From 796f4d362629f0bff55d705de550ff68932ec3b8 Mon Sep 17 00:00:00 2001
From: stephane <stephane.dervaux@inrae.fr>
Date: Wed, 16 Oct 2024 12:58:13 +0200
Subject: [PATCH 1/4] setting changelog

---
 src/main/resources/resources/changelog.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/resources/resources/changelog.txt b/src/main/resources/resources/changelog.txt
index e3db45df..36fb44d4 100644
--- a/src/main/resources/resources/changelog.txt
+++ b/src/main/resources/resources/changelog.txt
@@ -1,4 +1,5 @@
 ------------------ NEXT ------------------
+    * Enhancement (PO2-Tools/po2manager#106) : Ajout d'une option pour afficher / masquer les concepts dépréciés.
     * Enhancement (PO2-Tools/po2manager#105) : Ajout d'une confirmation lors du clique sur "reset node position"
     * Enhancement (PO2-Tools/po2manager#104) : Amélioration du texte de la légende du graphe
 
-- 
GitLab


From ce814b808c2b576a59a410d3007c9ae072a8b4ed Mon Sep 17 00:00:00 2001
From: stephane <stephane.dervaux@inrae.fr>
Date: Mon, 21 Oct 2024 18:18:20 +0200
Subject: [PATCH 2/4] add show deprecated management

---
 .../po2vocabmanager/view/RootLayoutController.java   | 12 +++++++++++-
 .../view/ontoView/OntologyOverviewController.java    |  9 +++------
 .../fr/inra/po2vocabmanager/view/RootLayout.fxml     |  1 +
 3 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/src/main/java/fr/inra/po2vocabmanager/view/RootLayoutController.java b/src/main/java/fr/inra/po2vocabmanager/view/RootLayoutController.java
index 32f5ace9..2613c50d 100644
--- a/src/main/java/fr/inra/po2vocabmanager/view/RootLayoutController.java
+++ b/src/main/java/fr/inra/po2vocabmanager/view/RootLayoutController.java
@@ -83,6 +83,8 @@ public class RootLayoutController {
     @FXML
     Menu conceptScheme;
     @FXML
+    CheckMenuItem showDeprecated;
+    @FXML
     MenuItem addConceptScheme;
     @FXML
     MenuItem itemNewProject;
@@ -110,7 +112,8 @@ public class RootLayoutController {
         itemNewProject.setDisable(true);
         itemNewOntology.setVisible(true);
         itemNewOntology.setDisable(true);
-
+        showDeprecated.setDisable(false);
+        showDeprecated.setSelected(false);
     }
 
     /**
@@ -155,6 +158,13 @@ public class RootLayoutController {
                 mainApp.run(null);
             }
         });
+
+        showDeprecated.setOnAction(event -> {
+            if(MainApp.getOntologyControler() != null && MainApp.getOntologyControler().getCurrentOntology() != null) {
+                MainApp.getOntologyControler().getCurrentOntology().setShowDeprecated(showDeprecated.selectedProperty().get());
+                MainApp.getOntologyControler().rebuildTree(true);
+            }
+        });
     }
 
     public void exportOnto() {
diff --git a/src/main/java/fr/inra/po2vocabmanager/view/ontoView/OntologyOverviewController.java b/src/main/java/fr/inra/po2vocabmanager/view/ontoView/OntologyOverviewController.java
index 51804f4d..827d62cf 100644
--- a/src/main/java/fr/inra/po2vocabmanager/view/ontoView/OntologyOverviewController.java
+++ b/src/main/java/fr/inra/po2vocabmanager/view/ontoView/OntologyOverviewController.java
@@ -176,6 +176,7 @@ TableView<SimpleStringProperty> tableClose;
     private BooleanProperty canEdit = new SimpleBooleanProperty(false);
     private BooleanProperty syncCloud = new SimpleBooleanProperty(false);
     private BooleanProperty isOnMainScheme = new SimpleBooleanProperty(false);
+    private BooleanProperty showDeprecated = new SimpleBooleanProperty(false);
 
     private TreeItem<VocabConcept> rootItem;
     private StringProperty title = new SimpleStringProperty();
@@ -585,11 +586,7 @@ TableView<SimpleStringProperty> tableClose;
 
