### Local Development Setup

Source: https://github.com/quartzbio/quartzbio-python/blob/main/README.md

Set up the quartzbio-python project for local development by cloning the repository and installing it in develop mode.

```bash
git clone https://github.com/quartzbio/quartzbio-python.git
cd quartzbio-python/
python setup.py develop
```

```bash
pip install -e .
```

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

### Install Libraries

Source: https://github.com/quartzbio/quartzbio-python/blob/main/examples/Python_Template.ipynb

Installs the quartzbio and plotly libraries. Run this cell before proceeding.

```python
!pip install quartzbio
!pip install plotly
```

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

### Install QuartzBio from Git

Source: https://github.com/quartzbio/quartzbio-python/blob/main/README.md

Install the quartzbio package directly from its GitHub repository using pip.

```bash
pip install -e git+https://github.com/quartzbio/quartzbio-python.git#egg=quartzbio
```

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

### Install QuartzBio Python Client

Source: https://github.com/quartzbio/quartzbio-python/blob/main/README.md

Install the quartzbio package using pip. For interactive use, also install IPython and gnureadline.

```bash
pip install quartzbio
```

```bash
pip install ipython
```

```bash
pip install gnureadline
```

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

### Install QuartzBio Python Client

Source: https://github.com/quartzbio/quartzbio-python/blob/main/CLAUDE.md

Clone the repository and install the client in development mode using pip. This command is useful for setting up the project for local development.

```bash
git clone https://github.com/quartzbio/quartzbio-python.git
cd quartzbio-python/
pip install -e .
```

```bash
python -m venv .venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate
pip install -e .
```

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

### Install QuartzBio Python Library

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/authentication.md.txt

Install or upgrade the QuartzBio Python package using pip. Ensure you are using a compatible Python version.

```bash
pip install --upgrade quartzbio
```

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

### Example Output: Commit Object

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/metadata_and_global_beacons.md.txt

This is an example of the output structure for a commit object, showing its properties and current status.

```python
{
'id': 125,
'datastore_id': 6,
'dataset_id': 1658666726768179211,
'status': 'destroying',
'progress_percent': 0,
'is_deleted': False
}
```

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

### Query String Syntax Examples

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/filters.html

Examples of Lucene-based query strings for field-specific searches, wildcards, and existence checks.

```text
status:active
gene:"BRCA1"
gene:(TTN)
gene:(TTN OR BRCA1)
gene_family:(Olfactory AND receptors)
_missing_:sample_id
_exists_:sample_id
BRCA*
```

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

### Creating a New Dataset with Fields

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/creating_and_migrating_datasets.html

Example demonstrating how to create a new dataset with predefined fields.

```APIDOC
## POST /api/datasets

### Description
Creates a new dataset with specified fields and capacity.

### Method
POST

### Endpoint
`/api/datasets`

### Parameters
#### Request Body
- **fields** (list of objects) - Required - A list of dictionaries, where each dictionary defines a dataset field with properties like 'name', 'description', 'data_type', 'is_list', 'is_hidden', and 'ordering'.
- **capacity** (string) - Optional - The capacity setting for the dataset (e.g., 'small').

### Request Example
```json
{
  "fields": [
    {
      "name": "my_string_field",
      "description": "Just a string",
      "data_type": "string",
      "is_list": false,
      "is_hidden": false,
      "ordering": 0
    },
    {
      "name": "gene_symbol",
      "description": "HUGO gene symbol",
      "data_type": "string",
      "entity_type": "gene"
    }
  ],
  "capacity": "small"
}
```

### Response
#### Success Response (200)
- **dataset_id** (string) - The unique identifier of the created dataset.
- **message** (string) - Confirmation message.

#### Response Example
```json
{
  "dataset_id": "some_dataset_id",
  "message": "Dataset created successfully."
}
```
```

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

### Run Tests with Tox

Source: https://github.com/quartzbio/quartzbio-python/blob/main/README.md

Install tox and run tests for the project. This is useful for ensuring code quality and compatibility.

```bash
pip install tox
tox
```

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

### Example Output Dictionary

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/metadata_and_global_beacons.md

Represents the structure of the returned object from the QuartzBio Python project.

```python
{'id': 125,
'datastore_id': 6,
'dataset_id': 1658666726768179211,
'status': 'destroying',
'progress_percent': 0,
'is_deleted': False}
```

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

### Get or Create Dataset

Source: https://context7.com/quartzbio/quartzbio-python/llms.txt

Retrieves a dataset by its full path, creating it if it does not already exist.

```python
# Get or create a dataset (creates if not exists)
dataset = Dataset.get_or_create_by_full_path("~/my-project/analysis-results")
```

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

### String Expression Example

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/expressions.md.txt

Illustrates a basic string concatenation expression.

```Python
# String expression
"hello" + " world"
# output: "hello world"
```

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

### JSONL File Format Example

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/import_parameters.md.txt

Illustrates the structure of a JSON Lines file, where each line is a complete JSON object.

```json
{"field": 1}
{"field": 2}
{"field": 3}
```

