SouthGreenPlatform · WoodenMaiden · Apr 29, 2024 · Apr 4, 2024 · Apr 4, 2024 · Apr 4, 2024
diff --git a/.github/workflows/test_helm_chart.yaml b/.github/workflows/test_helm_chart.yaml
@@ -17,6 +17,9 @@ jobs:
 
       - name: Install Helm
         uses: azure/setup-helm@v3
+        with:
+          version: 'latest'
+          token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Helm Check Action
         uses: hopisaurus/helm-check-action@v0.1.0

diff --git a/agrold-javaweb/Dockerfile b/agrold-javaweb/Dockerfile
@@ -1,5 +1,5 @@
 # Build stage
-FROM maven:3.9-amazoncorretto-8 as build
+FROM maven:3.9-amazoncorretto-17 as build
 # Shared arguments between build and run stages
 
 ARG AGROLD_NAME=aldp
@@ -11,7 +11,7 @@ COPY . /build_dir
 RUN mvn clean install -Dagrold.name=${AGROLD_NAME}
 
 # Run stage
-FROM bitnami/tomcat:8.5
+FROM bitnami/tomcat:9.0
 
 ARG GIT_COMMIT=unknown
 ARG AGROLD_NAME=aldp

diff --git a/agrold-javaweb/README.md b/agrold-javaweb/README.md
@@ -4,32 +4,33 @@
 
 ### Cloner l'appli
 
-- `git clone --branch dev `
--
+- `git clone --branch dev`
 
 Vous pourrez voir comment paramétrer votre IDE dans [la section appropriée sur le Notion](https://agrold-wiki.notion.site/Configurer-et-utiliser-son-IDE-pour-les-projets-cbf2dc48224f48009a9c0775a173a6d5)
 
 ### Deployer l'appli web
 
 #### Pré requis
 
-- Tomcat 7/8
+- Tomcat 7/8/9
+- JDK 17
+- Maven
 - mysql (sera bientôt agnostique ou retiré)
+- Docker (optionnel)
 
 #### Paramètres
 
 Le déploiement de l'application se fait premièrement avec des propriétés Java passées à tomcat.
 
-|            Name            |                                                                    Description                                                                    |       Valeur par défaut       |
-| :------------------------: | :-----------------------------------------------------------------------------------------------------------------------------------------------: | :---------------------------: |
-|       `agrold.name`        | Nom de l'archive et du contexte (le nom apparait après `agrold.baseurl` , par exemple si on met la valeur à `aldp` on a `https://someurl/agrold`) |            `aldp`             |
-|    `agrold.description`    |                                                         Description affichée dans Tomcat                                                          |              :x:              |
-|      `agrold.baseurl`      |                                                              L'URL de base de l'app                                                               |   `http://localhost:8080/`    |
-|  `agrold.sparql_endpoint`  |                                                             Url de l'endpoint SPARQL                                                              | `http://sparql.southgreen.fr` |
-| `agrold.db_connection_url` |                                             Url de la base de données ex: `[host]:[port]/[db]?[opt]`                                              |         :x: (requis)          |
-|    `agrold.db_username`    |                                                         Utilisateur de la base de données                                                         |         :x: (requis)          |
-|    `agrold.db_password`    |                                                        Mot de passe de la base de données                                                         |         :x: (requis)          |
-|      `agrold.rf_link`      |                                                   Lien vers une instance de RelFinder[Reformed]                                                   |  `http://rf.southgreen.fr/`   |
+|            Name            |                                Description                                 |       Valeur par défaut       |
+| :------------------------: | :------------------------------------------------------------------------: | :---------------------------: |
+|       `agrold.name`        | Nom de l'archive et du contexte `aldp` on a `https://<un domaine>/agrold`) |            `aldp`             |
+|    `agrold.description`    |                      Description affichée dans Tomcat                      |              :x:              |
+|  `agrold.sparql_endpoint`  |                          Url de l'endpoint SPARQL                          | `http://sparql.southgreen.fr` |
+| `agrold.db_connection_url` |          Url de la base de données ex: `[host]:[port]/[db]?[opt]`          |              :x:              |
+|    `agrold.db_username`    |                     Utilisateur de la base de données                      |              :x:              |
+|    `agrold.db_password`    |                     Mot de passe de la base de données                     |              :x:              |
+|      `agrold.rf_link`      |               Lien vers une instance de RelFinder[Reformed]                |  `http://rf.southgreen.fr/`   |
 
