Updated and reorganized documentation and images for LabIMotion featu…

…res and components.

docs/labimotion/design-principles.mdx

@@ -14,7 +14,7 @@ import designBase from "@site/static/img/labimotion/design-base.png";
 
 <SubTitle text="Generic Elements, Segments, and Datasets are organized by layers and fields." />
 
-Generic **[Elements](./guides/designer/elements/)**, **[Segments](./guides/designer/segments/)**, and **[Datasets](./guides/designer/datasets/)** are structured using **[Components](./guides/designer/components/)**, which are introduced as layers and fields. Each generic element, segment, or dataset has the capacity to encompass multiple layers, and within each layer, there is the potential for multiple fields to be present. This hierarchical arrangement allows for a flexible and comprehensive organization of data and information.
+Generic **[Elements](./designer/elements/)**, **[Segments](./designer/segments/)**, and **[Datasets](./designer/datasets/)** are structured using **[Components](./designer/components/)**, which are introduced as layers and fields. Each generic element, segment, or dataset has the capacity to encompass multiple layers, and within each layer, there is the potential for multiple fields to be present. This hierarchical arrangement allows for a flexible and comprehensive organization of data and information.
 
 <img
   src={require("@site/static/img/labimotion/labimotion_modules.png").default}
@@ -30,7 +30,7 @@ In case you are not familiar with the terms **Element**, **Segment**, and **Data
 
 - **Element**: An element is a fundamental enetity which represent an essential aspect within your domain. For example, the sample element or reaction element in Chemotion ELN.
 - **Segment**: A segment is a distinct section that usually has its own identifiable characteristics. You can use it to represent a specific subset of an element.
-- **Dataset**: Within the system, a predefined segment named "Analyses" is provided to capture analysis results. The dataset of the analysis comprises individual data points. Additionally, through **[integration with the ChemConverter service](./guides/user/datasets/converter-metadata)**, metadata extraction from raw files is automatically triggered, facilitating mapping into the dataset.
+- **Dataset**: Within the system, a predefined segment named "Analyses" is provided to capture analysis results. The dataset of the analysis comprises individual data points. Additionally, through **[Metadata Auto Mapper](./user/datasets/metadata-mapper)**, metadata extraction from raw files is automatically triggered, facilitating mapping into the dataset.
 
 <p align="center">
   <img src={designBase} alt="LabIMotion - Generic Element, Segment, and Dataset" />
@@ -43,11 +43,11 @@ In case you are not familiar with the terms **Element**, **Segment**, and **Data
 
 ### 🎨 Designer Role
 
-The Designer role is dedicated to creating templates that align with specific applications. These templates serve as the foundation for user interfaces. Take a moment to explore the **[Designer View](./guides/designer)** and uncover the possibilities that await you!
+The Designer role is dedicated to creating templates that align with specific applications. These templates serve as the foundation for user interfaces. Take a moment to explore the **[Designer Guides](./designer)** and uncover the possibilities that await you!
 
 ### 🔬 User Role
 
-Users are individuals who can choose from a range of pre-designed templates, each meticulously crafted by Designers to suit different applications. Visit the **[User View](./guides/user)** and delve into the available functionalities.
+Users are individuals who can choose from a range of pre-designed templates, each meticulously crafted by Designers to suit different applications. Visit the **[User Guides](./user)** and delve into the available functionalities.
 
 :::info
 

docs/labimotion/guides/designer/components/fields/index.mdx → docs/labimotion/designer/components/fields/index.mdx

@@ -55,10 +55,14 @@ A distinctive identifier within the field. It won't be editable once the layer i
 
 ### Term(Ontology Terminology)
 
-A terminology used to express the concept of this data field, providing a link to the terminology service.
+A terminology used to define this data field, ensuring standardized and consistent definitions across templates. A link to the definition and the terminology service is provided for users.
+
+:::note
+If you get an empty list, please check with your administrator if the ontology service is correctly configured. (See [Allowing access to Terminology Service](/docs/labimotion/preparation#allowing-access-to-terminology-service))
+:::
 
