### Example Environment Configuration

Source: https://docs.isabl.io/production-deployment

This snippet provides an example of environment variable configuration, specifically for an admin user. This is typically used in production setups.

```javascript
{
 "ADMIN_USER": "isablbot",
```

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

### Install Isabl CLI

Source: https://docs.isabl.io/quick-start

Install the CLI and apps, and configure environment variables.

```bash
# install isabl-cli from github (Use a virtualenv as a good practice)
pip install -e ./isabl_cli
pip install -e ./isabl_apps

# point to your API URL
export ISABL_API_URL=http://localhost:8000/api/v1/

# set environment variable for demo client
export ISABL_CLIENT_ID="demo-cli-client"
```

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

### Getting Instances from Database

Source: https://docs.isabl.io/retrieve-data

To get started, retrieve specific instances from the database.

```python
To get started, we can retrieve specific instances from the database:
```

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

### Install Isabl CLI

Source: https://docs.isabl.io/quick-start

Instructions for installing the Isabl CLI from GitHub, ideally within a virtual environment.

```bash
# install isabl-cli from github (Use a virtualenv as a good practice)
```

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

### Install Cookiecutter and Bootstrap Project

Source: https://docs.isabl.io/writing-applications

First, ensure cookiecutter is installed. Then, use it to bootstrap your project from the provided template. Finally, navigate to your project directory and install dependencies.

```bash
# first make sure you have cookiecutter installed
pip install cookiecutter

# now lets bootstrap your project
cookiecutter https://github.com/isabl-io/cookiecutter-apps

# finally install you project in a new virtual environment
cd <project-name> && pip install -r requirements.txt
```

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

### Run Docker Hello World

Source: https://docs.isabl.io/quick-start

Verifies that Docker is installed and running correctly on your system.

```bash
docker run hello-world
```

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

### Install and Configure Isabl CLI

Source: https://docs.isabl.io/llms-full.txt

Install the isabl-cli and isabl-apps from local paths. Set the ISABL_API_URL and ISABL_CLIENT_ID environment variables to configure the CLI to connect to your API.

```bash
pip install -e ./isabl_cli
pip install -e ./isabl_apps
```

```bash
export ISABL_API_URL=http://localhost:8000/api/v1/
```

```bash
export ISABL_CLIENT_ID="demo-cli-client"
```

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

### Run Application Instance

Source: https://docs.isabl.io/writing-applications

Example of executing a HelloWorldApp instance with custom run arguments.

```python
    HelloWorldApp().run(
        tuples=[([target_experiment], [])],
        run_args=dict(message="custom message"),
        commit=True,
    )
```

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

### Install Isabl CLI from GitHub

Source: https://docs.isabl.io/production-deployment

Use this command to install the isabl-cli package directly from a GitHub repository. Ensure you have pip installed.

```bash
# install isabl-cli from Github
pip install git+https://github.com/papaemmelab/isabl_cli#eggs=isabl-cli
```

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

### Run Production Services

Source: https://docs.isabl.io/production-deployment

Start the production services using the specified configuration file.

```bash
docker-compose -f production.yml up
```

```bash
docker-compose -f production.yml up -d
```

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

### Start Demo Containers

Source: https://docs.isabl.io/quick-start

Launch the demo containers in detached mode.

```bash
demo-compose up -d
```

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

### Install isabl_io_llms Package

Source: https://docs.isabl.io/production-deployment

Use this command to install the isabl_io_llms package. Ensure you have pip installed.

```bash
pip install -e <your-dir>/isabl_cli
```

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

### Check Isabl CLI Help

Source: https://docs.isabl.io/llms-full.txt

Verify the installation and view available commands for the Isabl CLI.

```bash
isabl --help
```

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

### Install Isabl CLI from GitHub

Source: https://docs.isabl.io/production-deployment

Use this command to install the Isabl CLI directly from its GitHub repository. This is useful for ensuring you have the latest version or for development purposes.

```bash
# install isabl-cli from Github
pip install git+https://github.com/papaemmelab/isabl_cli#eggs=isabl-cli
```

```bash
# or clone locally and install as editable
git clone https://github.com/papaemmelab/isabl_cli <your-dir>/isabl_cli
pip install -e <your-dir>/isabl_cli
```

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

### Setting Name Configuration

Source: https://docs.isabl.io/import-data

Example of how a setting name might be configured within the system.

```json
{
  "object": "block",
  "type": "code-line",
  "isVoid": false,
  "data": {},
  "nodes": [
    {
      "object": "text",
      "leaves": [
        {
          "object": "leaf",
          "text": "Setting Name",
          "marks": []
        }
      ],
      "key": "0"
    }
  ]
}
```

