NMRium

https://docs.nmrium.org/
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NMRium is a web-based NMR spectroscopy software that enables users to load, process, analyze, and...
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### Example .env File with Tokens

Source: https://docs.nmrium.org/help/zenodo

This example shows how to populate your .env file with both production and sandbox Zenodo API tokens, including comments for clarity.

```dotenv
# Zenodo production token
# Generated from: https://zenodo.org/account/settings/applications/tokens/new/
ACCESS_TOKEN=your_production_token_here

# Zenodo sandbox token
# Generated from: https://sandbox.zenodo.org/account/settings/applications/tokens/new/
ACCESS_TOKEN_SANDBOX=your_sandbox_token_here
```

--------------------------------

### Install and run zenodo-nmrium globally

Source: https://docs.nmrium.org/help/zenodo

Install the package globally via npm and execute it.

```bash
npm install -g zenodo-nmrium
```

```bash
zenodo-nmrium <path> [options]
```

--------------------------------

### Install and run zenodo-nmrium on Linux x64

Source: https://docs.nmrium.org/help/zenodo

Download the pre-built binary for Intel-based Linux and execute it.

```bash
curl -o zenodo-nmrium https://www.lactame.com/lib/zenodo-nmrium/HEAD/zenodo-nmrium-linux-x64 && chmod 555 zenodo-nmrium
```

```bash
./zenodo-nmrium <path> [options]
```

--------------------------------

### Example index.yml Metadata

Source: https://docs.nmrium.org/help/zenodo

This is an example of the index.yml file required at the root of your dataset folder. It contains metadata about your entire dataset, including title, description, copyright, keywords, and authors.

```yaml
title: "My NMR Dataset"
description: "<p>This dataset contains 1H NMR data for compound X.</p>"
copyright: "cc-by-4.0"
keywords:
  - NMR
  - compound X
authors:
  - family-name: "Doe"
    given-name: "Jane"
    affiliation: "University of Example"
    orcid: "0000-0000-0000-0001"
  - family-name: "Smith"
    given-name: "John"
    affiliation: "Institute of Research"
    orcid: "0000-0000-0000-0002"
```

--------------------------------

### Install and run zenodo-nmrium on macOS ARM64

Source: https://docs.nmrium.org/help/zenodo

Download the pre-built binary for Apple Silicon and execute it.

```bash
curl -o zenodo-nmrium https://www.lactame.com/lib/zenodo-nmrium/HEAD/zenodo-nmrium-darwin-arm64 && chmod 555 zenodo-nmrium
```

```bash
./zenodo-nmrium <path> [options]
```

--------------------------------

### Combine Submission Options

Source: https://docs.nmrium.org/help/zenodo

This example demonstrates combining multiple options for submission, including specifying the access token, enabling production environment, and auto-publishing.

```bash
./zenodo-nmrium ./my-nmr-dataset --access-token YOUR_TOKEN --production --auto-publish
```

--------------------------------

### Implement HelloDocusaurus Component

Source: https://docs.nmrium.org/contribute-to-doc/markdown_features

Examples of a simple React component structure for use in documentation.

```javascript
function HelloDocusaurus() {  
    return (  
        <h1>Hello, Docusaurus!</h1>  
    )  
}  

```

```javascript
function HelloDocusaurus() {  
  return <h1>Hello, Docusaurus!</h1>;  
}  

```

--------------------------------

### Example dataset folder structure

Source: https://docs.nmrium.org/help/zenodo

Required directory layout for organizing NMR samples and metadata before submission.

```text
my-nmr-dataset/  
├── index.yml                    # Dataset metadata (required)  
├── sample_1/                    # First sample (name will be reused in the table of content)  
│   ├── structure.mol            # Optional: chemical structure file (molfile format)  
│   ├── 12/                      # Experiment number of a native Bruker folder  
│   │   ├── fid  
│   │   ├── acqu  
│   │   ├── acqus  
│   │   ├── pdata/               # Processed data folder  
│   │   │   └── 1/  
│   │   │       ├── proc  
│   │   │       ├── procs  
│   │   │       └── ...  
│   │   └── ...  
│   ├── 13/                      # Another experiment  
│   └── ...  
├── sample_2.nmrium.zip          # Second sample was processed using NMRium. It could contain assignment  
├── sample_3/  
│   ├── structure.mol            # Optional: chemical structure file (molfile format)  
│   └── spectrum.jdx             # JCAMP-DX file (e.g., exported from Topspin using `tojdx` or from MNova with peak assignments)  
└── ...
```

--------------------------------

### Run zenodo-nmrium via npx

Source: https://docs.nmrium.org/help/zenodo

Execute the tool directly without permanent installation using npx.

```bash
npx zenodo-nmrium <path> [options]
```

--------------------------------

### Provide Zenodo Token via Command Line

Source: https://docs.nmrium.org/help/zenodo

You can provide your Zenodo API token directly using the -t or --access-token option when running the zenodo-nmrium command.

```bash
./zenodo-nmrium ./my-nmr-dataset -t YOUR_SANDBOX_TOKEN
```

--------------------------------

### Implement Collapsible Details Section

Source: https://docs.nmrium.org/contribute-to-doc/details

Use the <details> and <summary> tags to create a section that users can expand or collapse.

```html
<details>  
  <summary>Epcot Center</summary>  
  <p>  
    Epcot is a theme park at Walt Disney World Resort featuring exciting  
    attractions, international pavilions, award-winning fireworks and seasonal  
    special events.  
  </p>  
  <p>A second paragraphe</p>  
</details>  
```