 Pour injecter ces variables dans tomcat, il faut déclarer les sous forme d'argument en ligne de commande sous cette forme `-Dnomdelapropriété=valeur` et les placer dans la variable d'environnement `CATALINA_OPTS`
 
@@ -40,26 +41,18 @@ Par exemple:
 
 ```bash
 # Directement sur l'hôte
-export CATALINA_OPTS="-Dagrold.db_connection_url=someurlhere -Dagrold.db_username=usr -Dagrold.db_password=pwd"
+export CATALINA_OPTS="-Dagrold.blabla=valeur"
 catalina.sh
 ```
 
-```java
-...
-String URL = System.getProperty("agrold.db_connection_url");
-String usr = System.getProperty("agrold.db_username");
-String pwd = System.getProperty("agrold.db_password");
-...
-```
-
 Si vous lancez tomcat avec systemd le remplissage des variables d'environnement se fait ainsi
 
 ```bash
-sudo systemctl edit tomcat8 #ou tomcat7
+sudo systemctl edit tomcat8 #ou tomcat7/9
 
 # dans l'éditeur
 [Service]
-Environment="CATALINA_OPTS='-Dagrold.db_connection_url=someurlhere -Dagrold.db_username=usr -Dagrold.db_password=pwd'"
+Environment="CATALINA_OPTS='-Dagrold.blabla=valeur'"
 ```
 
 Pour compiler lancez maven à la racine du projet, Il est possible de passer la propriété `agrold.name` en argument de maven
@@ -72,24 +65,22 @@ mvn clean install
 mvn clean install -Dagrold.name=un_nom # vous accéderez à l'application via https://<votre url>/un_nom
 ```
 
-````
-
 Si vous utilisez docker:
 
 ```bash
 cd agrold-javaweb/
 
 # Vous pouvez utiliser le dockerfile
-#                          le mot de passe du manager
-docker build . -t <tag> --build-arg TOMCAT_PASSWORD=a --build-arg AGROLD_NAME=agrolddev
+#                          la valeur de agrold.name
+docker build . -t <tag> --build-arg AGROLD_NAME=agrolddev
 
 # Ou pull l'image stockée depuis le registre dans l'environnement de développement,
 docker login 10.9.2.21:8080 -u <user> -p <password>
 docker pull 10.9.2.21:8080
 
 # Lancer le conteneur
-docker run -p 8080:8080 -e CATALINA_OPTS="-Dagrold.db_connection_url=someurl -Dagrold.db_username=usr -Dagrold.db_password=pwd -Dagrold.baseurl=http://localhost:8080/ -Dagrold.sparql_endpoint=a" <tag>
-````
+docker run -p 8080:8080 <tag>
+```
 
 > [!NOTE]
 > À noter que l'image docker crée prend pour base l'image [bitnami/tomcat](https://hub.docker.com/r/bitnami/tomcat/). Cela veut dire que vous pouvez configurer l'image d'AgroLD comme celle de bitnami sur certain points nottament la configuration de l'utilisateur manager de tomcat.

