts'/>
+
+## 5. Generate Artifact
+
+After having all tests working _(not mandatory but recommanded)_ we can now install the `gazelle-objects-checker` module and generate the artifact.
+<br>
+The Artifact generated is a `.jar` suffixed by `jar-with-dependencies` as it's created as a **standalone** application.
+<br><br>
+To do we run the following command:
+>`mvn clean install`
+> 
+> or
+> 
+> `mvn clean install -DskipTests=true` (to skip tests)
+
+> Alert: even if GOC is in Standalone mode, it's need to have the Archetype installed locally at **Runtime**
+> 
+> This could be improved in a future release
+
+The Artifcat is generated at _**gazelle-objects-checker/hl7templates-packager-jar/target/hl7templates-packager-jar-X.X.X-SNAPSHOT-jar-with-dependencies.jar**_
+
+> The X.X.X refers to the current SNAPSHOT version
+>
+
+> _**HINT**_: if you still have compile errors, you can install just the archetypes module (as it's required at runtime) with:
+> 
+> `cd gazelle-objects-checker/archetype/generated-validator`
+> 
+> `mvn clean install`
+> 
+> And retrieve GOC Artifact from nexus.
+> 
+> here: [GOC Artifact Nexus](#)  /!\ to be updated after GOC Release
+
+<div id='generateValidator'/>
+
+## 6. Generate Validator
+This section remains to **run** Gazelle Objects Checker and generate the CDA MBval validator. 
+
+>Reminder: you need to have at least the Archetype installed as it's used at **Runtime**
+
+we will need the following parameters to run GOC and generate the validator: 
+<table>
+  <thead>
+    <th>Parameters</th>
+    <th>Description</th>
+    <th>Type</th>
+    <th>Example</th>
+    <th>is Required</th>
+  </thead>
+  <tr>
+    <td>-bbr</td>
+    <td>Path to the BBR file (provided by ART-DECOR)</td>
+    <td>XML File</td>
+    <td>/home/mylap/Documents/bbr-eHDSI-5.0.1.xml</td>
+    <td><b>Required</b></td>
+  </tr>
+  <tr>
+    <td>-out</td>
+    <td>Path where to generate the validator</td>
+    <td>Directory</td>
+    <td>/home/mylap/Documents/CDA-Validators/output-pivot-19-10-2021</td>
+    <td><b>Required</b></td>
+  </tr>
+  <tr>
+    <td>-mvn</td>
+    <td>Path to maven <b>binary</b></td>
+    <td>Binary (executable)</td>
+    <td>/opt/apache-maven-3.5.4/bin/mvn</td>
+    <td><b>Required</b></td>
+  </tr>
+  <tr>
+    <td>-serviceName</td>
+    <td>Validation Service Name</td>
+    <td>String</td>
+    <td>Pivot</td>
+    <td>not Required</td>
+  </tr>
+  <tr>
+    <td>-HL7TEMP_CDACONFFOLDERNAME </td>
+    <td>HL7template CDA config folder name</td>
+    <td>cdabasic or cdaepsos</td>
+    <td>cdaepsos</td>
+    <td>not Required (default=cdabasic)</td>
+  </tr>
+  <tr>
+    <td>-ignoreTemplateIdRequirements</td>
+    <td>ignore TemplateId Requirements when generating the constraints (useful for C-CDA validation tools) name</td>
+    <td>Boolean</td>
+    <td>VOID, parameter persent ==> it's true, not presenet ==> it's false</td>
+    <td>not Required (default=false [Not present])</td>
+  </tr>
+  <tr>
+    <td>-ignoreCdaBasicRequirements</td>
+    <td>ignore TemplateId Requirements when generating the constraints (useful for C-CDA validation tools) name</td>
+    <td>Boolean</td>
+    <td>VOID, parameter persent ==> it's true, not presenet ==> it's false</td>
+    <td>not Required (default=false [Not present])</td>
+  </tr>
+  <tr>
+    <td>-versionLabel</td>
+    <td>VersionLabel that will be used during the generation</td>
+    <td>String</td>
+    <td>2.1</td>
+    <td>not Required</td>
+  </tr>
+  <tr>
+    <td>-rootClassName</td>
+    <td><i>DEPRECATED:</i>Root class name of generated classes</td>
+    <td>Path to java class (see example)</td>
+    <td>net.ihe.gazelle.cdaepsos3.POCDMT000040ClinicalDocument</td>
+    <td>not Required</td>
+  </tr>
+  <tr>
+    <td>-HL7TEMP_RESOURCES_PATH</td>
+    <td><i>DEPRECATED</i>: Path to hl7templates resources folder</td>
+    <td>String</td>
+    <td>/home/mylap/Documents/hl7templates-resources</td>
+    <td>not Required</td>
+  </tr>
+</table>
+
+Move to the hl7templates-packager-jar/target directory and run the following command with java 11:
+
+Generic command with all possible parameters: <br>
+
+>`java -jar hl7templates-packager-jar-X.X.X[-SNAPSHOT]-jar-with-dependencies.jar -bbr <Path_To_BBR> 
+-out <Path_To_Output> -mvn <Path_To_MVN> [-serviceName <Service_Name>] [-HL7TEMP_CDACONFFOLDERNAME <cdabasic|cdaepsos>] 