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

### Define Dataset Paths

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/creating_and_migrating_datasets.md

Examples of path formats for identifying datasets within domains, vaults, and folders.

```default
<domain>:<vault>:<path>
```

```default
myDomain:MyVault:/folder/dataset
```

```default
~/folder/dataset
```

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

### QuartzBio CLI Interactive Shell

Source: https://context7.com/quartzbio/quartzbio-python/llms.txt

Command to start an interactive shell session with QuartzBio.

```bash
quartzbio shell
```

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

### Query a dataset

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/expression_functions.md.txt

Syntax and examples for querying datasets with optional filters, fields, and entity constraints.

```text
dataset_query(dataset, fields, limit, entities, filters, query)
```

```text
dataset_query("quartzbio:public:/ClinVar/5.1.0-20200720/Variants-GRCh38", fields=["clinical_significance"], query="*cancer*")
```

```text
dataset_query("quartzbio:public:/ClinVar/5.1.0-20200720/Variants-GRCh38", entities=[["variant", "GRCH38-13-32357842-32357842-TA"]])
```

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

### Configure CLI Entry Point

Source: https://github.com/quartzbio/quartzbio-python/blob/main/CLAUDE.md

Register the console script in the setup.py file.

```python
entry_points={
    'console_scripts': ['quartzbio = quartzbio.cli.main:main']
}
```

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

### Importing QuartzBio Library and Logging In

Source: https://github.com/quartzbio/quartzbio-python/blob/main/examples/global_search.ipynb

Demonstrates how to import the necessary QuartzBio modules and log in to the EDP environment.

```APIDOC
## Importing QuartzBio library and logging in

### Description
Import the `login`, `Filter`, and `GlobalSearch` classes from the `quartzbio` library and authenticate with the EDP.

### Code Example

```python
# Importing quartzbio library
from quartzbio import login
from quartzbio import Filter
from quartzbio import GlobalSearch

# Logging to EDP
login()
```
```

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

### Example XML Document Structure

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/import_parameters.md.txt

A sample XML document used to demonstrate how item_depth affects record enumeration during import.

```xml
<xml>
    <library>
        <shelf>
            <book lang="eng">
                <title>EDP Docs, 3rd Edition</title>
                <publish_date></publish_date>
                <summary></summary>
            </book>
            <book lang="eng">
                <title></title>
                <publish_date></publish_date>
                <summary></summary>
            </book>
        </shelf>
        <shelf>
            <book>
                <title></title>
            </book>
        </shelf>
    </library>
</xml>
```

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

### UploadProgressTracker Get Average Speed

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/genindex.html

Gets the average upload speed from the tracker.

```APIDOC
## UploadProgressTracker Get Average Speed

### Description
Calculates and returns the average upload speed recorded by the tracker.

### Method
GET

### Endpoint
/quartzbio.resource.object.UploadProgressTracker.get_average_speed

### Parameters
None

### Response
#### Success Response (200)
- **average_speed** (float) - The average upload speed in bytes per second.

#### Response Example
```json
{
  "average_speed": 102400.5
}
```
```

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

### Adding Fields to an Existing Dataset

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/creating_and_migrating_datasets.html

Example showing how to add a new field to a dataset that already exists.

```APIDOC
## POST /api/datasets/{dataset_id}/fields

### Description
Adds a new field to an existing dataset.

### Method
POST

### Endpoint
`/api/datasets/{dataset_id}/fields`

### Parameters
#### Path Parameters
- **dataset_id** (string) - Required - The ID of the dataset to which the field will be added.

#### Request Body
- **name** (string) - Required - The name of the new field.
- **data_type** (string) - Required - The data type of the new field (e.g., 'string').

### Request Example
```json
{
  "dataset_id": "existing_dataset_id",
  "name": "my_new_field",
  "data_type": "string"
}
```

### Response
#### Success Response (200)
- **field_id** (string) - The unique identifier of the newly created field.
- **message** (string) - Confirmation message.

#### Response Example
```json
{
  "field_id": "new_field_id",
  "message": "Field added successfully."
}
```
```

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

### QuartzBio Client Initialization

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/modules.html

Demonstrates how to initialize the QuartzBio client to interact with the API.

```APIDOC
## QuartzBio Python Client

### Description
The QuartzBio Python client provides an interface to interact with the QuartzBio API for various bioinformatics tasks.

### Usage
```python
from quartzbio.client import QuartzBioClient

# Initialize the client
client = QuartzBioClient(api_key='YOUR_API_KEY')
```
```

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

### Flattening Algorithm Example

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/exporting_data.md.txt

Illustrates how list fields in JSON records are expanded into multiple columns during CSV/XLSX export.

```Python
{"a": "a", "b": ["x"]}
{"a": "a", "b": ["x", "y"]}
{"a": "a", "b": ["x", "y", "z"]}
```

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

### View import help

Source: https://github.com/quartzbio/quartzbio-python/blob/main/examples/import/README.md