diff --git a/agrold-javaweb/charts/agrold-javaweb/Chart.yaml b/agrold-javaweb/charts/agrold-javaweb/Chart.yaml
@@ -9,7 +9,7 @@ annotations:
       image: docker.io/bitnami/tomcat:10.1.20-debian-12-r0
   licenses: Apache-2.0
 apiVersion: v2
-appVersion: 2.1.0
+appVersion: 2.1.1
 dependencies:
 - name: common
   repository: oci://registry-1.docker.io/bitnamicharts
@@ -46,4 +46,4 @@ name: agrold
 sources:
 - https://github.com/bitnami/charts/tree/main/bitnami/tomcat
 - https://github.com/SouthGreenPlatform/AgroLD_webapp
-version: 2.0.0
+version: 2.0.1
diff --git a/agrold-javaweb/charts/agrold-javaweb/templates/_helpers.tpl b/agrold-javaweb/charts/agrold-javaweb/templates/_helpers.tpl
@@ -97,9 +97,9 @@ Return the proper CATALINA_OPTS value
 {{- define "tomcat.catalinaOpts" -}}
 {{- $agrold := include "tomcat.flattenIntoSysProperties" .Values.agroldProperties -}}
 {{- if .Values.metrics.jmx.enabled -}}
-{{- default "" (cat .Values.catalinaOpts .Values.metrics.jmx.catalinaOpts (printf "-Dagrold.baseurl=%q" (ternary (print "https://" .Values.ingress.hostname) (print "http://" .Values.ingress.hostname) .Values.ingress.tls)) $agrold) | trim  -}}
+{{- default "" (cat .Values.catalinaOpts .Values.metrics.jmx.catalinaOpts $agrold) | trim  -}}
 {{- else -}}
-{{- default "" (cat .Values.catalinaOpts (printf "-Dagrold.baseurl=%q" (ternary (print "https://" .Values.ingress.hostname) (print "http://" .Values.ingress.hostname) .Values.ingress.tls)) $agrold) | trim -}}
+{{- default "" (cat .Values.catalinaOpts $agrold) | trim -}}
 {{- end -}}
 {{- end -}}
 

diff --git a/agrold-javaweb/charts/agrold-javaweb/values.yaml b/agrold-javaweb/charts/agrold-javaweb/values.yaml
@@ -8,8 +8,6 @@
 ##
 
 agroldProperties:
-  # The property below is set to ingress.hostname, set this value to override it
-  # baseurl: "http://agrold.org"
   db_connection_url: someurl
   db_username: user
   db_password: password
@@ -77,7 +75,7 @@ extraDeploy: []
 image:
   registry: ghcr.io
   repository: southgreenplatform/agrold
-  tag: 2.0.0
+  tag: 2.1.1
   digest: ""
   ## Specify a imagePullPolicy
   ## Defaults to 'Always' if image tag is 'latest', else set to 'IfNotPresent'

diff --git a/agrold-javaweb/charts/virtuoso/Chart.yaml b/agrold-javaweb/charts/virtuoso/Chart.yaml
@@ -16,7 +16,7 @@ type: application
 # This is the chart version. This version number should be incremented each time you make changes
 # to the chart and its templates, including the app version.
 # Versions are expected to follow Semantic Versioning (https://semver.org/)
-version: 1.0.0
+version: 1.0.1
 
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application. Versions are not expected to

diff --git a/agrold-javaweb/charts/virtuoso/templates/secrets.yaml b/agrold-javaweb/charts/virtuoso/templates/secrets.yaml
@@ -5,6 +5,6 @@ metadata:
   name: secrets-{{ $fullName }}
 type: Opaque
 data:
-  DAVPassword: {{ .Values.DAVPassword | b64enc | quote }}
-  DBAPassword: {{ .Values.DBAPassword | b64enc | quote }}
+  DAVPassword: {{ .Values.DAVPassword | default (randAlphaNum 32) | b64enc | quote }}
+  DBAPassword: {{ .Values.DBAPassword | default (randAlphaNum 32) | b64enc | quote }}
 
diff --git a/agrold-javaweb/charts/virtuoso/values.yaml b/agrold-javaweb/charts/virtuoso/values.yaml
@@ -89,10 +89,8 @@ initdb:
   enabled: true
   name: sparql-initdb
   kind: ConfigMap
-  data:
-    init.sh: |
-      #!/bin/bash
-      echo "Ready to go!"
+  data: {}
+
 
 persistence:
   enabled: true

diff --git a/agrold-javaweb/pom.xml b/agrold-javaweb/pom.xml
@@ -4,7 +4,7 @@
 
     <groupId>agrold</groupId>
     <artifactId>agrold</artifactId>
-    <version>2.1.0</version>
+    <version>2.1.1</version>
     <packaging>war</packaging>
 