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

### Install ISABL CLI and Apps

Source: https://docs.isabl.io/quick-start

Install the ISABL CLI and associated applications using pip. Ensure you are in the correct project directory.

```bash
pip install -e ./isabl_cli
```

```bash
pip install -e ./isabl_apps
```

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

### Start Isabl Web Development Server

Source: https://docs.isabl.io/llms-full.txt

Command to start the React development server for the isabl_web project using Yarn.

```bash
yarn serve
```

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

### Install and Configure Isabl CLI

Source: https://docs.isabl.io/llms-full.txt

Commands to install the Isabl CLI from GitHub and configure the required environment variables for production use.

```bash
# install isabl-cli from Github
pip install git+https://github.com/papaemmelab/isabl_cli#eggs=isabl-cli

# or clone locally and install as editable
git clone https://github.com/papaemmelab/isabl_cli <your-dir>/isabl_cli
pip install -e <your-dir>/isabl_cli
```

```bash
# let the client know what API should be used
export ISABL_API_URL="https://isabl.mskcc.org/api/v1/"

# set client id, you can create a new client in the admin site
export ISABL_CLIENT_ID="<replace with client primary key>"
```

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

### Start Isabl API Backend

Source: https://docs.isabl.io/llms-full.txt

Command to start the backend development server for the isabl_api project using docker-compose.

```bash
docker-compose up
```

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

### Bash: Install Cookiecutter and Bootstrap Project

Source: https://docs.isabl.io/llms-full.txt

Steps to install Cookiecutter and use it to bootstrap a new Isabl project. This includes installing the package and setting up requirements.

```bash
# first make sure you have cookiecutter installed
pip install cookiecutter

# now lets bootstrap your project
cookiecutter https://github.com/isabl-io/cookiecutter-apps

# finally install you project in a new virtual environment
cd <project-name> && pip install -r requirements.txt

```

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

### Get Help on a Method

Source: https://docs.isabl.io/retrieve-data

Use `?` to get help on a method, for example, `ii.get_instances?`.

```python
ipython
```

```python
?
```

```python
ii.get_instances?
```

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

### Isabl CLI Example

Source: https://docs.isabl.io/retrieve-data

This snippet demonstrates a basic interaction with the Isabl CLI. Further details on specific commands and their usage would typically be found in the CLI documentation.

```bash
# Using Isabl CLI
```

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

### Install Project Dependencies

Source: https://docs.isabl.io/writing-applications

Install project dependencies using pip from a requirements file. Ensure you are in the project directory.

```bash
cd <project-name> && pip install -r requirements.txt
```

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

### Bootstrap Isabl API Project

Source: https://docs.isabl.io/production-deployment

Install cookiecutter and initialize the project from the official template.

```bash
pip install cookiecutter 

# then bootstrap the project
cookiecutter https://github.com/papaemmelab/cookiecutter-api
```

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

### Bootstrap New Application Project

Source: https://docs.isabl.io/writing-applications

Installs cookiecutter and bootstraps a new application project from the Isabl template.

```bash
# first make sure you have cookiecutter installed
pip install cookiecutter

# now lets bootstrap your project
cookiecutter https://github.com/isabl-io/cookiecutter-apps

# finally install you project in a new virtual environment
```

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

### AbstractApplication Usage Examples

Source: https://docs.isabl.io/writing-applications

The `AbstractApplication` class provides a base for applications. This section shows common usage patterns and examples.

```text
AbstractApplication comes with
```

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

### Install isabl_io_llms via pip

Source: https://docs.isabl.io/production-deployment

Install the isabl_io_llms repository using pip. This is useful for making the library available in your Python environment.

```bash
pip install --editable /path/to/my/isabl/apps
```

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

### Install Isabl Web Dependencies

Source: https://docs.isabl.io/llms-full.txt

Command to install project dependencies for the isabl_web project using Yarn.

```bash
yarn install
```

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

### Format Python Projects

Source: https://docs.isabl.io/llms-full.txt

Install and run the Black formatter for Python-based components.

```bash
pip install black && black .
```

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

### Import BED Files Help Command

Source: https://docs.isabl.io/llms-full.txt

Execute this command to get assistance on importing BED files for sequencing techniques, which will be compressed, indexed, and registered.

```bash
isabl import-bedfiles --help
```

