installation-guide.md

---
title:  Installation & usage documentation
subtitle: Instalation Guide of Gazelle Objects Checker
authors: Achraf Achkari
date: 19/10/2021
---

# 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:
```bash
> 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**
```bash
> cd gazelle-objects-checker

> mvn test
```

**Run Integration Tests**
```bash
> 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:
```bash
> 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:
> 
> ```bash
> 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>

```bash
> 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:
```bash
> 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:**
> Go to the root folder of the provided output path
> 
> `cd /home/mylap/Documents/GOC-OUTPUT/logs/logs-[generation_date_time]`

**Logs are separated as follow:**
- **generated_report.log:** contains synthetic report about the generation process (`Warnings` and `Errors`)
- **detailed_report.log:** contains all the logging information from the generation process (`Infos`, `Warnings`, `Errors`)
- **cmdOutput.log:** contains the Stanrd Output of executed commands during generation (maven command to init project with archetype, generate code from OLC, packaging...)
- **cdeModelsErros.txt:** contains all detected inconsetencies between the provided BBR and pre-defined models used by GOC

![Logs Conception](Improved_Logging_Conception_v2.jpg "LogsConception")

<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:
```bash
> 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: 

```bash
> ./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