COCONUT

https://steinbeck-lab.github.io/coconut/
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### Install COCONUT Application Chart

Source: https://steinbeck-lab.github.io/coconut/local-instance.html

Install the COCONUT application using Helm. Ensure you have generated an application key and provided it in the `.Values.appProperties.key` property before installation.

```bash
helm install my-coconut-app repo-helm-charts/coconut-app
```

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

### Start PostgreSQL Docker Container

Source: https://steinbeck-lab.github.io/coconut/data.html

Use this command to start a PostgreSQL Docker container for the COCONUT database. Ensure Docker is installed.

```bash
docker run --name coconut-postgres -e POSTGRES_PASSWORD=yourpassword -e POSTGRES_USER=coconut -e POSTGRES_DB=coconut -p 5432:5432 -d postgres:15
```

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

### Start Laravel Horizon for Local Development

Source: https://steinbeck-lab.github.io/coconut/collection-submission.html

To process queued compounds during local development, start the Laravel Horizon service.

```bash
sail artisan horizon
```

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

### Install JS Dependencies with NPM

Source: https://steinbeck-lab.github.io/coconut/installation.html

Install the JavaScript dependencies for the project using NPM.

```bash
npm install
```

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

### Install PHP Dependencies with Composer

Source: https://steinbeck-lab.github.io/coconut/installation.html

Install the required PHP dependencies for the project using Composer.

```bash
composer install
```

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

### Copy Environment File

Source: https://steinbeck-lab.github.io/coconut/installation.html

Copy the example environment file to create the actual environment file for configuration.

```bash
cp .env.example .env
```

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

### Start Docker Containers with Sail

Source: https://steinbeck-lab.github.io/coconut/installation.html

Run the Sail command to start the Docker containers in detached mode.

```bash
./vendor/bin/sail up -d
```

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

### Get Organisms

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Get the details of organisms where the molecules are reported to be found in.

```APIDOC
## GET /api/organisms

### Description
Get the details of organisms where the molecules are reported to be found in.

### Method
GET

### Endpoint
/api/organisms
```

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

### Run Vite Local Development Server

Source: https://steinbeck-lab.github.io/coconut/installation.html

Start the Vite local development server for front-end assets. This command is used for development purposes.

```bash
npm run dev
```

```bash
yarn dev
```

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

### Basic Example for Searching Reports

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

This JSON payload demonstrates how to filter, sort, and paginate search results for reports.

```json
{
  "search": {
    "filters": [
      {
        "field": "title",
        "operator": "like",
        "value": "%molecule%"
      }
    ],
    "sorts": [
      {
        "field": "title",
        "direction": "desc"
      }
    ],
    "page": 1,
    "limit": 10
  }
}
```

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

### Get Citations

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Get details about the citations connected to various resources on COCONUT.

```APIDOC
## GET /api/citations

### Description
Get details about the citations connected to various resources on COCONUT.

### Method
GET

### Endpoint
/api/citations
```

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

### Get Molecules

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Retrieves all details about available molecules.

```APIDOC
## GET /api/molecules

### Description
Retrieves all details about available molecules.

### Method
GET

### Endpoint
/api/molecules
```

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

### Clone COCONUT Repository

Source: https://steinbeck-lab.github.io/coconut/installation.html

Clone the COCONUT project repository from Github. This is the first step in the installation process.

```bash
git clone https://github.com/Steinbeck-Lab/coconut.git
```

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

### Get Properties

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Exclusively search for molecule properties.

```APIDOC
## GET /api/properties

### Description
Exclusively search for molecule properties.

### Method
GET

### Endpoint
/api/properties
```

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

### Get Collections

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Retrieves details about the collections hosted on COCONUT.

```APIDOC
## GET /api/collections

### Description
Retrieves details about the collections hosted on COCONUT.

### Method
GET

### Endpoint
/api/collections
```

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

### Get Molecules Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Retrieve all details about a specific molecule.

```http
GET /api/molecules
```

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

### Get Collections Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Retrieve details about the collections hosted on COCONUT.

```http
GET /api/collections
```

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

### Get Citations API Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Retrieve details about citations connected to various resources on COCONUT.

```http
GET /api/citations
```

