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update structure editor and designer #289

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33 changes: 23 additions & 10 deletions docs/eln/install_configure/configuration.mdx
Original file line number Diff line number Diff line change
Expand Up @@ -206,33 +206,46 @@ For each registered Device, a collection job can be set up through the administr

## Structure editor

Chemotion ELN uses Ketcher as the default structure editor. To use other editors, configure the required files and the license (if needed) in the `structure_editors.yml` file. After editing the `structure_editors.yml` the service needs to be restarted.
The default structure editor for Chemotion ELN is Ketcher, specifically version v1, seamlessly integrated through the ketcher-rails project; therefore, no additional configuration is needed.
If you wish to utilize other supported structure editors, such as Ketcher v2, ChemDraw, or Marvin JS, additional configuration is required. In such cases, you'll need to adjust the necessary files and, potentially, provide a license. Please be aware that any modifications to the `structure_editors.yml` file will necessitate a service restart for the changes to take effect.

The `structure_editors.yml` configuration file is in the `config` folder. To create the file for the first time,
The `structure_editors.yml` configuration file is located in the `config` folder. To configure other structure editors, follow these steps:

1. Navigate to the application directory (/var/www/chemotion_ELN/current).
```sh
cd /var/www/chemotion_ELN/current
```

2. Copy the example configuration file to create a new one if the file doesn't exist yet.
```sh
# from the application dir (/var/www/chemotion_ELN/current) copy the config file
cp config/structure_editors.yml.example config/structure_editors.yml
```

# edit it
vim config/structure_editors.yml
3. Open the file and edit it. Make the necessary edits, followed by [Complete structure_editors.yml example](#complete-structure_editorsyml-example).

# restart the application (assuming Passenger is being used)
4. Restart the application (assuming Passenger is being used)
```sh
touch tmp/restart.txt
```

# keep the configuration for future Chemotion ELN updates (assuming Capistrano is used)
5. Keep the configuration for future Chemotion ELN updates (assuming Capistrano is used)
```sh
mv config/structure_editors.yml /var/www/chemotion_ELN/shared/config/structure_editors.yml
ln -s /var/www/chemotion_ELN/shared/config/structure_editors.yml /var/www/chemotion_ELN/current/config/structure_editors.yml
```

### Currently supported editors
### Supported editors

| Name | Version |
| ----------- | ------------------------------------------------------------------------------------------- |
| ChemDraw JS | 17, 20 |
| ChemDraw JS | 17+ |
| Ketcher 2 | [2.4](https://drive.google.com/drive/folders/1TZLEVyKs0Fhz8vmjOHK6Xii8MFfrifFI?usp=sharing) |
| Marvin JS | 21.8 |

### Complete structure_editors.yml example

```yaml

```yaml
### example of structure_editors.yml
production:
Expand Down Expand Up @@ -362,7 +375,7 @@ Chemotion ELN provides users with an easy way to query information in SciFinder<
This is managed by the Chemotion team at KIT to facilitate the process.

:::caution Important note
At the moment, CAS offers a process for Chemotion users in Germany to request SciFinder access through the API. This is managed by the consortium HBZ. For all oher institutions not located in Germany: please let us know about your need to integrate the SciFinder API - we will try to clarify the options with CAS.
At the moment, CAS offers a process for Chemotion users in Germany to request SciFinder access through the API. This is managed by the consortium HBZ. For all oher institutions not located in Germany: please let us know about your need to integrate the SciFinder API - we will try to clarify the options with CAS.
:::

#### Instance Registration
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,30 @@ title: Restriction Setting
author: Claire Lin
sidebar_position: 1
---

import { Reader } from '@site/src/js/layout';
import { FontAwesomeIcon } from "@fortawesome/react-fontawesome";
import { faCogs } from "@fortawesome/free-solid-svg-icons";
import { FigCaption, SubTitle, YouTubeFrame, Reader } from '@site/src/js/layout';

<Reader text="Designer" />

When a restriction is applied, the layer is hidden. It will only be shown when the criteria are met. If there are multiple restrictions that have been applied, the layer will be displayed when any one of them is matched.

Just few steps to set up the restriction:

1. Click the **Restriction Setting** <FontAwesomeIcon icon={faCogs} /> button on the top right corner of the layer.
2. Start to set up the condition - Layer, Field, and Value.
3. Done!

:::tip
Use **Preview Design** function to see how your design look like.
:::

Quick cath up with the video below to see how to set up the restriction.

<YouTubeFrame src="https://www.youtube-nocookie.com/embed/VuEFAd8HzzU" title="Designer: Layer Restriction Setting." />

<FigCaption text="Designer: Layer Restriction Setting." />

:::info
If there are more than one condition are set, the layer shows when one of the conditions got matched.
:::
5 changes: 4 additions & 1 deletion docs/labimotion/guides/user/datasets/converter-metadata.mdx
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,10 @@ import { FigCaption, SubTitle, YouTubeFrame, Reader } from '@site/src/js/layout'
<SubTitle text="Converter-Metadata." />
<Reader text="User" />

The ChemConverter service provides automatic metadata extraction and mapping to the generic dataset.
Combined with the power of the **[ChemConverter](/docs/services/chemconverter)** service, enabling automatic metadata extraction from raw files and seamless mapping to the Generic Dataset.

<YouTubeFrame src="https://www.youtube-nocookie.com/embed/OeY4ebfzfDg" title="Converter Metadata." />

:::tip
Dive deeper into **[ChemConverter](/docs/services/chemconverter)** for more insights and information.
:::