--------------------------------

### Configure Zenodo Tokens via .env File

Source: https://docs.nmrium.org/help/zenodo

Store your Zenodo API tokens in a .env file for automatic loading. The tool checks for .env files in the current directory, your home directory, or ~/.zenodo-nmrium.

```dotenv
ACCESS_TOKEN=<ZENODO_PRODUCTION_TOKEN>
ACCESS_TOKEN_SANDBOX=<ZENODO_SANDBOX_TOKEN>
```

--------------------------------

### Zenodo Submit Command Line Usage

Source: https://docs.nmrium.org/help/zenodo

This displays the usage information for the zenodo-submit command, outlining positional arguments and available options for submitting datasets.

```bash
Usage: zenodo-submit <path> [options]  

Positional Arguments:  
  path                                    Path to dataset folder with index.yml and data  

Options:  
  -t, --access-token <token>              Zenodo API access token (required)  
  -s, --sandbox                           Use sandbox environment (default)  
  -p, --production                        Use production environment  
  -a, --auto-publish                      Auto-publish after submission  
  -d, --data-selection <type>             Data selection for NMRium visualization  
                                          Choices: ft, fid, both, preferFT, preferFID  
                                          Default: ft  
  -l, --log-level <level>                 Logger level  
                                          Choices: trace, debug, info, warn, error, fatal, silent  
                                          Default: info  
  -h, --help                              Show this help message  
```

--------------------------------

### Submit Data to Production

Source: https://docs.nmrium.org/help/zenodo

This command submits your NMR dataset to the Zenodo production environment. Ensure you use your production API token and the -p flag.

```bash
./zenodo-nmrium ./my-nmr-dataset -t YOUR_PRODUCTION_TOKEN -p
```

--------------------------------

### NMRium CLI Configuration Flags

Source: https://docs.nmrium.org/help/zenodo

Configuration options for the NMRium CLI to manage Zenodo submissions.

```APIDOC
## CLI Configuration Options

### Description
Configuration flags for the NMRium CLI to authenticate with Zenodo, select environments, and control submission behavior.

### Parameters
#### Options
- **--access-token, -t** (string) - Required - API token for Zenodo authentication. Can also be set via ACCESS_TOKEN or ACCESS_TOKEN_SANDBOX environment variables.
- **--sandbox, -s** (flag) - Optional - Submit to Zenodo sandbox (default).
- **--production, -p** (flag) - Optional - Submit to production environment.
- **--auto-publish, -a** (flag) - Optional - Automatically publish the record after submission. If omitted, record is created in draft state.
- **--data-selection, -d** (string) - Optional - Controls NMR data types shown. Choices: ft (default), fid, both, preferFT, preferFID.
- **--log-level, -l** (string) - Optional - Sets logger verbosity. Choices: trace, debug, info (default), warn, error, fatal, silent.
```

--------------------------------

### Submit Data Using Environment Variables

Source: https://docs.nmrium.org/help/zenodo

When using environment variables, you can omit the -t option. The tool will automatically use ACCESS_TOKEN_SANDBOX for sandbox submissions or ACCESS_TOKEN for production if the -p flag is used.

```bash
# Uses ACCESS_TOKEN_SANDBOX from .env file
./zenodo-nmrium ./my-nmr-dataset

# Uses ACCESS_TOKEN from .env file
./zenodo-nmrium ./my-nmr-dataset -p
```

--------------------------------

### Create Markdown Links

Source: https://docs.nmrium.org/contribute-to-doc/markdown_features

Reference other documents using standard Markdown link syntax with relative file paths.

```markdown
Let's see how to [Create a document](../20_create/20_create).  

```

--------------------------------

### Auto-Publish Submission to Sandbox

Source: https://docs.nmrium.org/help/zenodo

This command submits your NMR dataset to the Zenodo sandbox and automatically publishes it after a successful submission. Requires a sandbox API token.

```bash
./zenodo-nmrium ./my-nmr-dataset -t YOUR_SANDBOX_TOKEN -a
```

--------------------------------

### Create Admonitions with MDX

Source: https://docs.nmrium.org/contribute-to-doc/admonitions

Use triple colons to define admonition blocks. Titles are optional and content supports standard Markdown formatting.

```markdown
:::note
The content and title _can_ include markdown.
:::

:::note You can specify an optional title
Heads up! Here's a pro-tip.
:::

:::info
Useful information.
:::

:::caution
Warning! You better pay attention!
:::

:::danger
Danger danger, mayday!
:::
```

--------------------------------

### Create a new markdown document

Source: https://docs.nmrium.org/contribute-to-doc/create

Define the document title using front matter and add content in markdown format.

```markdown
---
title: Hello, World!
---

## Hello, World!

This is your first document in **Docusaurus**, Congratulations!
```

--------------------------------

### Embed Markdown Images

Source: https://docs.nmrium.org/contribute-to-doc/markdown_features

Display images stored in the static directory using standard Markdown image syntax.

```markdown
![Docusaurus logo](/img/docusaurus.png)  

```

--------------------------------

### Define Front Matter Metadata

Source: https://docs.nmrium.org/contribute-to-doc/markdown_features

Use YAML-formatted metadata at the top of Markdown files to configure document properties like ID, title, and sidebar labels.

```yaml
---
  
id: my-doc  
title: My document title  
description: My document description  
sidebar_label: My doc  
---  
  
Markdown content  

```

--------------------------------

### Define React Components in MDX

Source: https://docs.nmrium.org/contribute-to-doc/markdown_features

Use MDX to define and render interactive React components directly within Markdown files.

```jsx
export const Highlight = ({children, color}) => (  
  <span  
    style={{
      backgroundColor: color,  
      borderRadius: '2px',  
      color: 'red',  
      padding: '0.2rem',  
    }}>
    {children}  
  </span>  
);
  
<Highlight color="#c7401e">Docusaurus green</Highlight> and <Highlight color="#1877F2">Facebook blue</Highlight> are my favorite colors.  

```
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