Displays all available command line arguments for the import command.

```bash
quartzbio import -h
```

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

### Get the Count of Subjects for an Entity Search

Source: https://github.com/quartzbio/quartzbio-python/blob/main/examples/global_search.ipynb

To get the number of subjects associated with an entity search, use the .subjects_count() method. This returns an integer count.

```python
# Subjects count
search.subjects_count()
```

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

### Query Facets Examples

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/quartzbio.md

Demonstrates how to request facets for specific fields using string arguments or keyword arguments with configuration options.

```python
q.facets(‘field_1’, ‘field_2’)
```

```python
q.facets(field_1={‘limit’: 0}, field_2={‘limit’: 10})
```

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

### Define Dataset Template Fields

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/dataset_templates.md.txt

Example structure for defining fields within a dataset template. Each field includes properties like name, title, data type, and optional dependencies or expressions. Note the comma placement in the example.

```Python
fields = [{
    "name": "reason",
    "title": "Reason"
    "description": "The reasons for the significance value",
    "data_type": "string",
    "depends_on": [
        "reason_list"
    ],
    "expression": ", ".join(record.reason_list) if record.reason_list else None",
    "ordering": 1
},{...}]
```

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

### Querying Datasets with Python

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/querying_datasets_and_files.html

Examples demonstrating how to limit results, order by single or multiple columns, and handle ascending or descending sort orders.

```python
# Users can set how many records they want to retrieve with the "limit" parameter
Dataset.get_by_full_path('quartzbio:Public:/ClinVar/5.2.0-20210110/Variants-GRCH37').query(limit=1000)

# Users can order query results using the ordering argument

# Order the query results by clinical_significance ascending
Dataset.get_by_full_path('quartzbio:Public:/ClinVar/5.2.0-20210110/Variants-GRCH37').query(ordering='clinical_significance')

# Order the query results by clinical_significance descending
Dataset.get_by_full_path('quartzbio:Public:/ClinVar/5.2.0-20210110/Variants-GRCH37').query(ordering='-clinical_significance')

# Query results can be ordered by multiple columns

# Order the query results by clinical_significance descending and gene_symbol ascending
Dataset.get_by_full_path('quartzbio:Public:/ClinVar/5.2.0-20210110/Variants-GRCH37').query(ordering=['-clinical_significance', 'gene'])
```

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

### GET /beacons

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/quartzbio.resource.beacon.md

Lists available Beacon resources.

```APIDOC
## GET /beacons

### Description
Retrieves a list of Beacon resources.

### Method
GET

### Endpoint
/beacons

### Response
- **id** (string) - ID
- **title** (string) - Title
- **description** (string) - Description
- **vault_object_id** (string) - Object ID
```

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

### Run QuartzBio Tests

Source: https://github.com/quartzbio/quartzbio-python/blob/main/CLAUDE.md

Execute all tests using setup.py or make commands. Specific test modules can be run using make targets or by directly invoking the unittest module. Ensure API credentials are set as environment variables.

```bash
python setup.py test
```

```bash
make check
```

```bash
make test-sample              # Runs quartzbio.test.test_sample
```

```bash
make test-dataset             # Runs quartzbio.test.test_dataset
```

```bash
python -m unittest quartzbio.test.test_query
```

```bash
pip install tox
tox
```

```bash
export QUARTZBIO_API_HOST=https://api.quartzbio.com
export QUARTZBIO_ACCESS_TOKEN=your_token_here
```

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

### QuartzBioClient Get

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/genindex.html

Retrieves a resource using the QuartzBio client.

```APIDOC
## QuartzBioClient Get

### Description
Fetches a specific resource using the QuartzBio client.

### Method
GET

### Endpoint
/quartzbio.client.QuartzBioClient.get
/quartzbio.QuartzBioClient.get

### Parameters
#### Query Parameters
- **resource_id** (string) - Required - The unique identifier of the resource to retrieve.

### Response
#### Success Response (200)
- **resource** (object) - The retrieved resource object.

#### Response Example
```json
{
  "resource": {
    "id": "resource_123",
    "name": "Example Resource"
  }
}
```
```

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

### Initialize QuartzBio and Plotly

Source: https://github.com/quartzbio/quartzbio-python/blob/main/examples/generating_icgc_survival_curves.ipynb

Imports necessary modules and authenticates the session with EDP credentials.

```python
from quartzbio import login, Dataset, Filter
import plotly.plotly as py
import plotly.tools as tls
from plotly.graph_objs import *

# Load local EDP credentials
login()
```

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

### GET /v2/datasets/{DATASET_ID}

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/creating_and_migrating_datasets.html

Retrieve metadata about a specific dataset.

```APIDOC
## GET /v2/datasets/{DATASET_ID}

### Description
Retrieve metadata about a dataset. This request requires an authorized user with permission to view the target dataset.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/datasets/{DATASET_ID}

### Parameters
#### Path Parameters
- **DATASET_ID** (integer) - Required - The unique identifier of the dataset.

### Response
#### Success Response (200)
- **Dataset** (object) - The requested Dataset resource.
```