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

### GET /isabl --help

Source: https://docs.isabl.io/llms-full.txt

Displays the help menu for the Isabl command-line tool, listing all available commands and options.

```APIDOC
## GET isabl --help

### Description
Displays the help menu for the Isabl command-line tool, listing all available commands and options.

### Method
CLI Command

### Endpoint
isabl --help

### Parameters
#### Options
- **--version** (flag) - Optional - Show the version and exit.
- **--help** (flag) - Optional - Show this message and exit.
```

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

### Environment Variable Setup and Client Configuration

Source: https://docs.isabl.io/isabl-settings

Before interacting with the API, ensure you set the necessary environment variables. Subsequently, configure your client object with the provided settings, referencing the default configurations for further details.

```APIDOC
## Environment Variable Setup and Client Configuration

### Description
Before anything, you must set the following environment variables. Once this is set, you can configure your client object settings with the following configurations (see to check default settings).

### Method
N/A (Configuration Steps)

### Endpoint
N/A (Configuration Steps)

### Parameters
N/A (Configuration Steps)

### Request Example
N/A (Configuration Steps)

### Response
N/A (Configuration Steps)

## API Endpoint Details (Example Table Structure)

### Description
This section outlines the structure of API data, potentially representing different endpoints or data types. The table below provides a sample of available data fields.

### Method
N/A (Table Structure)

### Endpoint
N/A (Table Structure)

### Parameters
N/A (Table Structure)

### Request Example
N/A (Table Structure)

### Response
#### Success Response (200)
- **Field Name** (Type) - Description

#### Response Example
N/A (Table Structure)

| Header 1 | Header 2 | Header 3 |
|---|---|---|
| Value 1a | Value 2a | Value 3a |
| Value 1b | Value 2b | Value 3b |
| Value 1c | Value 2c | Value 3c |
```

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

### Configure TLS with Certificate and Key Paths

Source: https://docs.isabl.io/production-deployment

Configure TLS by providing the paths to your certificate and key files. This is a common setup for production environments.

```bash
 tls /path/to/cert path/to/key
```

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

### Create Superuser for Isabl

Source: https://docs.isabl.io/llms-full.txt

Create a superuser account for the Isabl application using the provided example credentials. This is necessary for logging into the web interface.

```bash
demo-django createsuperuser
```

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

### Define a new application class

Source: https://docs.isabl.io/writing-applications

This example demonstrates how to define a new application class by inheriting from AbstractApplication. It includes a placeholder for application-specific logic.

```python
class MyApp(AbstractApplication):
    def __init__(self):
        super().__init__()

```

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

### Build and Run Production Stack

Source: https://docs.isabl.io/llms-full.txt

Commands to build, start, and manage the lifecycle of the production Docker containers.

```bash
docker-compose -f production.yml build
```

```bash
docker-compose -f production.yml up
```

```bash
docker-compose -f production.yml up -d
```

```bash
docker-compose -f production.yml run --rm django python manage.py migrate
```

```bash
docker-compose -f production.yml run --rm django python manage.py createsuperuser
```

```bash
docker-compose -f production.yml run --rm django python manage.py shell
```

```bash
docker-compose -f production.yml logs
```

```bash
docker-compose -f production.yml scale django=4
docker-compose -f production.yml scale celeryworker=2
```

```bash
docker-compose -f production.yml ps
```

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

### Get Count Function Example

Source: https://docs.isabl.io/retrieve-data

Demonstrates the usage of the 'get-count' function, likely for retrieving the number of items or results.

```javascript
self.__next_f.push([1,"e5:[\"$\",\"div\",null,{\"aria-labelledby\":\"$undefined\",\"className\":\"blocks w-full space-y-2 lg:space-y-3 leading-normal self-center **:text-left text-left\",\"children\":[[ \"$\",\"p\",\"2199\",{\"className\":\"has-\\[.button,input\\]:flex has-\\[.button,input\\]:flex-wrap has-\\[.button,input\\]:gap-2 has-\\[.button,input\\]:items-center mx-auto page-width-wide:mx-0 decoration-primary/6 print:break-inside-avoid w-full max-w-\\[unset\"],\"children\":[[ \"$\",\"$1\",\"2198\",{\"children\":[[ \"$\",\"$1\",\"0\",{\"children\":[ \"$\",\"strong\",\"mark\",{\"className\":\"font-bold\",\"children\":\"get-count\"}]}]}]}]}]])
```