 <YouTubeFrame
-  src="https://www.youtube-nocookie.com/embed/P5OOXB0RyqU?list=PLZoVOhxCsajnl5_tveYUvtD0Y57devzdn"
+  src="https://www.youtube-nocookie.com/embed/P5OOXB0RyqU"
   title="Designer - Linking an Ontology Term to a Field (HD)"
 />
 <FigCaption text="Designer - Linking an Ontology Term to a Field" />

docs/labimotion/guides/designer/components/fields/types/drag-element.mdx → docs/labimotion/designer/components/fields/types/drag-element.mdx

@@ -18,5 +18,5 @@ An icon with drag & drop function to let the user add a prior created element.
 </p>
 
 :::info
-To see how will it look like in the User view, check out the [User View > Elements > Drag Element](/docs/labimotion/guides/user/elements/drag-element).
+To see how will it look like in the User view, check out the [User View > Elements > Drag Element](/docs/labimotion/user/elements/drag-element).
 :::

docs/labimotion/guides/designer/components/fields/types/drag-sample.mdx → docs/labimotion/designer/components/fields/types/drag-sample.mdx

@@ -18,5 +18,5 @@ An icon with drag & drop function to let the user add a sample. It will display
 </p>
 
 :::info
-To see how will it look like in the User view, check out the [User View > Elements > Drag Sample](/docs/labimotion/guides/user/elements/drag-sample).
+To see how will it look like in the User view, check out the [User View > Elements > Drag Sample](/docs/labimotion/user/elements/drag-sample).
 :::

docs/labimotion/guides/designer/elements/template-sync.mdx → docs/labimotion/designer/elements/template-sync.mdx

@@ -18,7 +18,7 @@ import {
 
 Effortlessly synchronize templates suitable for your application from the Template Hub, enabling you to harness the collaborative contributions of scientists. This approach is highly recommended.
 
-As a [Designer](/docs/labimotion/design-principles#-designer-role), you can sync collective contributed templates from the Template Hub to your instance. This allows users to seamlessly work with the templates and publish their work step-by-step. See [Template Sync. & Publish](../../../template-sync-and-publish).
+As a [Designer](/docs/labimotion/design-principles#-designer-role), you can sync collective contributed templates from the Template Hub to your instance. This allows users to seamlessly work with the templates and publish their work step-by-step. See [Template Sync. & Publish](/docs/labimotion/template-sync-and-publish).
 
 ## Exchange Across Instances
 

docs/labimotion/guides/designer/index.mdx → docs/labimotion/designer/index.mdx

@@ -1,13 +1,12 @@
 ---
-title: Designer View
+title: Designer Guides
 author: Claire Lin
-sidebar_position: 3
+sidebar_position: 4
 ---
 import { FontAwesomeIcon } from "@fortawesome/react-fontawesome";
 import {
   faArrowUpRightFromSquare,
 } from "@fortawesome/free-solid-svg-icons";
-import DocCardList from "@theme/DocCardList";
 import {
   FigCaption,
   SubTitle,
@@ -84,7 +83,3 @@ Starting from LabIMotion v2.1, you can use **Quick Filter** to quickly find a te
 />
 
 <FigCaption text="Designer, you design what you need." />
-
-## Topics
-
-<DocCardList />

docs/labimotion/guides/designer/template-features/preview-design.mdx → docs/labimotion/designer/template-features/preview-design.mdx

@@ -59,6 +59,14 @@ The **Version List** displays the latest 10 released template versions, includin
 
 <FigCaption text="Designer - Version List" />
 
+### Version number
+
+The version number is displayed in the format `X.Y`, where `X` represents the major version and `Y` the minor version, highlighted in blue.
+
+:::info
+Refer to the [Save and Release](/docs/labimotion/designer/template-features/workarea#-save-and-release-major) guidelines for more information.
+:::
+
 ### <FontAwesomeIcon icon={faEye} /> Preview this version
 
 The preview feature is available not only for the current version but also for all versions.

docs/labimotion/index.mdx

@@ -23,7 +23,7 @@ LabIMotion ELN extends the software Chemotion ELN systematically with respect to
 
 :::tip
 
-Explore the **[Designer View](labimotion/guides/designer/)** to gain proficiency in creating templates that perfectly align with your specific applications.
+Explore the **[Designer Guides](labimotion/designer/)** to gain proficiency in creating templates that perfectly align with your specific applications.
 