 
@@ -45,17 +45,17 @@
         <dependency>
             <groupId>javax.xml.bind</groupId>
             <artifactId>jaxb-api</artifactId>
-            <version>2.2.11</version>
+            <version>2.4.0-b180830.0359</version>
         </dependency>
         <dependency>
             <groupId>com.sun.xml.bind</groupId>
             <artifactId>jaxb-core</artifactId>
-            <version>2.2.11</version>
+            <version>4.0.5</version>
         </dependency>
         <dependency>
             <groupId>com.sun.xml.bind</groupId>
             <artifactId>jaxb-impl</artifactId>
-            <version>2.2.11</version>
+            <version>4.0.5</version>
         </dependency>
         <dependency>
             <groupId>javax.activation</groupId>
@@ -70,57 +70,57 @@
         <dependency>
             <groupId>javax</groupId>
             <artifactId>javaee-web-api</artifactId>
-            <version>6.0</version>
+            <version>8.0.1</version>
             <scope>provided</scope>
         </dependency>
         <dependency>
             <groupId>javax.ws.rs</groupId>
             <artifactId>javax.ws.rs-api</artifactId>
-            <version>2.1</version>
+            <version>2.1.1</version>
         </dependency>
         <dependency>
             <groupId>org.glassfish.jersey.containers</groupId>
             <artifactId>jersey-container-servlet</artifactId>
-            <version>2.26</version>
+            <version>2.42</version>
         </dependency>
         <dependency>
             <groupId>org.glassfish.jersey.core</groupId>
             <artifactId>jersey-server</artifactId>
-            <version>2.26</version>
+            <version>2.42</version>
         </dependency>
         <dependency>
             <groupId>org.glassfish.jersey.inject</groupId>
             <artifactId>jersey-hk2</artifactId>
-            <version>2.26</version>
+            <version>2.42</version>
         </dependency>
         <dependency>
             <groupId>org.glassfish.jersey.media</groupId>
             <artifactId>jersey-media-multipart</artifactId>
-            <version>2.26</version>
+            <version>2.42</version>
         </dependency>
         <!-- https://mvnrepository.com/artifact/junit/junit -->
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
-            <version>4.12</version>
+            <version>4.13.2</version>
             <scope>test</scope>
         </dependency>
         <!-- https://mvnrepository.com/artifact/org.json/json -->
         <dependency>
             <groupId>org.json</groupId>
             <artifactId>json</artifactId>
-            <version>20180813</version>
+            <version>20240303</version>
         </dependency>
         <!-- https://mvnrepository.com/artifact/mysql/mysql-connector-java -->
         <dependency>
             <groupId>mysql</groupId>
             <artifactId>mysql-connector-java</artifactId>
-            <version>5.1.6</version>
+            <version>8.0.33</version>
         </dependency>
         <dependency>
             <groupId>com.google.code.gson</groupId>
             <artifactId>gson</artifactId>
-            <version>2.2.4</version>
+            <version>2.10.1</version>
         </dependency>
     </dependencies>
 

diff --git a/agrold-javaweb/src/main/java/agrold/ogust/config/MySQLProperties.java b/agrold-javaweb/src/main/java/agrold/ogust/config/MySQLProperties.java
@@ -30,7 +30,7 @@ private MySQLProperties(){
         /* prevent usage of constructor bcause it's a static class */
     }
 
-
+    // TODO: Change how it is handled, this will be replaced by cookies since it is just for history purposes
     /**
      *
      * @return an ArrayList of String with the lines of the text in the same
@@ -39,13 +39,9 @@ private MySQLProperties(){
     public static List<String> readLoginConfigurations() {
         List<String> lines = new ArrayList<>();
         try {
-            String URL = System.getProperty("agrold.db_connection_url");
-            String usr = System.getProperty("agrold.db_username");
-            String pwd = System.getProperty("agrold.db_password");
-
-            if (URL == null) throw new NullPointerException("Missing system property: agrold.db_connection_url");
-            if (usr == null) throw new NullPointerException("Missing system property: agrold.db_username");
-            if (pwd == null) throw new NullPointerException("Missing system property: agrold.db_password");
+            String URL = System.getProperty("agrold.db_connection_url", "");
+            String usr = System.getProperty("agrold.db_username", "");
+            String pwd = System.getProperty("agrold.db_password", "");
 
             lines.add(URL);
             lines.add(usr);

