From eb42720864cc6a8e995b0b96d30fc61b6a2dbd01 Mon Sep 17 00:00:00 2001 From: "chia-lin.lin" Date: Wed, 1 Nov 2023 03:14:44 +0100 Subject: [PATCH] Add files via upload --- docs/eln/admin/features.mdx | 98 +++++++++---------- docs/eln/admin/generic_config.mdx | 5 +- .../guides/designer/datasets/index.mdx | 20 +++- docs/labimotion/index.mdx | 30 +++++- 4 files changed, 94 insertions(+), 59 deletions(-) diff --git a/docs/eln/admin/features.mdx b/docs/eln/admin/features.mdx index 567cd61e..1810d0ea 100644 --- a/docs/eln/admin/features.mdx +++ b/docs/eln/admin/features.mdx @@ -1,5 +1,6 @@ --- title: UI Features +author: Claire Lin --- # UI features @@ -8,41 +9,45 @@ For functions that require authorized access, the administrator can grant or den ![adminui-uifeatures](@site/static/img/admin_ui/features.png) -**Edit Permission** +## Edit Permission -- Enable globally - when the function is enabled globally, it is available for all users except the users in the "Exclude Users" list -- Include Users - the user who can access the function -- Exclude Users - the user who cannot access the function +When it comes to editing permissions, there are three crucial aspects to consider: + +- **Global Enablement**: This setting enables the functionality for all users by default, excluding those specified in the "Exclude Users" list. +- **Include Users**: These are the users who are allowed to access the specific function. +- **Exclude Users**: This category comprises users who are explicitly denied access to the function. ![adminui-uifeatures-edit_permission](@site/static/img/admin_ui/features-permission.gif) -**Edit JSON** +## Edit JSON + +Each feature has its own unique characteristics and administrators have the right to fine-tune the configuration. -Each function has its own unique features and the administrator can adjust the setting by editing the configuration. Please make sure to find the corresponding information and read the content carefully before changing the settings. +:::caution WARNING +It is important to be fully informed before making any changes. +::: + +Here are the features available for customization: -- User Label - Computed Prop - Reaction Prediction -- Sample Decoupled -- Generic Element -- Generic Segment -- Generic Dataset - [ChemDraw Editor](#chemdraw-editor) -- Ketcher Editor +- Ketcher 2 Editor +- [User Authentication (userProvider)](#user-authentication-userprovider) -## ChemDraw Editor +### ChemDraw Editor -**Supported Versions** +**Compatible Versions** -| Chemotion ELN | ChemDraw | +| Chemotion ELN | ChemDraw | | ----------------- | ---------- | | 1.5.3 and after | 22 | -| 1.0.2 ~ 1.5.3 | 17, 19, 20 | +| 1.0.2 to 1.5.3 | 17, 19, 20 | | 1.0.2 and earlier | 17 | -**JSON** +**Configuration in JSON** -To active ChemDraw in Chemotion ELN, use +To activate ChemDraw in Chemotion ELN, use the following JSON configuration: ```json { @@ -50,46 +55,35 @@ To active ChemDraw in Chemotion ELN, use } ``` -By default, the web service in enabled. To disable the web service, use - -```json -{ - "editor": "chemdraw", - "features": { - "disabled": ["WebService"] - } -} -``` - -To set up ChemDraw, please see [Structure editor](../install_configure/configuration#structure-editor). +For detailed setup instructions for ChemDraw, please refer to [Structure editor](../install_configure/configuration#structure-editor){:target="_blank" rel="noopener noreferrer"}. -## User Authentication (userProvider) +### User Authentication (userProvider) **Supported Versions** -| Chemotion ELN | protocol/services | +| Chemotion ELN | Protocol/Services | | ------------- | ----------------- | | 1.6. | OIDC, shibboleth | **Setting** -After having saved the settings, the ELN service needs to be restarted to apply changes. +Once the settings have been saved, the ELN service requires a restart to apply the changes. Configuration example: ```sh { -  extra_rules: { - enable: false, - disable_signup: true,      - disable_db_login: false    - },    - shibboleth: {      - enable: false,      - uid: 'pairwise-id',      - email: 'mail', - last_name: 'sn',      - first_name: 'givenName'    +  extra_rules: { + enable: false, + disable_signup: true,     + disable_db_login: false   + },   + shibboleth: {  + enable: false, + uid: 'pairwise-id', + email: 'mail', + last_name: 'sn', + first_name: 'givenName' }, openid_connect: { enable: true, @@ -111,20 +105,24 @@ Configuration example: } ``` -| OIDC params | value | +#### OIDC Parameters + +| Parameter | Value | | ---------------------- | -------------------------------------------------------------- | | enable | `true` or `false` | | host | address of the service | | icon | path to a public image to display on the sign-in page | -| issuer | url of the issuer | +| issuer | URL of the issuer | | scheme | 'https' | | client_id | client ID | -| redirect_uri | your chemotion ELN url + '/users/auth/openid_connect/callback' | +| redirect_uri | your chemotion ELN URL + '/users/auth/openid_connect/callback' | | client_secret | secret | | token_endpoint | '/oauth2/token' | | authorization_endpoint | '/oauth2/auth' | -| Shibboleth params | value | +#### Shibboleth Parameters + +| Parameters | Value | | ----------------- | ----------------------------- | | enable | `true` or `false` | | uid | 'pairwise-id' | @@ -132,7 +130,9 @@ Configuration example: | last_name | 'sn' | | first_name | 'givenName' | -| Extra rules params | value | +#### Extra Rules Parameters + +| Parameters | Value | | ------------------ | ----------------------------- | | enable | `true` or `false` | | disable_signup | `true` or `false` | diff --git a/docs/eln/admin/generic_config.mdx b/docs/eln/admin/generic_config.mdx index d32b724a..92c9a883 100644 --- a/docs/eln/admin/generic_config.mdx +++ b/docs/eln/admin/generic_config.mdx @@ -1,5 +1,6 @@ --- title: Generic Configuration +authors: Nicole Jung, Claire Lin, Pei-Chi Huang, Noura Rayya --- import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; @@ -32,8 +33,8 @@ import { } from "@fortawesome/free-solid-svg-icons"; import { Btn } from "@site/src/js/btn.js"; -:::danger Caution -This page is still being edited and reviewed. +:::caution Important +This document pertains to the Beta version of LabIMotion, formerly known as "Generic Module." We highly encourage you to refer to the documentation of the official release **[LabIMotion](../../labimotion/)** for comprehensive information. ::: ## Generic segments, elements and datasets diff --git a/docs/labimotion/guides/designer/datasets/index.mdx b/docs/labimotion/guides/designer/datasets/index.mdx index 616e2d38..9ca0188f 100644 --- a/docs/labimotion/guides/designer/datasets/index.mdx +++ b/docs/labimotion/guides/designer/datasets/index.mdx @@ -4,8 +4,13 @@ author: Claire Lin sidebar_position: 3 --- -Shares commonalities with both the Elements and Segments functions and is -associated with the Chemical Methods Ontology. +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { faList } from "@fortawesome/free-solid-svg-icons"; +import { FigCaption, SubTitle, YouTubeFrame, Reader } from '../../../layout'; +import elementList from '@site/static/img/labimotion/element-designer-list.png'; + + + The **Datasets** function shares commonalities with both the [Elements](elements/) and [Segments](segments/) functions, affording you the ability to intricately design the user interface through the integration of [Layers](components/layers/) and [Fields](components/fields/). Notably, the distinctive aspect of the "Datasets" function lies in its association with the Chemical Methods Ontology. To initiate the design of a Dataset, you are required to first select the relevant Ontology. Subsequently, they can seamlessly begin shaping and refining the Dataset's user interface using [Layers](components/layers/) and [Fields](components/fields/), thus offering a specialized and comprehensive approach to interface design tailored to chemical methodologies. @@ -13,14 +18,21 @@ The **Datasets** function shares commonalities with both the [Elements](elements ### Dataset Template List +Following the same approach of delivering a user-friendly user interface in a grid format, Dataset templates are displayed in a grid layout for your ease of use. + +- :white_check_mark: **Sort** the grid by clicking on the column headers. +- :white_check_mark: **Filter** the grid by clicking on the filter icon located at the right of the column headers. + +For a practical demonstration of sorting and filtering tasks in a list, you can watch the video in the [Element Template List](../designer/elements#element-template-list) section. + ![Designer - Generic Dataset](/img/labimotion/designer-generic-dataset.png) -## Attributes +## Dataset Attributes ### Chemical Methods Ontology -A more easily readable and understandable name