From cf14c6e9bd4557facec4580ffa97d4b9c8009e22 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Tue, 16 Jul 2024 10:48:28 +0200
Subject: [PATCH 1/5] remove study / assay help menus

---
 packages/renderer/src/docs/assay.vue | 167 ---------------------------
 packages/renderer/src/docs/study.vue | 152 ------------------------
 2 files changed, 319 deletions(-)
 delete mode 100644 packages/renderer/src/docs/assay.vue
 delete mode 100644 packages/renderer/src/docs/study.vue

diff --git a/packages/renderer/src/docs/assay.vue b/packages/renderer/src/docs/assay.vue
deleted file mode 100644
index f7a78b5b..00000000
--- a/packages/renderer/src/docs/assay.vue
+++ /dev/null
@@ -1,167 +0,0 @@
-<script setup>
-import a_input from '../components/a_input.vue';
-import a_btn from '../components/a_btn.vue';
-</script>
-
-<template>
-  <div class="q-pt-sm">
-
-    <h5 style="margin-bottom:0.5em;">Assay</h5>
-    <div class="text-body2 text-justify" style="padding-bottom:1em;">
-      In the Assay menu you can adapt the metadata of one assay added to your ARC.
-    </div>
-
-    <q-card>
-
-      <q-card-section>
-
-        <q-item>
-          <q-item-section avatar>
-            <q-icon color="grey-8" name="biotech" />
-          </q-item-section>
-          <q-item-section>Assay</q-item-section>
-        </q-item>
-
-        <q-list class="q-gutter-xs">
-          <q-item>
-            <q-item-section>
-              <a_input label='Identifier' v-model='{ _: "YourIdentifier" }._' readonly />
-            </q-item-section>
-            <q-item-section>
-              The assay identifier is automatically added when adding the assay to your ARC and cannot be changed
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <a_input label='Studies' readonly-hidden />
-            </q-item-section>
-            <q-item-section>
-              List or adapt the studies this assay is linked to
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <a_input label='Measurement Type' readonly-hidden />
-            </q-item-section>
-            <q-item-section>
-              Add a measurement type for this assay
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <a_input label='Technology Type' readonly-hidden />
-            </q-item-section>
-            <q-item-section>
-              Add a technology type for this assay
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <a_input label='Technology Platform' readonly-hidden />
-            </q-item-section>
-            <q-item-section>
-              Add a technology platform for this assay
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <div>
-                <a_btn label="delete" icon='delete' color="red-9" />
-              </div>
-            </q-item-section>
-            <q-item-section>
-              Completely delete this assay from the ARC
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <div>
-                <a_btn label="edit table" icon='edit' color="secondary" />
-              </div>
-            </q-item-section>
-            <q-item-section>
-              Edit experimental metadata using <a
-                href="https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/implementation/Swate.html"
-                target="_blank">Swate</a>
-            </q-item-section>
-          </q-item>
-        </q-list>
-
-      </q-card-section>
-
-      <q-separator inset size="0.3em" />
-
-      <q-card-section>
-
-        <q-item>
-          <q-item-section avatar>
-            <q-icon color="grey-8" name="groups" />
-          </q-item-section>
-          <q-item-section>People</q-item-section>
-        </q-item>
-
-        <q-list class="q-gutter-xs">
-          <q-item>
-            <q-item-section>
-              In the people section you can add authors and collaborators of the assay.
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <div>
-                <a_btn label="add person" icon='person_add_alt_1' color="secondary" />
-              </div>
-            </q-item-section>
-            <q-item-section>
-              Click to add a person
-            </q-item-section>
-          </q-item>
-        </q-list>
-
-      </q-card-section>
-
-      <q-separator inset size="0.3em" />
-
-      <q-card-section>
-
-        <q-item>
-          <q-item-section avatar>
-            <q-icon color="grey-8" name="menu_book" />
-          </q-item-section>
-          <q-item-section>
-            Publications
-          </q-item-section>
-        </q-item>
-
-        <q-list class="q-gutter-xs">
-          <q-item>
-            <q-item-section>
-              In the publications section you can add publications to the assay.
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <div>
-                <a_btn label="add publication" icon='bookmark_add' color="secondary" />