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

### Import data via command line

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/importing_data.md.txt

Use the quartzbio CLI to import files with options for dataset creation and commit modes.

```bash
# Import a file (create the dataset if necessary):
quartzbio import --create-dataset --follow ~/test-dataset data.vcf.gz

# Import files in upsert mode (create the dataset from a template if necessary):
quartzbio import --create-dataset --template-file template.json --commit-mode=upsert --follow ~/test-dataset data.vcf.gz
```

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

### GET /v2/vaults/{ID}

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/vaults_and_objects.md.txt

Retrieve the metadata for a specific vault.

```APIDOC
## GET https://<EDP_API_HOST>/v2/vaults/{ID}

### Description
Retrieve a vault's metadata. This request requires an authorized user with "read" permission or higher on the vault.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/vaults/{ID}

### Parameters
#### Path Parameters
- **ID** (string) - Required - The unique identifier of the vault.

### Response
#### Success Response (200)
- **vault** (object) - The Vault resource.
```

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

### GET /v2/vaults

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/vaults_and_objects.md.txt

List all available vaults accessible to the user.

```APIDOC
## GET https://<EDP_API_HOST>/v2/vaults

### Description
List all available vaults. All public vaults are included in this response. If the request is sent by an authenticated user, vaults which the user has "read" permission or higher on are also returned.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/vaults

### Response
#### Success Response (200)
- **vaults** (array) - A list of vaults matching the provided filters.
```

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

### Launch QuartzBio IPython Shell (General)

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/quartzbio.cli.ipython.md

Launches the QuartzBio shell, a general wrapper for IPython.

```APIDOC
## quartzbio.cli.ipython.launch_ipython_shell(args)

### Description
Open the QuartzBio shell (IPython wrapper)

### Method
Not applicable (Python function call)

### Endpoint
Not applicable (Python function call)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```python
quartzbio.cli.ipython.launch_ipython_shell(args)
```

### Response
None (Launches an interactive shell)
```

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

### GET /v2/dataset_restore_tasks

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/dataset_versioning.html

Lists all available dataset restore tasks.

```APIDOC
## GET /v2/dataset_restore_tasks

### Description
Retrieve a list of available dataset restore tasks.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/dataset_restore_tasks

### Response
#### Success Response (200)
- **list** (array) - A list of DatasetRestoreTask resources.
```

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

### Function: main()

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/quartzbio.cli.main.md

The primary entry point for the QuartzBio CLI application.

```APIDOC
## Function: main()

### Description
Main entry point for the QuartzBio CLI application.
```

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

### GET /v2/dataset_templates

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/dataset_templates.md.txt

Retrieves a list of available dataset templates.

```APIDOC
## GET /v2/dataset_templates

### Description
Retrieve a list of available dataset templates.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/dataset_templates

### Parameters
#### Query Parameters
- **limit** (integer) - Optional - The number of objects to return per page.
- **offset** (integer) - Optional - The offset within the list of available objects.

### Response
#### Success Response (200)
- **list** (array) - A list of resources visible to the requesting user.
```

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

### GET /v2/saved_queries

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/querying_datasets_and_files.md

List all Saved Queries available to the authenticated user.

```APIDOC
## GET /v2/saved_queries

### Description
Retrieves all Saved Queries available to the current user.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/saved_queries

### Response
#### Success Response (200)
- **SavedQueries** (array) - A list of SavedQuery resources.
```

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

### Build Documentation Locally

Source: https://github.com/quartzbio/quartzbio-python/blob/main/README.md

Build the project documentation locally using Sphinx and Sphinx Autobuild. This allows you to preview the documentation before deploying.

```bash
make sphinx-autobuild
```

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

### Running the Streamlit Demo App

Source: https://github.com/quartzbio/quartzbio-python/blob/main/quartzbio/contrib/streamlit/README.md

Execute the secured Streamlit application using the command line interface.

```bash
streamlit run app.py
```

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

### GET /v2/saved_queries/{ID}

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/querying_datasets_and_files.md

Retrieve a specific Saved Query by its ID.

```APIDOC
## GET /v2/saved_queries/{ID}

### Description
Retrieve a Saved Query resource by its unique identifier.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/saved_queries/{ID}

### Parameters
#### Path Parameters
- **ID** (string) - Required - The unique identifier of the saved query.

### Response
#### Success Response (200)
- **SavedQuery** (object) - The SavedQuery resource.
```

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

### GET /v2/dataset_fields/{ID}

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/creating_and_migrating_datasets.md

Retrieve a specific dataset field by its ID.

```APIDOC
## GET /v2/dataset_fields/{ID}

### Description
Retrieve a dataset field. This request requires an authorized user with read permission on the dataset.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/dataset_fields/{ID}

### Parameters
#### Path Parameters
- **ID** (string) - Required - The unique identifier of the dataset field.

### Response
#### Success Response (200)
- **DatasetField** (object) - The requested DatasetField resource.
```

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

### Manage QuartzBio Documentation

Source: https://github.com/quartzbio/quartzbio-python/blob/main/CLAUDE.md

Commands to build, serve, and generate documentation for the QuartzBio project. Use 'make sphinx-autobuild' for local development with live reloading.