diff --git a/agrold-javaweb/src/main/java/agrold/webservices/API.java b/agrold-javaweb/src/main/java/agrold/webservices/API.java
@@ -31,6 +31,7 @@
 import javax.ws.rs.PathParam;
 import javax.ws.rs.Produces;
 import javax.ws.rs.QueryParam;
+import javax.ws.rs.HeaderParam;
 import javax.ws.rs.WebApplicationException;
 import javax.ws.rs.client.Client;
 import javax.ws.rs.client.ClientBuilder;
@@ -95,15 +96,15 @@ String inputStream2String(InputStream incomingData){
     @GET
     // @Consumes(MediaType.APPLICATION_JSON) // for "in body parameters"
     @Path("/customizable/{serviceLocalName}")
-    public Response genericGet(@PathParam("serviceLocalName") String serviceLocalName, @Context UriInfo uriInfo, @Context  HttpHeaders headers) throws IOException {        
+    public Response genericGet(@PathParam("serviceLocalName") String serviceLocalName, @Context UriInfo uriInfo, @Context HttpHeaders headers) throws IOException {        
         List<MediaType> mediaTypes = headers.getAcceptableMediaTypes();
         MediaType reponseMediaType = mediaTypes.get(0);
         if (reponseMediaType == null) {
             return Response.serverError()
                     .entity("[AgroLD Web Services] - Format Error: The requested resource is not available in the format \"" + mediaTypes.get(0) + "\"")
                     .build();
         }
-        String content = CustomizableServicesManager.queryCustomizableService(serviceLocalName, uriInfo.getQueryParameters(), "get", reponseMediaType);
+        String content = CustomizableServicesManager.queryCustomizableService(serviceLocalName, uriInfo.getQueryParameters(), "get", reponseMediaType, headers.HOST);
         return buildResponse(content, reponseMediaType.toString());
     }
 
@@ -122,8 +123,8 @@ public Response genericGet(@PathParam("serviceLocalName") String serviceLocalNam
     // generic web service for modifiables ones    
     @GET
     @Path("/webservices")
-    public Response getAPISpecification() throws IOException {
-        String content = CustomizableServicesManager.readAPISpecification(Utils.AGROLDAPIJSONURL);
+    public Response getAPISpecification(@HeaderParam("Host") String host) throws IOException {
+        String content = CustomizableServicesManager.readAPISpecification(Utils.AGROLDAPIJSONURL, host);
         return buildResponse(content, Utils.JSON);
     }
 
@@ -132,24 +133,24 @@ public Response getAPISpecification() throws IOException {
     @DELETE
     @Produces(MediaType.TEXT_PLAIN)
     @Path("/webservices")
-    public Response deleteService(@QueryParam("name") String name, @QueryParam("httpMethod") String httpMethod) throws IOException {        
-        String content = CustomizableServicesManager.deleteService(name, httpMethod); 
+    public Response deleteService(@QueryParam("name") String name, @QueryParam("httpMethod") String httpMethod, @HeaderParam("Host") String host) throws IOException {        
+        String content = CustomizableServicesManager.deleteService(name, httpMethod, host); 
         return buildResponse(content, MediaType.TEXT_PLAIN);
     }
 
     @RolesAllowed("ADMIN")
     @PUT
     @Path("/webservices")
-    public Response addService(@QueryParam("name") String name, @QueryParam("httpMethod") String httpMethod, InputStream specificationDataStream) throws IOException {       
-        String content = CustomizableServicesManager.addService(name, httpMethod, inputStream2String(specificationDataStream));
+    public Response addService(@QueryParam("name") String name, @QueryParam("httpMethod") String httpMethod, InputStream specificationDataStream, @HeaderParam("Host") String host) throws IOException {       
+        String content = CustomizableServicesManager.addService(name, httpMethod, inputStream2String(specificationDataStream), host);
         return buildResponse(content, MediaType.TEXT_PLAIN);
     }
 
     @RolesAllowed("ADMIN")
     @POST
     @Path("/webservices")
-    public Response updateService(@QueryParam("name") String name, @QueryParam("httpMethod") String httpMethod, InputStream specificationDataStream) throws IOException {
-        String content = CustomizableServicesManager.updateService(name, httpMethod, inputStream2String(specificationDataStream));
+    public Response updateService(@QueryParam("name") String name, @QueryParam("httpMethod") String httpMethod, InputStream specificationDataStream, @HeaderParam("Host") String host) throws IOException {
+        String content = CustomizableServicesManager.updateService(name, httpMethod, inputStream2String(specificationDataStream), host);
         return buildResponse(content, MediaType.TEXT_PLAIN);
     }