 :::
 

docs/labimotion/guides/preparation/index.mdx → docs/labimotion/preparation.mdx

@@ -1,7 +1,7 @@
 ---
 title: Preparation
 author: Claire Lin
-sidebar_position: 1
+sidebar_position: 3
 ---
 
 import DocCardList from "@theme/DocCardList";
@@ -20,11 +20,11 @@ import menu from "@site/static/img/labimotion/menu.png";
 
 ## Before You Start...
 
-LabIMotion divides users into two distinct roles: [Designer](../designer/index.mdx) and [User](../user/index.mdx), each with specific responsibilities and permissions tailored to their needs. We strongly recommend that you have a clear understanding of your role before proceeding.
+LabIMotion divides users into two distinct roles: [**Designer**](./designer/index.mdx) and [**User**](./user/index.mdx), each with specific responsibilities and permissions tailored to their needs. We strongly recommend that you have a clear understanding of your role before proceeding.
 
-## Words for System Administrators
+## Words for **System Administrators**
 
-### Assigning the **Designer** role
+### Assigning the Designer role
 
 Given the importance of this **Designer** role, we recommend that you assign it to users who are responsible for creating and managing templates.
 
@@ -46,7 +46,11 @@ Navigate to the **UI features** menu, choose the generic feature (Element, Segme
   <img src={permissionUI} alt="UI Feature" width="500" />
 </div>
 
-## Words for Designers
+### Allowing access to Terminology Service
+
+Ensure your instance can connected to the Terminology Service (https://service.tib.eu and https://api.terminology.tib.eu) to retrieve complete and up-to-date ontology terms and data. If access to these URLs is restricted, the related functionality will still work, but users may receive incomplete information.
+
+## Words for **Designers**
 
 To access the Designer function, you must have the necessary permissions. If you can't find the **Generic Designer** option in the menu, please contact your system administrator for assistance.
 
@@ -56,8 +60,8 @@ To access the Designer function, you must have the necessary permissions. If you
 
 ### Recommended practices
 
-Utilize the Template Hub, a user-friendly collaboration center designed for scientists to effortlessly share templates across different applications. Learn how to synchronize templates from the Template Hub in the **[Template Sync & Publish](../../template-sync-and-publish.mdx)**.
+Utilize the Template Hub, a user-friendly collaboration center designed for scientists to effortlessly share templates across different applications. Learn how to synchronize templates from the Template Hub in the **[Template Sync & Publish](./template-sync-and-publish.mdx)**.
 
-## Words for Users
+## Words for **Users**
 
 Make sure you have the necessary permissions to access **Generic Elements, Segments, or  Datasets**. If these generic features are not visible, please contact your system administrator for assistance.

docs/labimotion/template-sync-and-publish.mdx

@@ -14,7 +14,7 @@ Template synchronization enables you to synchronize templates from the Template
 
 In your role as a designer, you have the capability to request templates to be integrated into your instance. Once these templates are requested, they will be generated and subsequently made available within your instance, allowing users to promptly commence their utilization.
 
-Additionally, users have the option to acquire DOIs for their work in the [Chemotion Repository](https://www.chemotion-repository.net/welcome) and facilitate the process of publication.
+Additionally, users have the option to acquire DOIs for their work in the [**Chemotion Repository**](https://www.chemotion-repository.net/welcome) and facilitate the process of publication.
 