-              </div>
-            </q-item-section>
-            <q-item-section>
-              Click to add a publication
-            </q-item-section>
-          </q-item>
-        </q-list>
-
-      </q-card-section>
-
-    </q-card>
-
-  </div>
-</template>
diff --git a/packages/renderer/src/docs/study.vue b/packages/renderer/src/docs/study.vue
deleted file mode 100644
index 5ee5d062..00000000
--- a/packages/renderer/src/docs/study.vue
+++ /dev/null
@@ -1,152 +0,0 @@
-<script setup>
-import a_input from '../components/a_input.vue';
-import a_btn from '../components/a_btn.vue';
-</script>
-
-<template>
-  <div class="q-pt-sm">
-
-    <h5 style="margin-bottom:0.5em;">Study</h5>
-    <div class="text-body2 text-justify" style="padding-bottom:1em;">
-      In the Study menu you can adapt the metadata of one study added to your ARC.
-    </div>
-
-    <q-card>
-
-      <q-card-section>
-
-        <q-item>
-          <q-item-section avatar>
-            <q-icon color="grey-8" name="biotech" />
-          </q-item-section>
-          <q-item-section>Study</q-item-section>
-        </q-item>
-
-        <q-list class="q-gutter-xs">
-          <q-item>
-            <q-item-section>
-              <a_input label='Identifier' v-model='{ _: "YourIdentifier" }._' readonly />
-            </q-item-section>
-            <q-item-section>
-              The study identifier is automatically added when adding the study to your ARC and cannot be changed
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <a_input label='Title' v-model='{ _: "Your study title" }._' readonly-hidden />
-            </q-item-section>
-            <q-item-section>
-              Give your study a short title
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <a_input label='Description' readonly-hidden />
-            </q-item-section>
-            <q-item-section>
-              Add a description about your study
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <div>
-                <a_btn label="delete" icon='delete' color="red-9" />
-              </div>
-            </q-item-section>
-            <q-item-section>
-              Completely delete this study from the ARC
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <div>
-                <a_btn label="edit table" icon='edit' color="secondary" />
-              </div>
-            </q-item-section>
-            <q-item-section>
-              Edit experimental metadata using <a
-                href="https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/implementation/Swate.html"
-                target="_blank">Swate</a>
-            </q-item-section>
-          </q-item>
-        </q-list>
-
-
-      </q-card-section>
-
-      <q-separator inset size="0.3em" />
-
-      <q-card-section>
-
-        <q-list>
-          <q-item>
-            <q-item-section avatar>
-              <q-icon color="grey-8" name="groups" />
-            </q-item-section>
-            <q-item-section>People</q-item-section>
-          </q-item>
-        </q-list>
-
-        <q-list class="q-gutter-xs">
-          <q-item>
-            <q-item-section>
-              In the people section you can add authors and collaborators of the study.
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <div>
-                <a_btn label="add person" icon='person_add_alt_1' color="secondary" />
-              </div>
-            </q-item-section>
-            <q-item-section>
-              Click to add a person
-            </q-item-section>
-          </q-item>
-        </q-list>
-
-      </q-card-section>
-
-      <q-separator inset size="0.3em" />
-
-      <q-card-section>
-
-        <q-list class="q-gutter-xs">
-          <q-item v-ripple>
-            <q-item-section avatar>
-              <q-icon color="grey-8" name="menu_book" />
-            </q-item-section>
-            <q-item-section>Publications</q-item-section>
-          </q-item>
-        </q-list>
-
-        <q-list>
-          <q-item>
-            <q-item-section>
-              In the publications section you can add publications to the study.
-            </q-item-section>
-          </q-item>
-
-          <q-item>
-            <q-item-section>
-              <div>
-                <a_btn label="add publication" icon='bookmark_add' color="secondary" />
-              </div>
-            </q-item-section>
-            <q-item-section>
-              Click to add a publication
-            </q-item-section>
-          </q-item>
-        </q-list>
-
-      </q-card-section>
-
-    </q-card>
-
-  </div>
-</template>

From 10ad1ba9798a85b043d40505e965defc67068454 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Tue, 16 Jul 2024 11:25:48 +0200
Subject: [PATCH 2/5] add validation help