 
     public void rebuildTree(boolean rebuildConstraint) {
-        if(isOnMainScheme().get()) {
-            rootItem = new RecursiveTreeItem<VocabConcept>(currentOntology.getRootNode(), VocabConcept::getGraphic , VocabConcept::getSubNode, this);
-        } else {
-            rootItem = new RecursiveTreeItem<VocabConcept>(currentOntology.getRootNode(), VocabConcept::getGraphic , VocabConcept::getSubNodeInScheme, this);
-        }
+        rootItem = new RecursiveTreeItem<>(currentOntology.getRootNode(), VocabConcept::getGraphic, VocabConcept::getSubNodeInScheme, this);
         setTree(rootItem);
         if(rebuildConstraint) {
             currentOntology.rebuildConstraints();
@@ -677,8 +674,8 @@ TableView<SimpleStringProperty> tableClose;
                         minorVersion.bind(onto.getMinorVersion());
 
                         currentOntology = onto;
+                        showDeprecated.bind(currentOntology.showDeprecatedProperty());
 
-//                        rebuildConstraints();
                         currentOntology.setCurrentSkosScheme(currentOntology.getMainScheme());
                         MainApp.getOntologyControler().setIsOnMainScheme(true);
 
diff --git a/src/main/resources/fr/inra/po2vocabmanager/view/RootLayout.fxml b/src/main/resources/fr/inra/po2vocabmanager/view/RootLayout.fxml
index efcc17d2..73754c12 100644
--- a/src/main/resources/fr/inra/po2vocabmanager/view/RootLayout.fxml
+++ b/src/main/resources/fr/inra/po2vocabmanager/view/RootLayout.fxml
@@ -49,6 +49,7 @@
                 <Menu fx:id="view" mnemonicParsing="false" text="View">
                     <items>
                         <Menu fx:id="conceptScheme" mnemonicParsing="false" text="Concept Scheme" />
+                  <CheckMenuItem fx:id="showDeprecated" mnemonicParsing="false" text="Show deprecated concepts" />
                     </items>
                 </Menu>
                 <Menu mnemonicParsing="false" text="Tools">
-- 
GitLab


From 4d50fb3781bb8ede32973e209eba0b1eb2fd7fcc Mon Sep 17 00:00:00 2001
From: stephane <stephane.dervaux@inrae.fr>
Date: Mon, 21 Oct 2024 18:35:31 +0200
Subject: [PATCH 3/4] fix for the changelog

---
 src/main/resources/resources/changelog.txt | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/main/resources/resources/changelog.txt b/src/main/resources/resources/changelog.txt
index f89c8951..d84fcaec 100644
--- a/src/main/resources/resources/changelog.txt
+++ b/src/main/resources/resources/changelog.txt
@@ -1,5 +1,7 @@
------------------- V1.8.5.0 ------------------
+------------------ NEXT ---------------------
     * Enhancement (PO2-Tools/po2manager#106) : Ajout d'une option pour afficher / masquer les concepts dépréciés.
+
+------------------ V1.8.5.0 ------------------
     * Enhancement (PO2-Tools/po2manager#107) : Ajout d'une option lors de l'ajout d'étape existante à l'itinéraire pour y inclure les liens entre étapes
     * Enhancement (PO2-Tools/po2manager#95) : uniformiser les fonctionnalités de copies (step / itinerary / ....)
 
-- 
GitLab


From f2e71a90eaed62c26214bd77689d92da7a84572c Mon Sep 17 00:00:00 2001
From: stephane <stephane.dervaux@inrae.fr>
Date: Thu, 7 Nov 2024 09:47:47 +0100
Subject: [PATCH 4/4] set version of PO2Engine to 2.3.1.3

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index d4650387..3693c7d3 100644
--- a/pom.xml
+++ b/pom.xml
@@ -332,7 +332,7 @@
         <dependency>
             <groupId>fr.inrae.po2engine</groupId>
             <artifactId>PO2Engine</artifactId>
-            <version>2.3.0.5</version>
+            <version>2.3.1.3</version>
             <exclusions>
                 <exclusion>
                     <groupId>ch.qos.logback</groupId>
-- 
GitLab