 ## Synchronize templates
 

docs/labimotion/user/datasets/metadata-mapper.mdx

@@ -0,0 +1,57 @@
+---
+title: Metadata Auto Mapper
+author: Claire Lin
+sidebar_position: 4
+---
+
+import {
+  FigCaption,
+  SubTitle,
+  YouTubeFrame,
+  Reader,
+} from "@site/src/js/layout";
+
+import mapperConcept from "@site/static/img/labimotion/metadata-mapper.png";
+
+<SubTitle text="Metadata Auto Mapper extract the metadata and fill into the dataset for you" />
+<Reader text="User" />
+
+The **Metadata Auto Mapper** automatically maps file data to the corresponding dataset template, displaying it in the predefined form.
+
+:::info[Prerequisites]
+
+Ensure the following prerequisites are met before proceeding:
+
+1. The corresponding dataset template exists and is active in your system.
+2. The file format is supported by the Metadata Auto Mapper.
+
+:::
+
+<p align="center">
+  <img src={mapperConcept} alt="LabIMotion - Generic Dataset: Metadata Auto Mapper" />
+  <FigCaption text="LabIMotion - Generic Dataset: Metadata Auto Mapper" />
+</p>
+
+Let's take a look at the following examples:
+
+### NMR File
+
+The video demonstrates how the Metadata Auto Mapper extracts the metadata from an NMR file and fills it into the dataset.
+
+<YouTubeFrame
+  src="https://www.youtube-nocookie.com/embed/dUSl0yTDTvk"
+  title="Metadata Auto Mapper"
+/>
+
+<FigCaption text="Generic Dataset: Metadata Auto Mapper - NMR file data extraction" />
+
+### BagIt format file
+
+The video demonstrates how the Metadata Auto Mapper extracts the metadata from a BagIt format file and fills it into the dataset.
+
+<YouTubeFrame
+  src="https://www.youtube-nocookie.com/embed/OeY4ebfzfDg"
+  title="Converter Metadata"
+/>
+
+<FigCaption text="Generic Dataset: Metadata Auto Mapper - BagIt file data extraction" />

docs/labimotion/guides/user/elements/details.mdx → docs/labimotion/user/elements/details.mdx

@@ -31,4 +31,4 @@ By uploading Word files, Excel files, and presentation files, you can directly e
 
 ### Segment tab
 
-If segments are released and activated for this element, you can view them in the tab list. For additional information, please refer to the **[Segments](/docs/labimotion/guides/user/segments)** section.
+If segments are released and activated for this element, you can view them in the tab list. For additional information, please refer to the **[Segments](/docs/labimotion/user/segments)** section.

docs/labimotion/guides/user/features/revisions.mdx → docs/labimotion/user/features/revisions.mdx

@@ -29,14 +29,19 @@ The **Revision** function includes:
 
 ![Revision](/img/labimotion/revision-modal-user.png)
 
-### Viewing Versions <FontAwesomeIcon icon={faEye} />
+
+### Version number
+
+The version number indicates the template version, displayed in the format `X.Y`, where `X` represents the major version and `Y` the minor version, highlighted in blue.
+
+### <FontAwesomeIcon icon={faEye} /> Viewing this version
 
 Each change made to the content is recorded upon saving. This allows for easy viewing and tracing back to previous versions.
 
-### Reverting Changes <FontAwesomeIcon icon={faReply} />
+### <FontAwesomeIcon icon={faReply} /> Reverting Changes
 
-Users can choose to revert back to a specific version. This action restores the data to the selected version, effectively undoing any changes made after that point in time.
+You can choose to revert back to a specific version. This action restores the data to the selected version, effectively undoing any changes made after that point in time.
 
-### Delete Version <FontAwesomeIcon icon={faTrashCan} />
+### <FontAwesomeIcon icon={faTrashCan} /> Delete Version
 
 If the old version is no longer needed, it can be deleted. This action is irreversible and  cannot be undone once completed.

docs/labimotion/guides/user/index.mdx → docs/labimotion/user/index.mdx

@@ -1,10 +1,9 @@
 ---
-title: User View
+title: User Guides
 author: Claire Lin
-sidebar_position: 4
+sidebar_position: 5
 ---
 
-import DocCardList from "@theme/DocCardList";
 import {
   FigCaption,
   SubTitle,
@@ -30,5 +29,3 @@ Explore the available generic templates on **[Template Hub](https://www.chemotio
 Moreover, please don't hesitate to **[contact us](mailto:[email protected])** if you wish to share the templates.
 
 ## Topics
-
-<DocCardList />