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

### Get Properties API Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Exclusively search for molecule properties.

```http
GET /api/properties
```

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

### Get Organisms API Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Retrieve details of organisms where molecules are reported to be found.

```http
GET /api/organisms
```

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

### Seed the Database (Optional)

Source: https://steinbeck-lab.github.io/coconut/installation.html

Run the database seeders to populate the database with initial data, if available.

```bash
./vendor/bin/sail artisan db:seed
```

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

### Run Database Migrations

Source: https://steinbeck-lab.github.io/coconut/installation.html

Execute the database migrations to create the necessary tables for the application.

```bash
./vendor/bin/sail artisan migrate
```

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

### Navigate to Project Directory

Source: https://steinbeck-lab.github.io/coconut/installation.html

Change the current directory to the cloned COCONUT project folder.

```bash
cd coconut
```

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

### Register

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Registers a new user with the provided details.

```APIDOC
## POST /api/auth/register

### Description
Registers a new user with the provided details.

### Method
POST

### Endpoint
/api/auth/register

### Request Body
#### application/json
- **first_name** (string) - Required
- **last_name** (string) - Required
- **username** (string) - Required
- **affiliation** (string) - Required
- **email** (string) - Required
- **password** (string) - Required
- **password_confirmation** (string) - Required

### Request Example
```json
{
  "first_name": "John",
  "last_name": "Doe",
  "username": "JDoe",
  "affiliation": "JD",
  "email": "john@example.com",
  "password": "password",
  "password_confirmation": "password"
}
```

### Response
#### Success Response (200)
- **success** (boolean) - Indicates if the registration was successful.
- **message** (string) - A message describing the result of the registration.
- **token** (string) - The authentication token for the newly registered user.

#### Response Example
```json
{
  "success": true,
  "message": "string",
  "token": "string"
}
```
```

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

### Access Application

Source: https://steinbeck-lab.github.io/coconut/installation.html

Access the Laravel application in your browser. Ensure Docker containers are running.

```bash
http://localhost
```

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

### Add Helm Repository

Source: https://steinbeck-lab.github.io/coconut/local-instance.html

Add the Helm repository containing COCONUT charts to your Helm client. Run `helm repo update` if the repo was previously added.

```bash
helm repo add repo-helm-charts https://nfdi4chem.github.io/repo-helm-charts/
```

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

### Load PostgreSQL Dump with Docker

Source: https://steinbeck-lab.github.io/coconut/data.html

Load a text format SQL dump into the running COCONUT PostgreSQL Docker container. Replace '/path/to/coconut_dump.sql' with the actual path to your dump file.

```bash
docker exec -i coconut-postgres psql -U coconut -d coconut < /path/to/coconut_dump.sql
```

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

### Register Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Use this endpoint to register a new user. Requires all user details including password confirmation.

```http
POST /api/auth/register
```

```json
{
  "first_name": "John",
  "last_name": "Doe",
  "username": "JDoe",
  "affiliation": "JD",
  "email": "john@example.com",
  "password": "password",
  "password_confirmation": "password"
}
```

```json
{
  "success": true,
  "message": "string",
  "token": "string"
}
```

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

### Create Report

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Create a new report.

```APIDOC
## POST /api/reports

### Description
Create a new report.

### Method
POST

### Endpoint
/api/reports

### Parameters
#### Request Body
(The request body schema for creating a report is not detailed in the source.)
```

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

### Generate Application Key

Source: https://steinbeck-lab.github.io/coconut/installation.html

Generate the application key using the Sail artisan command. This is necessary for secure session handling and encryption.

```bash
./vendor/bin/sail artisan key:generate
```

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

### SQL Query for Download Count

Source: https://steinbeck-lab.github.io/coconut/data.html

This SQL query calculates the molecule count for downloads, including active molecules and parent molecules without variants. It joins the molecules, collection_molecule, and collections tables.

```sql
SELECT count(*) 
FROM molecules m
JOIN collection_molecule cm ON m.id = cm.molecule_id
JOIN collections c ON cm.collection_id = c.id
WHERE c.title = 'Australian natural products' 
  AND m.active=true 
  AND (m.is_parent=false OR (m.is_parent=true AND has_variants=false));
```