```bash
make sphinx-autobuild
# Build and serve docs locally (http://localhost:8080)
```

```bash
make sphinx-apidoc
```

```bash
make sphinx-build
```

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

### Importing Quartzbio Library

Source: https://github.com/quartzbio/quartzbio-python/blob/main/examples/global_search.ipynb

Initializes the necessary modules for interacting with the Quartzbio API.

```python
# Importing quartzbio library
from quartzbio import login
from quartzbio import Filter
from quartzbio import GlobalSearch
```

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

### GET /v2/vaults

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/vaults_and_objects.html

List all available vaults accessible to the authenticated user.

```APIDOC
## GET /v2/vaults

### Description
List all available vaults. All public vaults are included in this response. If the request is sent by an authenticated user, vaults which the user has “read” permission or higher on are also returned.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/vaults

### Response
#### Success Response (200)
- **vaults** (array) - A list of vaults matching the provided filters.
```

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

### Get Dataset Import

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/import_parameters.md

Retrieves details of a specific dataset import.

```APIDOC
## GET /v2/dataset_imports/{ID}

### Description
Retrieves the details of a specific dataset import.

### Method
GET

### Endpoint
`/<EDP_API_HOST>/v2/dataset_imports/{ID}`

### Parameters
#### Path Parameters
- **ID** (string) - Required - The unique identifier of the dataset import to retrieve.

### Authorization
This request requires an authorized user with write permissions on the dataset.

### Response
#### Success Response (200)
- **details** (object) - Contains the details of the dataset import. The response returns “HTTP 200 OK” when successful.

#### Response Example
```json
{
  "message": "HTTP 200 OK"
}
```
```

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

### Build Dash Auth JS Components

Source: https://github.com/quartzbio/quartzbio-python/blob/main/quartzbio/contrib/dash/js/README.md

Run these commands to build the Dash Auth JavaScript components. Ensure you have Node.js and Yarn installed.

```bash
yarn
```

```bash
yarn run build
```

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

### QuartzBioClient Initialization

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/quartzbio.client.md

Initializes the QuartzBio API client with host and token information.

```APIDOC
## quartzbio.client.QuartzBioClient

### Description
A requests-based HTTP client for QuartzBio API resources.

### Parameters
- **host** (str) - Optional - The host URL for the API.
- **token** (str) - Optional - The authentication token.
- **token_type** (Literal['Bearer', 'Token']) - Optional - The type of token, defaults to 'Bearer'.
- **include_resources** (bool) - Optional - Whether to include resources, defaults to True.
- **retry_all** (bool) - Optional - Whether to retry all requests.
```

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

### Dataset Get By Full Path

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/genindex.html

Retrieves a Dataset by its full path.

```APIDOC
## Dataset Get By Full Path

### Description
Retrieves a Dataset object using its complete path.

### Method
GET

### Endpoint
/quartzbio.Dataset.get_by_full_path
/quartzbio.Object.get_by_full_path

### Parameters
#### Query Parameters
- **full_path** (string) - Required - The full path to the dataset.

### Response
#### Success Response (200)
- **dataset** (Dataset) - The retrieved Dataset object.

#### Response Example
```json
{
  "dataset": {
    "id": "dataset_abc",
    "name": "MyDataset"
  }
}
```
```

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

### Create Dataset Template with Fields

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/dataset_templates.html

Example of preparing a list of DatasetField objects to create a new template. Includes required and optional attributes for data transformation.

```python
fields = [
    {
    'name': 'sample',
    "depends_on": ['subject'],
    "entity_type": "sample",
    'description': 'Sample ID from SUBJECT',
    'data_type': 'string',
    'ordering': 1 ,
    'expression': "record.subject"},{
    'name': 'study',
    'title': 'STUDY',
    'description': 'Study Code',
    'ordering': 2 ,
    'expression': "None if value == 'UNASSIGNED' else value",
    'data_type': 'string'},{
    "data_type": "string",
    "depends_on": [
        "hgvs_c"
    ],
    "description": "EDP variant entity, computed from the short variant CDS change",
    "expression": "entity_ids('variant', record.hgvs_c) if record.hgvs_c else None",
    "is_transient": True,
    "name": "variant_cdna_grch38"
}
]
```

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

### GET /user

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/expression_functions.html

Retrieves the profile information for the currently authenticated user.

```APIDOC
## GET /user

### Description
Returns the currently authenticated user's profile information.

### Method
GET

### Endpoint
/user

### Response
#### Success Response (200)
- **name** (string) - The user’s full name.
- **email** (string) - The user’s email address.
```

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

### Launch QuartzBio IPython Shell (IPython 5+)

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/quartzbio.cli.ipython.md

Launches the QuartzBio shell using IPython version 5 or newer.