is presented to end-users, aiding them in recognizing and understanding the segment they are interacting with. +A more easily readable and understandable name is presented to end-users, aiding them in recognizing and understanding the dataset they are interacting with. ### Version diff --git a/docs/labimotion/index.mdx b/docs/labimotion/index.mdx index 5d489fb4..ff405fb3 100644 --- a/docs/labimotion/index.mdx +++ b/docs/labimotion/index.mdx @@ -5,6 +5,8 @@ sidebar_label: LabIMotion Extension sidebar_position: 3 --- +import ContactUs from './_contact-us.mdx'; + LabIMotion is a software that was built as a generic extension of the established Software Chemotion-ELN. LabIMotion was developed at KIT in the institute IBCS-FMS and was funded by the research data management initiative ExU-RDM at KIT. ![LabImotion](/img/logos/LabIMotion_logo_cut.png) @@ -13,10 +15,30 @@ LabIMotion is a software that was built as a generic extension of the establishe The software development team at IBCS-FMS is developing with many other developers and scientists in Germany the electronic lab notebook Chemotion ELN. This development was included to the strategic projects of the National Research Data Infrastructure NFDI4Chem in 2019. The functions of Chemotion ELN are specifically designed for chemistry purposes. Many requests with respect to the use of the software in other disciplines were not covered, therefore, its use was recommended for chemists only. During the last years, the direct need for ELN software in other disciplines was expressed at KIT in particular from scientists in engineering, natural sciences and materials sciences. The project LabIMotion ELN was started to offer solutions for those scientists. The development team at IBCS extended Chemotion ELN in a generic manner to allow its use by other disciplines. -## Current status, improvements and options +## The Power of LabIMotion ELN + +### Customized Functionality for Scientists + +LabIMotion ELN extends the software Chemotion ELN systematically with respect to functions and available modules. The extension allows to use the ELN software either with or without chemistry functionality. The most important change that comes with the implementation of LabIMotion ELN is the option to design new modules which can be adapted to the needs of the scientists. The modules can be connected to each other and therefore, a clear assignment of materials and samples to processes and workflows can be gained. + +:::tip +Explore the **[Designer View](labimotion/guides/designer/)** to gain proficiency in creating templates that perfectly align with your specific applications. +::: + +### Collaboration and Efficiency -LabIMotion ELN extends the software Chemotion ELN systematically with respect to functions and available modules. The extension allows to use the ELN software either with or without chemistry functionality. The most important change that comes with the implementation of LabIMotion ELN is the option to design new modules which can be adapted to the needs of the scientists. The modules can be connected to each other and therefore, a clear assignment of materials and samples to processes and workflows can be gained. The functions of LabIMotion are described on the documentation page of our software development team: +LabIMotion ELN also introduces a user-friendly collaboration centre. Scientists can easily share templates between various applications and synchronise them effortlessly via the Template Hub. -:::tip Contact us -Please contact us using the [LabIMotion Team](mailto:chemotion-labimotion@lists.kit.edu) for information regarding latest developments in LabIMotion. +:::tip +Learn more about **Template Hub**, a platform designed to enhance resource sharing and streamline access to invaluable templates contributed by fellow researchers and professionals.. ::: + +### Streamlined Research Publication + +The LabIMotion ELN, in addition to its extensive functionality, helps scientists access Digital Object Identifiers (DOIs) and streamlines the online research publication process. This support simplifies the process of publishing research results and ensures that scientists from different disciplines can efficiently share their research with the world. + +:::tip +Discover the features of **[Chemotion Repository](repo/)** and unlock the potential to publish your work efficiently. +::: + +