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

### Molecule Actions

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Launches specific actions related to molecules.

```APIDOC
## POST /api/molecules/actions/{action}

### Description
Launches specific actions related to molecules.

### Method
POST

### Endpoint
/api/molecules/actions/{action}

### Parameters
#### Path Parameters
- **action** (string) - Required - The action to perform on the molecule.
```

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

### Verify PostgreSQL Data Load with Docker

Source: https://steinbeck-lab.github.io/coconut/data.html

Execute a SQL query within the COCONUT PostgreSQL Docker container to verify that data has been loaded correctly. This command counts the number of molecules.

```bash
docker exec -it coconut-postgres psql -U coconut -d coconut -c "SELECT count(*) FROM molecules;"
```

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

### Login

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Authenticates a user and returns an access token. The token is of Bearer type and must be included in the request headers.

```APIDOC
## POST /api/auth/login

### Description
Authenticates a user and returns an access token.

### Method
POST

### Endpoint
/api/auth/login

### Request Body
#### application/json
- **email** (string) - Required
- **password** (string) - Required

### Request Example
```json
{
  "email": "john@example.com",
  "password": "password"
}
```

### Response
#### Success Response (200)
- **access_token** (string) - The authentication token.
- **token_type** (string) - The type of the token (e.g., Bearer).

#### Response Example
```json
{
  "access_token": "string",
  "token_type": "string"
}
```
```

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

### Create Report API Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Use this endpoint to create a new report. It accepts JSON content.

```http
POST /api/reports
```

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

### Molecule Actions Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Launch specific actions related to molecules. The action is specified as a path parameter.

```http
POST /api/molecules/actions/{action}
```

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

### Uninstall COCONUT Application Chart

Source: https://steinbeck-lab.github.io/coconut/local-instance.html

Remove the COCONUT application deployed via Helm.

```bash
helm delete my-coconut-app
```

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

### Login Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Use this endpoint to authenticate and obtain an access token. The token is of Bearer type and must be included in request headers.

```http
POST /api/auth/login
```

```json
{
  "email": "john@example.com",
  "password": "password"
}
```

```json
{
  "access_token": "string",
  "token_type": "string"
}
```

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

### Create Report

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Allows users to create a new report entry in the COCONUT system. This operation requires specific attributes for the molecule being reported.

```APIDOC
## Create Report

### Description
Allows users to create a new report entry in the COCONUT system. This operation requires specific attributes for the molecule being reported.

### Method
POST

### Endpoint
/api/reports

### Parameters
#### Request Body
- **mutate** (array) - Required - An array containing mutation operations.
  - **operation** (string) - Required - Must be "create".
  - **attributes** (object) - Required - Attributes of the new report.
    - **title** (string) - Required - The title of the report.
    - **evidence** (string) - Required - Evidence supporting the report.
    - **comment** (string) - Optional - Additional comments.
    - **suggested_changes** (object) - Optional - Suggested changes or new data.
      - **new_molecule_data** (object) - Required if suggested_changes is present.
        - **canonical_smiles** (string) - Required - The canonical SMILES string of the molecule.
        - **reference_id** (string) - Optional - An identifier for the reference.
        - **name** (string) - Optional - The name of the molecule.
        - **link** (string) - Optional - A URL link to more information.
        - **mol_filename** (string) - Optional - The filename for the molecule structure.
        - **structural_comments** (string) - Optional - Comments about the structure.
        - **references** (array) - Optional - An array of references.
          - **doi** (string) - Required - The Digital Object Identifier for the reference.
          - **organisms** (array) - Optional - Organisms associated with the reference.
            - **name** (string) - Required - The name of the organism.
            - **parts** (array) - Optional - Parts of the organism used.
            - **locations** (array) - Optional - Geographical locations.
              - **name** (string) - Required - The name of the location.
              - **ecosystems** (array) - Optional - Ecosystems of the location.

### Request Example
```json
{
  "mutate": [
    {
      "operation": "create",
      "attributes": {
        "title": "Isolation of Berberine from Berberis vulgaris",
        "evidence": "The compound was isolated from the root bark extract using column chromatography and structure confirmed by NMR and MS analysis.",
        "comment": "This alkaloid has shown significant antimicrobial activity against gram-positive bacteria.",
        "suggested_changes": {
          "new_molecule_data": {
            "canonical_smiles": "COc1ccc2cc3[n+](cc2c1OC)CCc1cc2c(cc1-3)OCO2",
            "reference_id": "ID if it has one",
            "name": "Berberine",
            "link": "https://pubchem.ncbi.nlm.nih.gov/compound/2353",
            "mol_filename": "berberine.mol",
            "structural_comments": "Quaternary isoquinoline alkaloid with a tetracyclic skeleton",
            "references": [
              {
                "doi": "10.1021/np50123a002",
                "organisms": [
                  {
                    "name": "Berberis vulgaris",
                    "parts": ["root", "bark", "rhizome"],
                    "locations": [
                      { "name": "Eastern Europe", "ecosystems": ["temperate forest", "woodland"] },
                      { "name": "Western Asia", "ecosystems": ["mountain slopes", "rocky terrain"] }
                    ]
                  },
                  {
                    "name": "Hydrastis canadensis",
                    "parts": ["rhizome", "roots"],
                    "locations": [
                      { "name": "Eastern North America", "ecosystems": ["deciduous forest", "shaded woodland"] }
                    ]
                  }
                ]
              },
              {
                "doi": "10.1016/j.jep.2019.112124",
                "organisms": [
                  {
                    "name": "Coptis chinensis",
                    "parts": ["rhizome", "roots"],
                    "locations": [
                      { "name": "Southern China", "ecosystems": ["mountain forests", "hillsides"] },
                      { "name": "Eastern Asia", "ecosystems": ["humid forest", "river valleys"] }
                    ]
                  },
                  {
                    "name": "Phellodendron amurense",
                    "parts": ["bark", "stem"],
                    "locations": [{ "name": "Northeast Asia", "ecosystems": ["deciduous forest", "mixed forest"] }]
                  }
                ]
              }
            ]
          }
        }
      },
      "relations": []
    }
  ]
}
```
```