```APIDOC
## quartzbio.cli.ipython.launch_ipython_5_shell(args)

### Description
Open the QuartzBio shell (IPython wrapper) with IPython 5+

### Method
Not applicable (Python function call)

### Endpoint
Not applicable (Python function call)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```python
quartzbio.cli.ipython.launch_ipython_5_shell(args)
```

### Response
None (Launches an interactive shell)
```

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

### GET /v2/dataset_commits/{ID}

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/dataset_versioning.html

Retrieves metadata for a specific dataset commit.

```APIDOC
## GET /v2/dataset_commits/{ID}

### Description
Retrieve metadata about a dataset commit.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/dataset_commits/{ID}

### Parameters
#### Path Parameters
- **ID** (string) - Required - The unique identifier of the dataset commit.

### Response
#### Success Response (200)
- **DatasetCommit** (object) - The resource containing metadata about the commit.
```

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

### GET /v2/dataset_templates/{ID}

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/dataset_templates.md.txt

Retrieves a specific dataset template by its ID.

```APIDOC
## GET /v2/dataset_templates/{ID}

### Description
Retrieve a dataset template.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/dataset_templates/{ID}

### Parameters
#### Path Parameters
- **ID** (string) - Required - The unique identifier of the template.

### Response
#### Success Response (200)
- **DatasetTemplate** (object) - The requested DatasetTemplate resource.
```

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

### quartzbio.cli Package Overview

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/quartzbio.cli.rst.txt

Overview of the available submodules within the quartzbio.cli package.

```APIDOC
## quartzbio.cli Package

### Description
The quartzbio.cli package provides the command-line interface tools for the QuartzBio platform. It includes modules for handling user authentication, managing credentials, interacting with data, and initializing IPython environments.

### Submodules
- **quartzbio.cli.auth**: Handles user authentication processes.
- **quartzbio.cli.credentials**: Manages user credentials and configuration.
- **quartzbio.cli.data**: Provides commands for data manipulation and retrieval.
- **quartzbio.cli.ipython**: Integration for IPython environments.
- **quartzbio.cli.ipython_init**: Initialization scripts for IPython.
- **quartzbio.cli.main**: The main entry point for the CLI application.
- **quartzbio.cli.tutorial**: Contains tutorial and onboarding command logic.
```

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

### Import Data using Command Line

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/importing_data.html

Import data files using the quartzbio import command. Supports creating datasets and specifying commit modes.

```bash
quartzbio import --create-dataset --follow ~/test-dataset data.vcf.gz
```

```bash
quartzbio import --create-dataset --template-file template.json --commit-mode=upsert --follow ~/test-dataset data.vcf.gz
```

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

### GET /v2/dataset_snapshot_tasks

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/dataset_versioning.md.txt

Retrieves a list of all available dataset snapshot tasks.

```APIDOC
## GET /v2/dataset_snapshot_tasks

### Description
Retrieve a list of available dataset snapshot tasks.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/dataset_snapshot_tasks

### Response
#### Success Response (200)
- **List** (array) - The response contains a list of DatasetSnapshotTask resources.
```

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

### Upload Files using Command Line

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/importing_data.html

Upload local folders to the personal vault using the quartzbio upload command. Only missing files and folders are uploaded.

```bash
quartzbio upload ./local_folder
```

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

### GET /v2/dataset_exports/{ID}

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/exporting_data.md.txt

Retrieve metadata about a specific dataset export.

```APIDOC
## GET /v2/dataset_exports/{ID}

### Description
Retrieve metadata about an export.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/dataset_exports/{ID}

### Parameters
#### Path Parameters
- **ID** (string) - Required - The unique identifier of the export.

### Response
#### Success Response (200)
- **DatasetExport** (object) - The DatasetExport resource.
```

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

### GET /v2/dataset_imports/{ID}

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/import_parameters.md.txt

Retrieves details for a specific dataset import.

```APIDOC
## GET /v2/dataset_imports/{ID}

### Description
Retrieves details for a specific dataset import.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/dataset_imports/{ID}

### Parameters
#### Path Parameters
- **ID** (string) - Required - The unique identifier of the dataset import.

### Response
#### Success Response (200)
- **Status** - HTTP 200 OK
```

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

### Launch QuartzBio IPython Shell (Legacy)

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/quartzbio.cli.ipython.md

Launches the QuartzBio shell for older IPython versions.

```APIDOC
## quartzbio.cli.ipython.launch_ipython_legacy_shell(args)

### Description
Open the QuartzBio shell (IPython wrapper) for older IPython versions

### Method
Not applicable (Python function call)

### Endpoint
Not applicable (Python function call)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```python
quartzbio.cli.ipython.launch_ipython_legacy_shell(args)
```

### Response
None (Launches an interactive shell)
```

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

### GET /v2/datasets/{DATASET_ID}/imports

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/import_parameters.html

Lists all imports associated with a specific dataset.