---
 packages/renderer/src/docs/validation.vue | 64 +++++++++++++++++++++++
 packages/renderer/src/views/HelpView.vue  |  6 +--
 2 files changed, 66 insertions(+), 4 deletions(-)
 create mode 100644 packages/renderer/src/docs/validation.vue

diff --git a/packages/renderer/src/docs/validation.vue b/packages/renderer/src/docs/validation.vue
new file mode 100644
index 00000000..fdc5772b
--- /dev/null
+++ b/packages/renderer/src/docs/validation.vue
@@ -0,0 +1,64 @@
+<script setup>
+import d_input from '../components/d_input.vue';
+import d_btn from '../components/d_btn.vue';
+import d_checkbox from '../components/d_checkbox.vue';
+</script>
+
+<template>
+  <div class="q-py-sm">
+
+    <h5 style="margin-bottom:0.5em;">
+      <q-icon color="grey-8" name="verified" />
+      Validation
+    </h5>
+    <q-card>
+      <q-card-section>
+        <q-item><div>
+        Here you can choose, how your ARC shall be validated.
+        The actual validation occurs in the DataHUB once you synchronize your ARC for the next time.
+        Please check out the <a
+          href="https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/DataHUB-Manual/cqc-pipelines/cqc-pipelines.html"
+          target="_blank">DataPLANT knowledge base</a> for more information.
+        </div></q-item>
+      </q-card-section>
+
+    </q-card>
+    
+    <q-separator inset />
+
+    <q-card>
+      <q-card-section>
+        <q-item><div>
+        By default every ARC is validated against the <a
+          href="https://github.com/nfdi4plants/ARC-specification"
+          target="_blank">"ARC specification"</a> to guarantee ARC intactness.
+        </div>
+      </q-item>                
+      
+        <q-item><div>
+        Under "Custom Validation Packages" you can add or remove additional validation packages.
+        For instance, if you want to publish your ARC and receive a DOI via the DataHUB, select and add the "invenio" validation. 
+        Please check out the <a
+          href="https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/DataHUB-Manual/datahub-data-publications.html"
+          target="_blank">DataPLANT knowledge base</a> for more information about publishing your ARC.        
+        </div>
+      </q-item>    
+    </q-card-section>
+    </q-card>
+
+
+    <q-separator inset />
+
+    <q-card>
+      <q-card-section>
+        <q-item><div>
+        By clicking
+        <d_btn label="Save" icon='verified' color="secondary" /> the file ".arc/validation_packages.yml" is edited
+        or added to your ARC.
+      </div>
+    </q-item>
+      </q-card-section>
+    </q-card>
+
+  </div>
+</template>
diff --git a/packages/renderer/src/views/HelpView.vue b/packages/renderer/src/views/HelpView.vue
index 1c21216c..1ba6f9a1 100644
--- a/packages/renderer/src/views/HelpView.vue
+++ b/packages/renderer/src/views/HelpView.vue
@@ -5,9 +5,8 @@ import appProperties from '../AppProperties.ts';
 import GitCommitHelp from '../docs/git-commit.vue';
 import GitSyncHelp from '../docs/git-sync.vue';
 import GitHistoryHelp from '../docs/git-history.vue';
-import AssayHelp from '../docs/assay.vue';
-import StudyHelp from '../docs/study.vue';
 import DataHubHelp from '../docs/datahub.vue';
+import ValidationHelp from '../docs/validation.vue';
 import HomeHelp from '../docs/home.vue';
 import SwateHelp from '../docs/swate.vue';
 
@@ -20,8 +19,7 @@ import SwateHelp from '../docs/swate.vue';
     <GitHistoryHelp v-else-if='appProperties.state===appProperties.STATES.GIT_HISTORY'></GitHistoryHelp>
     <SwateHelp v-else-if='appProperties.state===appProperties.STATES.EDIT_SWATE'></SwateHelp>
     <DataHubHelp v-else-if='appProperties.state===appProperties.STATES.OPEN_DATAHUB'></DataHubHelp>
-    <AssayHelp v-else-if='appProperties.state===appProperties.STATES.EDIT_ASSAY'></AssayHelp>
-    <StudyHelp v-else-if='appProperties.state===appProperties.STATES.EDIT_STUDY'></StudyHelp>
+    <ValidationHelp v-else-if='appProperties.state===appProperties.STATES.VALIDATION'></ValidationHelp>
     <HomeHelp v-else></HomeHelp>
   </div>
 </template>