+ [-ignoreTemplateIdRequirements <true|false>] [-ignoreCdaBasicRequirements <true|false>]
+[-versionLabel <version>] [-rootClassName <Root_ClassName>] [-HL7TEMP_RESOURCES_PATH <Path_To_Resources>]` 
+
+_The [X.X.X] to the current used version of GOC, and it's not present if we retrieve a release from Nexus._
+
+Example with SEQUOIA:
+>`java -jar hl7templates-packager-jar-3.0.0-SNAPSHOT-jar-with-dependencies.jar -bbr ~/Documents/BBR-SEQUOIA.xml
+> -out home/mylap/Documents/GOC-OUTPUT/output-sequoia-mu3 -mvn /opt/apache-maven-3.5.4/bin/mvn
+> -serviceName "HL7 - C-CDA R2.1 - Meaningful Use Stage 3" -ignoreTemplateIdRequirements 
+> -ignoreCdaBasicRequirements  -versionLabel 2.1`
+
+**For logs:**
+>Root folder of the provided output path
+> 
+> `cd /home/mylap/Documents/GOC-OUTPUT/logs/logs-[generation_date_time]`
+
+More details about logs will be provided later. 
+
+<div id='validateCDA'/>
+
+## 7. Validate CDA
+
+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 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:
+>`cd <Path_To_Output>/epsos5-validator-app/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:
+<table>
+  <thead>
+    <th>Parameters</th>
+    <th>Description</th>
+    <th>Type</th>
+    <th>Example</th>
+    <th>is Required</th>
+  </thead>
+  <tr>
+    <td>-path</td>
+    <td>Path to the CDA Document we want to validate</td>
+    <td>Path to an XML file</td>
+    <td>/home/mylap/Documents/eHDSI_CDA.xml</td>
+    <td><b>Required</b></td>
+  </tr>
+  <tr>
+    <td>-out</td>
+    <td>Path to save the generated results</td>
+    <td>Path to an XML file</td>
+    <td>../../results1.xml</td>
+    <td><b>Recomanded: </b>If not provided, output is redirected to STDOUT</td>
+  </tr>
+  <tr>
+    <td>-b64</td>
+    <td>Provide a path to a document in Base64</td>
+    <td>Path to an XML file</td>
+    <td>/home/mylap/Documents/eHDSI_CDA_B64.xml</td>
+    <td>Don't use it if you use the -path parameter</td>
+  </tr>
+  <tr>
+    <td>-html</td>
+    <td>Generate html as output of validation</td>
+    <td>Boolean</td>
+    <td>VOID, parameter persent ==> it's true, not presenet ==> it's false</td>
+    <td>Not Required</td>
+  </tr>
+  <tr>
+    <td>-resources</td>
+    <td>Full path to the resources folder (XSD schema + valueSets) </td>
+    <td>Path to directory</td>
+    <td>/home/mylap/resources/</td>
+    <td>Not Required</td>
+  </tr>
+
+</table>
+
+Here is an example to validate a document with normal case: 
+>`./validator.sh -path /home/mylap/eHDSI_CDA.xml -out ../../results1.xml`
+
+<div id='extra'/>
+
+## 8. Extras
+
+You can find some previous made documentation here _(belong the old GOC, and could propably not reperesent the actual version)_: 
+- [GOC Instalation guide fo developper](https://docs.google.com/document/d/1G5bmLhFKNjOvg_rxEllidTofYrwxBeZG_kigTM0pqXM/edit?usp=sharing)
+- [Gazelle Object Checker General Public info - GOC](https://docs.google.com/document/d/1265YcvKk983Fna2Y8TI6V9O1wnKqERFAibIlVGYgW20/edit?usp=sharing)
+
+#### Next released documentation
+
+- Functional description of GOC
+- Pepare validator for SEQUOIA
+- Use interactif scripts for generation
+- New Archetecture used for logging

hl7templates/gocmodel-jar/pom.xml

@@ -333,13 +333,6 @@
             <groupId>commons-io</groupId>
             <artifactId>commons-io</artifactId>
             <version>2.6</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>commons-io</groupId>
-            <artifactId>commons-io</artifactId>
-            <version>2.6</version>
-            <scope>compile</scope>
         </dependency>
 
     </dependencies>

hl7templates/hl7templates-packager-jar/src/main/java/net/ihe/gazelle/lib/hl7templatespackager/peripherals/HL7Templates2GOC.java

@@ -58,7 +58,7 @@ public class HL7Templates2GOC {
     private String rootClassName;
 
     @Option(name = "-HL7TEMP_CDACONFFOLDERNAME", metaVar = "hl7temp_cdaconffoldername", usage = "hl7temp cda conf folder name", required = false)
-    private String HL7TEMP_CDACONFFOLDERNAME;
+    private String HL7TEMP_CDACONFFOLDERNAME = "cdabasic";
 
     @Option(name="-HL7TEMP_RESOURCES_PATH", metaVar = "HL7TEMP_RESOURCES_PATH", usage = "path to hl7templates resources folder", required = false)
     private String HL7TEMP_RESOURCES_PATH;