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

### Search Molecules Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Search for molecules using various attributes from the 'molecules' and 'properties' tables. Fields from the 'properties' table require a 'properties.' prefix.

```http
POST /api/molecules/search
```

```json
{
  "search": {
    "scopes": [],
    "filters": [
      {
        "field": "standard_inchi",
        "operator": "=",
        "value": ""
      },
      {
        "field": "standard_inchi_key",
        "operator": "=",
        "value": ""
      },
      {
        "field": "canonical_smiles",
        "operator": "=",
        "value": ""
      },
      {
        "field": "sugar_free_smiles",
        "operator": "=",
        "value": ""
      }
    ]
  }
}
```

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

### Create New Molecule Report

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Use this endpoint to create a new molecule report. Ensure all required fields like title, canonical_smiles, and doi are provided. Only one molecule can be submitted per request.

```json
{
  "mutate": [
    {
      "operation": "create",
      "attributes": {
        "title": "Isolation of Berberine from Berberis vulgaris",
        "evidence": "The compound was isolated from the root bark extract using column chromatography and structure confirmed by NMR and MS analysis.",
        "comment": "This alkaloid has shown significant antimicrobial activity against gram-positive bacteria.",
        "suggested_changes": {
          "new_molecule_data": {
            "canonical_smiles": "COc1ccc2cc3[n+](cc2c1OC)CCc1cc2c(cc1-3)OCO2",
            "reference_id": "ID if it has one",
            "name": "Berberine",
            "link": "https://pubchem.ncbi.nlm.nih.gov/compound/2353",
            "mol_filename": "berberine.mol",
            "structural_comments": "Quaternary isoquinoline alkaloid with a tetracyclic skeleton",
            "references": [
              {
                "doi": "10.1021/np50123a002",
                "organisms": [
                  {
                    "name": "Berberis vulgaris",
                    "parts": ["root", "bark", "rhizome"],
                    "locations": [
                      { "name": "Eastern Europe", "ecosystems": ["temperate forest", "woodland"] },
                      { "name": "Western Asia", "ecosystems": ["mountain slopes", "rocky terrain"] }
                    ]
                  },
                  {
                    "name": "Hydrastis canadensis",
                    "parts": ["rhizome", "roots"],
                    "locations": [
                      { "name": "Eastern North America", "ecosystems": ["deciduous forest", "shaded woodland"] }
                    ]
                  }
                ]
              },
              {
                "doi": "10.1016/j.jep.2019.112124",
                "organisms": [
                  {
                    "name": "Coptis chinensis",
                    "parts": ["rhizome", "roots"],
                    "locations": [
                      { "name": "Southern China", "ecosystems": ["mountain forests", "hillsides"] },
                      { "name": "Eastern Asia", "ecosystems": ["humid forest", "river valleys"] }
                    ]
                  },
                  {
                    "name": "Phellodendron amurense",
                    "parts": ["bark", "stem"],
                    "locations": [{ "name": "Northeast Asia", "ecosystems": ["deciduous forest", "mixed forest"] }]
                  }
                ]
              }
            ]
          }
        }
      },
      "relations": []
    }
  ]
}
```