From c3fe07bd5c0c2ef55940eeb61f54b75504095d18 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Tue, 16 Jul 2024 11:29:10 +0200
Subject: [PATCH 3/5] fix commit icon

---
 packages/renderer/src/docs/git-commit.vue     |  2 +-
 packages/renderer/src/docs/home.vue           | 16 +++++++++++++++-
 packages/renderer/src/views/GitCommitView.vue |  2 +-
 3 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/packages/renderer/src/docs/git-commit.vue b/packages/renderer/src/docs/git-commit.vue
index ebce2bba..a89b8051 100644
--- a/packages/renderer/src/docs/git-commit.vue
+++ b/packages/renderer/src/docs/git-commit.vue
@@ -9,7 +9,7 @@ import d_checkbox from '../components/d_checkbox.vue';
   <div class="q-py-sm">
 
     <h5 style="margin-bottom:0.5em;"> 
-      <q-icon color="grey-8" name="verified" /> Commit Changes
+      <q-icon color="grey-8" name="rule" /> Commit Changes
     </h5>   
 
     <q-card>
diff --git a/packages/renderer/src/docs/home.vue b/packages/renderer/src/docs/home.vue
index 3d2fabf1..494f0965 100644
--- a/packages/renderer/src/docs/home.vue
+++ b/packages/renderer/src/docs/home.vue
@@ -208,7 +208,7 @@ export default {
 
           <q-item>
             <q-item-section avatar>
-              <q-icon color="grey-7" name="verified" />
+              <q-icon color="grey-7" name="rule" />
             </q-item-section>
             <q-item-section style="margin-left: -1.2em;">
               Commit
@@ -242,6 +242,20 @@ export default {
             </q-item-section>
           </q-item>
 
+          <q-separator inset />
+                    
+          <q-item>
+            <q-item-section avatar>
+              <q-icon color="grey-7" name="verified" />
+            </q-item-section>
+            <q-item-section style="margin-left: -1.2em;">
+              Validation
+            </q-item-section>
+            <q-item-section>
+              Choose ARC validation
+            </q-item-section>
+          </q-item>
+
           <q-separator inset />
 
           <q-item>
diff --git a/packages/renderer/src/views/GitCommitView.vue b/packages/renderer/src/views/GitCommitView.vue
index 1896c684..9f79bb2b 100644
--- a/packages/renderer/src/views/GitCommitView.vue
+++ b/packages/renderer/src/views/GitCommitView.vue
@@ -228,7 +228,7 @@ onUnmounted(()=>{
 <template>
   <q-list bordered class="rounded-borders">
     <ViewItem
-      icon="verified"
+      icon="rule"
       label="Commit Changes"
       caption="Track changes of the ARC with git"
       group="git"

From a0960cf7e617089f7b4a0b8b8d5ca48a837cb7d7 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Tue, 16 Jul 2024 11:31:24 +0200
Subject: [PATCH 4/5] default activate help menu

---
 packages/renderer/src/App.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/packages/renderer/src/App.vue b/packages/renderer/src/App.vue
index 21176f53..51e9e876 100644
--- a/packages/renderer/src/App.vue
+++ b/packages/renderer/src/App.vue
@@ -36,7 +36,7 @@ setCssVar('primary', '#2d3e50');
 const iProps = reactive({
   showToolbar: true,
   toolbarMinimized: false,
-  showHelp: false,
+  showHelp: true,
   splitterModel: 300,
   error: false,
   error_text: '',

From f257245856853e102eb21817018462ef8fed10ca Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Tue, 16 Jul 2024 11:37:13 +0200
Subject: [PATCH 5/5] add toggle note to home help

---
 packages/renderer/src/docs/home.vue | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/packages/renderer/src/docs/home.vue b/packages/renderer/src/docs/home.vue
index 494f0965..12530d97 100644
--- a/packages/renderer/src/docs/home.vue
+++ b/packages/renderer/src/docs/home.vue
@@ -93,6 +93,8 @@ export default {
 
     <h5 style="margin-bottom:0.5em;">Help</h5>
 
+    Click <q-icon color="grey-7" name="help" />Toggle Help in the sidebar to show or hide the help menu.
+
     <div class="q-pa-sm text-body2 text-justify">
       The ARCitect is divided into three panels: sidebar, file tree and main menu.
     </div>