```APIDOC
## GET /v2/datasets/{DATASET_ID}/imports

### Description
Lists all imports associated with a specific dataset.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/datasets/{DATASET_ID}/imports

### Parameters
#### Path Parameters
- **DATASET_ID** (string) - Required - The unique identifier of the dataset.

#### Query Parameters
- **limit** (integer) - Optional - The number of objects to return per page.
- **offset** (integer) - Optional - The offset within the list of available objects.

### Response
#### Success Response (200)
- Returns a list of DatasetImport resources.
```

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

### Login to QuartzBio

Source: https://github.com/quartzbio/quartzbio-python/blob/main/README.md

Log in to your QuartzBio account using the CLI. Ensure you have your credentials ready.

```bash
quartzbio login
```

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

### GET /v2/object_copy_tasks/{ID}

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/vaults_and_objects.md.txt

Retrieves metadata for a specific object copy task.

```APIDOC
## GET /v2/object_copy_tasks/{ID}

### Description
Retrieve metadata about an object copy task.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/object_copy_tasks/{ID}

### Parameters
#### Path Parameters
- **ID** (integer) - Required - The unique identifier of the copy task.
```

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

### GET /v2/object_copy_tasks

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/vaults_and_objects.md.txt

Lists all object copy tasks created by the current user.

```APIDOC
## GET /v2/object_copy_tasks

### Description
List object copy tasks created by the current user.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/object_copy_tasks
```

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

### Create Template and Dataset

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/dataset_templates.md.txt

Initialize a template object and create a dataset using the template's field structure.

```Python
from quartzbio import Dataset, DatasetTemplate 

template = DatasetTemplate.create(**template)
dataset = Dataset.get_or_create_by_full_path('your dataset path', fields=template.fields)
# Dataset will now have the non-transient fields from the template
# with desired titles/descriptions and expressions print(dataset.fields())
# But no records print(dataset.documents_count)
```

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

### Test Credentials with `whoami` Command

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/authentication.md.txt

Verify your authentication by running the `quartzbio whoami` command in the terminal. A successful output confirms your login status and domain.

```bash
$ quartzbio whoami
# You are logged-in to the "***" domain as ****@****.com with role member.
```

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

### GET /v2/objects

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/vaults_and_objects.md.txt

Retrieves a list of objects based on provided filter criteria.

```APIDOC
## GET /v2/objects

### Description
List all available objects that the user has read access to, with optional filtering.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/objects

### Parameters
#### Query Parameters
- **id** (integer) - Optional - The ID of an object.
- **vault_id** (integer) - Optional - The ID of the vault that will contain the object.
- **vault_name** (string) - Optional - The name of the vault containing objects.
- **vault_full_path** (text) - Optional - The full path of the vault containing objects.
- **parent_object_id** (integer) - Optional - The ID of the existing folder object to place the new object into.
- **filename** (string) - Optional - The filename of the object.
- **path** (string) - Optional - The path of the object, including its parent folder.
- **object_type** (string) - Optional - The type of the object. Must be one of "file", "folder", or "dataset".
- **depth** (integer) - Optional - The depth of the object in the Vault.
- **query** (string) - Optional - A string that matches any objects whose path contains that string.
- **regex** (regex) - Optional - A regular expression which searches objects for matching paths.

### Response
#### Success Response (200)
- **List** (array) - The response returns a list of objects matching the provided filters.
```

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

### GET /v2/dataset_restore_tasks/{RESTORE_TASK_ID}

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/dataset_versioning.html

Retrieves metadata for a specific dataset restore task.

```APIDOC
## GET /v2/dataset_restore_tasks/{RESTORE_TASK_ID}

### Description
Retrieve metadata about a dataset restore task.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/dataset_restore_tasks/{RESTORE_TASK_ID}

### Parameters
#### Path Parameters
- **RESTORE_TASK_ID** (string) - Required - The unique identifier of the restore task.

### Response
#### Success Response (200)
- **DatasetRestoreTask** (object) - The resource containing metadata about the restore task.
```

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

### Log out and Log in with Credentials

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/authentication.md.txt

Clear existing credentials and log in using a personal access token and your account's domain. This command creates or updates the credentials file.

```bash
# Clear your existing credentials
quartzbio logout

# Replace "TOKEN" with the Personal Access Token copied from the EDP web page
# Replace "DOMAIN" with your account's subdomain (i.e. your company name)
quartzbio login --access-token TOKEN --api-host https://DOMAIN.api.edp.aws.quartz.bio
```

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

### GET /v2/datasets/{DATASET_ID}/template

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/dataset_templates.md.txt

Creates a dataset template from an existing dataset.

```APIDOC
## GET /v2/datasets/{DATASET_ID}/template

### Description
Create a dataset template from an existing dataset.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/datasets/{DATASET_ID}/template

### Parameters
#### Path Parameters
- **DATASET_ID** (string) - Required - The unique identifier of the source dataset.

### Response
#### Success Response (200)
- **DatasetTemplate** (object) - An unsaved DatasetTemplate object for the specified dataset.
```

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

### GET /v2/dataset_snapshot_tasks/{SNAPSHOT_TASK_ID}

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/dataset_versioning.md.txt

Retrieves metadata for a specific dataset snapshot task.