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

### SQL Query for Search Count

Source: https://steinbeck-lab.github.io/coconut/data.html

This SQL query calculates the molecule count as displayed on search pages, considering active molecules that are not parents.

```sql
SELECT count(*) 
FROM molecules 
WHERE id IN (
   SELECT DISTINCT molecule_id 
   FROM entries 
   WHERE collection_id=55);
  
```

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

### Search Properties

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Search properties based on various attributes.

```APIDOC
## POST /api/properties/search

### Description
Search properties based on various attributes.

### Method
POST

### Endpoint
/api/properties/search

### Parameters
#### Request Body
- **total_atom_count** (integer) - Optional - The total number of atoms.
- **heavy_atom_count** (integer) - Optional - The number of heavy atoms.
- **molecular_weight** (number) - Optional - The molecular weight.
- **exact_molecular_weight** (number) - Optional - The exact molecular weight.
- **molecular_formula** (string) - Optional - The molecular formula.
- **alogp** (number) - Optional - The calculated logP value.
- **topological_polar_surface_area** (number) - Optional - The topological polar surface area.
- **rotatable_bond_count** (integer) - Optional - The number of rotatable bonds.
- **hydrogen_bond_acceptors** (integer) - Optional - The number of hydrogen bond acceptors.
- **hydrogen_bond_donors** (integer) - Optional - The number of hydrogen bond donors.
- **hydrogen_bond_acceptors_lipinski** (integer) - Optional - The number of hydrogen bond acceptors according to Lipinski's rule.
- **hydrogen_bond_donors_lipinski** (integer) - Optional - The number of hydrogen bond donors according to Lipinski's rule.
- **lipinski_rule_of_five_violations** (integer) - Optional - The number of Lipinski's rule of five violations.
- **aromatic_rings_count** (integer) - Optional - The number of aromatic rings.
- **qed_drug_likeliness** (number) - Optional - The Quantitative Estimate of Drug-likeness score.
- **formal_charge** (integer) - Optional - The formal charge of the molecule.
- **fractioncsp3** (number) - Optional - The fraction of sp3 hybridized carbons.
- **number_of_minimal_rings** (integer) - Optional - The number of minimal rings.
- **van_der_walls_volume** (number) - Optional - The van der Waals volume.
```

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

### Search Collections

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Search Collections using various attributes like title, description, identifier, and URL.

```APIDOC
## POST /api/collections/search

### Description
Search Collections using various attributes.

### Method
POST

### Endpoint
/api/collections/search

### Parameters
#### Request Body
- **title** (string) - Optional - The title of the collection.
- **description** (string) - Optional - The description of the collection.
- **identifier** (string) - Optional - The identifier of the collection.
- **url** (string) - Optional - The URL of the collection.
```

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

### Logout

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Logs out the currently authenticated user.

```APIDOC
## GET /api/auth/logout

### Description
Logs out the currently authenticated user.

### Method
GET

### Endpoint
/api/auth/logout

### Response
#### Success Response (200)
- **logout** (string) - A message indicating the logout status.

#### Response Example
```json
{
  "logout": "string"
}
```
```