```APIDOC
## GET /v2/dataset_snapshot_tasks/{SNAPSHOT_TASK_ID}

### Description
Retrieve metadata about a dataset snapshot task.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/dataset_snapshot_tasks/{SNAPSHOT_TASK_ID}

### Parameters
#### Path Parameters
- **SNAPSHOT_TASK_ID** (string) - Required - The unique identifier of the snapshot task.

### Response
#### Success Response (200)
- **DatasetSnapshotTask** (object) - The response contains a DatasetSnapshotTask resource.
```

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

### List Files and Folders

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs-source/source/quartzbio.cli.data.md

Lists files and folders at a given QuartzBio remote path.

```APIDOC
## GET /api/data/ls

### Description
Given a QuartzBio remote path, lists the files and folders.

### Method
GET

### Endpoint
/api/data/ls

### Parameters
#### Query Parameters
- **path** (string) - Required - The QuartzBio remote path.
```

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

### GET /v2/datasets/{DATASET_ID}/exports

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/exporting_data.md.txt

List all exports associated with a specific dataset.

```APIDOC
## GET /v2/datasets/{DATASET_ID}/exports

### Description
List the exports associated with a dataset.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/datasets/{DATASET_ID}/exports

### Parameters
#### Path Parameters
- **DATASET_ID** (string) - Required - The unique identifier of the dataset.

### Response
#### Success Response (200)
- **List[DatasetExport]** (array) - A list of DatasetExport resources.
```

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

### GET /v2/dataset_exports/{ID}/download

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/exporting_data.md.txt

Download a dataset export file by its ID.

```APIDOC
## GET /v2/dataset_exports/{ID}/download

### Description
Download a dataset export by its ID. Requires an authorized user with read permissions on the dataset. Note that exports may expire after 24 hours.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/dataset_exports/{ID}/download

### Parameters
#### Path Parameters
- **ID** (string) - Required - The unique identifier of the dataset export.

#### Query Parameters
- **redirect** (boolean) - Optional - Return a 302 redirect to the download location (default: true).

### Response
#### Success Response (302/200)
- **Response** (object) - Returns a 302 redirect to the download URL, or a URL to the file if redirect mode is disabled.
```

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

### GET /v2/object_copy_tasks/{ID}

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/vaults_and_objects.html

Retrieve metadata for a specific object copy task by its ID.

```APIDOC
## GET /v2/object_copy_tasks/{ID}

### Description
Retrieve metadata about an object copy task. This request requires that the authorized user is also the user who created the object copy task being retrieved.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/object_copy_tasks/{ID}

### Parameters
#### Path Parameters
- **ID** (string) - Required - The unique identifier of the object copy task.

### Response
#### Success Response (200)
- **task** (object) - An object copy task resource.
```

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

### Enable Global Beacon Indexing for a Dataset

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/_sources/metadata_and_global_beacons.md.txt

Demonstrates how to enable Global Beacon indexing for a dataset using the Python client. This process allows the dataset to be searched across the organization via specialized endpoints.

```Python
# Getting the dataset
dataset = Dataset.get_by_full_path('~/beacon-test-dataset')

# Enabling Global Beacon on dataset
dataset.enable_global_beacon()

# Example Output:
{'id': 125,
'datastore_id': 6,
'dataset_id': 1658666726768179211,
'status': 'indexing',
'progress_percent': 0,
'is_deleted': False}
```

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

### GET /v2/dataset_migrations/{ID}

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/creating_and_migrating_datasets.html

Retrieves metadata about a specific dataset migration. Requires permission.

```APIDOC
## GET /v2/dataset_migrations/{ID}

### Description
Retrieve metadata about a dataset migration.

This request requires an authorized user with permission.

The response contains a DatasetMigration resource.

### Method
GET

### Endpoint
https://<EDP_API_HOST>/v2/dataset_migrations/{ID}

### Parameters
#### Path Parameters
- **ID** (integer) - Required - The ID of the dataset migration to retrieve.
```

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

### Launch IPython Shell

Source: https://github.com/quartzbio/quartzbio-python/blob/main/docs/quartzbio.cli.ipython.html

Functions to open the QuartzBio shell wrapper for different IPython versions.

```APIDOC
## launch_ipython_shell(args)

### Description
Opens the standard QuartzBio shell (IPython wrapper).

### Parameters
- **args** (object) - Required - Arguments to pass to the shell initialization.

---

## launch_ipython_5_shell(args)

### Description
Opens the QuartzBio shell (IPython wrapper) specifically for IPython 5+.

### Parameters
- **args** (object) - Required - Arguments to pass to the shell initialization.

---

## launch_ipython_legacy_shell(args)

### Description
Opens the QuartzBio shell (IPython wrapper) for older IPython versions.

### Parameters
- **args** (object) - Required - Arguments to pass to the shell initialization.
```