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

### Search Organisms

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Search Organisms using various attributes like name, IRI, rank, and molecule count.

```APIDOC
## POST /api/organisms/search

### Description
Search Organisms using various attributes.

### Method
POST

### Endpoint
/api/organisms/search

### Parameters
#### Request Body
- **name** (string) - Optional - The name of the organism.
- **iri** (string) - Optional - The Internationalized Resource Identifier.
- **rank** (string) - Optional - The taxonomic rank.
- **molecule_count** (integer) - Optional - The number of molecules associated with the organism.
```

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

### Search Molecules

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Searches for molecules using various attributes from the 'molecules' and 'properties' tables. Searchable fields include InChI, SMILES, CAS, molecular weight, and more.

```APIDOC
## POST /api/molecules/search

### Description
Searches for molecules using various attributes from the 'molecules' and 'properties' tables.

### Method
POST

### Endpoint
/api/molecules/search

### Request Body
#### application/json
- **search** (object) - Required
  - **scopes** (array) - Optional. An array of scopes for the search.
  - **filters** (array) - Required. An array of filter objects.
    - **field** (string) - Required. The field to filter on (e.g., 'standard_inchi', 'properties.molecular_weight').
    - **operator** (string) - Required. The comparison operator (e.g., '=', '>', '<').
    - **value** (any) - Required. The value to compare against.

### Request Example
```json
{
  "search": {
    "scopes": [],
    "filters": [
      {
        "field": "standard_inchi",
        "operator": "=",
        "value": ""
      },
      {
        "field": "standard_inchi_key",
        "operator": "=",
        "value": ""
      },
      {
        "field": "canonical_smiles",
        "operator": "=",
        "value": ""
      },
      {
        "field": "sugar_free_smiles",
        "operator": "=",
        "value": ""
      }
    ]
  }
}
```
```

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

### Search Collections API Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Use this endpoint to search for collections using attributes like title, description, identifier, and URL.

```http
POST /api/collections/search
```

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

### Search Reports

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Search for reports with various filtering, sorting, and pagination options.

```APIDOC
## POST /api/reports/search

### Description
Search for reports with various filtering, sorting, and pagination options.

### Method
POST

### Endpoint
/api/reports/search

### Parameters
#### Request Body
- **search** (object) - Required - Object containing search criteria.
  - **filters** (array) - Optional - Array of filter objects.
    - **field** (string) - Required - The field to filter on.
    - **operator** (string) - Required - The comparison operator (e.g., 'like').
    - **value** (string) - Required - The value to filter by.
  - **sorts** (array) - Optional - Array of sort objects.
    - **field** (string) - Required - The field to sort by.
    - **direction** (string) - Required - The sort direction ('asc' or 'desc').
  - **page** (integer) - Optional - The page number for pagination.
  - **limit** (integer) - Optional - The number of results per page.
```

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

### Search Organisms API Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Search for organisms using attributes like name, IRI, rank, and molecule count.

```http
POST /api/organisms/search
```

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

### Search Properties API Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Search for properties based on various attributes including atom counts, molecular weight, and drug-likeness scores.

```http
POST /api/properties/search
```

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

### Search Citations API Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Search for citations using attributes such as DOI, title, and authors.

```http
POST /api/citations/search
```

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

### Search Citations

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Search Citations using various attributes like DOI, title, authors, and citation text.

```APIDOC
## POST /api/citations/search

### Description
Search Citations using various attributes.

### Method
POST

### Endpoint
/api/citations/search

### Parameters
#### Request Body
- **doi** (string) - Optional - The Digital Object Identifier.
- **title** (string) - Optional - The title of the citation.
- **authors** (string) - Optional - The authors of the citation.
- **citation_text** (string) - Optional - The text of the citation.
```

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

### Logout Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Use this endpoint to log out from the API. No request body is required.

```http
GET /api/auth/logout
```

```json
{
  "logout": "string"
}
```

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

### Search Reports API Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Search for reports with filtering, sorting, and pagination options.

```http
POST /api/reports/search
```

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

### Update Existing Report

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

This endpoint allows for updating an existing report using its ID. Note that this operation requires special access privileges and is typically performed by the Scientific Advisory Board.

```json
{
    "mutate": [
        {
            "operation": "update",
            "key": 43,
            "attributes": {"title": "new name"}
        }
    ]
}
```

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

### Mutate Organisms API Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

This endpoint is for updating organism details. It requires special access privileges and is not available to general users.

```http
POST /api/organisms/mutate
```

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

### Delete Reports

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Use this endpoint to permanently delete one or more reports by providing their IDs in a list. This action is restricted and requires special access privileges.

```json
{
  "resources": [
    42,
    43
  ]
}
```

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

### Mutate Collections API Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

This endpoint is for updating collection details. It requires special access privileges and is not available to general users.

```http
POST /api/collections/mutate
```

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

### Mutate Properties API Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

This endpoint is for updating molecule properties. It requires special access privileges and is not available to general users.

```http
POST /api/properties/mutate
```

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

### Mutate Citations API Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

This endpoint is for updating citation details. It requires special access privileges and is not available to general users.

```http
POST /api/citations/mutate
```

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

### Mutate Molecules Endpoint

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Update molecule properties. This endpoint requires special access privileges and is restricted to authorized users.

```http
POST /api/molecules/mutate
```

```json
{
  "mutate": [
    {
      "operation": "create",
      "attributes": {
        "standard_inchi": "",
        "standard_inchi_key": "",
        "canonical_smiles": "",
        "sugar_free_smiles": "",
        "identifier": "",
        "name": "",
        "cas": "",
        "iupac_name": "",
        "murko_framework": "",
        "structural_comments": "",
        "name_trust_level": "",
        "annotation_level": "",
        "variants_count": "",
        "status": "",
        "active": "",
        "has_variants": "",
        "has_stereo": "",
        "is_tautomer": "",
        "is_parent": ""
      }
    }
  ]
}
```

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

### Mutate Molecules

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Updates molecule properties. This endpoint is restricted and requires special access privileges.

```APIDOC
## POST /api/molecules/mutate

### Description
Updates molecule properties. This operation is restricted and requires special access privileges.

### Method
POST

### Endpoint
/api/molecules/mutate

### Request Body
#### application/json
- **mutate** (array) - Required. An array of mutation operations.
  - **operation** (string) - Required. The type of operation (e.g., 'create').
  - **attributes** (object) - Required. The attributes to mutate.

### Request Example
```json
{
  "mutate": [
    {
      "operation": "create",
      "attributes": {
        "standard_inchi": "",
        "standard_inchi_key": "",
        "canonical_smiles": "",
        "sugar_free_smiles": "",
        "identifier": "",
        "name": "",
        "cas": "",
        "iupac_name": "",
        "murko_framework": "",
        "structural_comments": "",
        "name_trust_level": "",
        "annotation_level": "",
        "variants_count": "",
        "status": "",
        "active": "",
        "has_variants": "",
        "has_stereo": "",
        "is_tautomer": "",
        "is_parent": ""
      }
    }
  ]
}
```
```

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

### Update Report

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Updates an existing report identified by its ID. This operation is restricted and requires special access privileges.

```APIDOC
## Update Report

### Description
Updates an existing report identified by its ID. This operation is restricted and requires special access privileges.

### Method
PATCH

### Endpoint
/api/reports/{id}

### Parameters
#### Path Parameters
- **id** (integer) - Required - The ID of the report to update.

#### Request Body
- **mutate** (array) - Required - An array containing mutation operations.
  - **operation** (string) - Required - Must be "update".
  - **key** (integer) - Required - The key (ID) of the report to update.
  - **attributes** (object) - Required - The attributes to update.
    - **title** (string) - Optional - The new title for the report.

### Request Example
```json
{
    "mutate": [
        {
            "operation": "update",
            "key": 43,
            "attributes": {"title": "new name"}
        }
    ]
}
```
```

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

### Delete Report

Source: https://steinbeck-lab.github.io/coconut/api-documentation.html

Permanently deletes one or more reports identified by their IDs. This operation is restricted and requires special access privileges.

```APIDOC
## Delete Report

### Description
Permanently deletes one or more reports identified by their IDs. This operation is restricted and requires special access privileges.

### Method
DELETE

### Endpoint
/api/reports

### Parameters
#### Request Body
- **resources** (array) - Required - An array of report IDs to delete.
  - (integer) - Required - The ID of a report to delete.

### Request Example
```json
{
  "resources": [
    42,
    43
  ]
}
```
```
Tokens:
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