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

### Rerun All Failed Signals

Source: https://docs.isabl.io/operational-automations

Use this command to rerun all signals that have previously failed. No additional setup is required beyond having isabl installed.

```bash
# rerun all failed signals
isabl rerun-signals
```

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

### Initialize and Configure HelloWorldApp

Source: https://docs.isabl.io/writing-applications

Instantiates the application and defines default settings for message and path configuration.

```python
 # create files if you may test with real data at some point
 app = HelloWorldApp()
 app.application.settings.default_client = {
 "default_message": "Hello from Elephant Island.",
 "echo_path": tmpdir.docker("ubuntu", "echo")
 }
```

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

### Install Isabl CLI Dependencies

Source: https://docs.isabl.io/llms-full.txt

Command to install project dependencies for isabl_cli using pip. It is recommended to perform this installation within a virtual environment.

```bash
pip install -r requirements.txt
```

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

### Using Isabl SDK

Source: https://docs.isabl.io/data-model

Demonstrates how to import the Isabl CLI module and interact with instances.

```python
import isabl_cli as ii

center = ii.get_instance(
 'centers',
 'MEMORIAL SLOAN KETTERING (MSK)'
)
individual = ii.create_instance(
```

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

### Isabl CLI Settings Configuration

Source: https://docs.isabl.io/llms-full.txt

Example configuration for the isabl CLI, specifying submission methods for analyses and merge operations, along with custom requirements and throttling settings.

```json
// isabl cli's settings
{
    ...
    "SUBMIT_ANALYSES": "isabl_cli.batch_systems.submit_slurm",
    "SUBMIT_CONFIGURATION": {
        "extra_args": " -p GPU_PARTITION ",
        "get_requirements": "my_isabl_extension.batch_systems.get_slurm_requirements",
        "throttle_by": 50,
        "unbuffer": True,
    },
    "SUBMIT_MERGE_ANALYSIS": "my_isabl_extension.batch_systems.submit_merge_analysis_to_slurm",
    ...
}
```

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

### Install Yarn Package Manager

Source: https://docs.isabl.io/llms-full.txt

Command to install Yarn, a JavaScript package manager, using Homebrew. This command installs Yarn without Node.js, assuming Node.js is managed separately.

```bash
brew install yarn --without-node
```

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

### Isabl Configuration Settings

Source: https://docs.isabl.io/production-deployment

Example of Isabl's core configuration settings, including user, group, storage, and application integrations. Ensure these match your production environment.

```json
{
  "ADMIN_USER": "isablbot",
  "DEFAULT_LINUX_GROUP": "isabl",
  "BASE_STORAGE_DIRECTORY": "/isabl/data",
  "SUBMIT_ANALYSES": "isabl_cli.batch_systems.submit_lsf",
  "ON_DATA_IMPORT": ["isabl_apps.signals.signal_data_import"],
  "CUSTOM_COMMANDS": ["isabl_apps.cli.one_click_genome"],
  "ON_STATUS_CHANGE": ["isabl_apps.signals.signal_apps_automation"],
  "INSTALLED_APPLICATIONS": ["isabl_apps.apps.BwaMemGRCh37"]
}
```

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

### Get Target Experiment or Tumor

Source: https://docs.isabl.io/retrieve-data

This code snippet is used to get the target experiment or tumor.

```python
# get the target experiment or tumor\n
```

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

### Filter by Starts With Query

Source: https://docs.isabl.io/retrieve-data

Use these parameters to filter results where a field starts with a specific substring.

```text
[i]startswith
```

```text
name__startswith=isab
```

```text
name__istartswith=iSab
```

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

### Build Demo Containers

Source: https://docs.isabl.io/quick-start

Build the Docker containers for the demo environment.

```bash
demo-compose build
```

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

### Define a Hello World Isabl Application

Source: https://docs.isabl.io/writing-applications

Inherit from AbstractApplication and override get_command to define the execution logic. The cli_options attribute specifies available command-line arguments.

```python
from isabl_cli import AbstractApplication
from isabl_cli import options


class HelloWorldApp(AbstractApplication):

    NAME = "HELLO WORLD"
    VERSION = "1.0.0"
    cli_options = [options.TARGETS]

    def get_command(self, analysis):
        experiment = analysis.targets[0]  
        return f"echo {experiment.sample.identifier} {experiment.raw_data} "
```

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

### Navigate to Demo Directory

Source: https://docs.isabl.io/quick-start

Change the current directory to the cloned ISABL demo repository.

```bash
cd isabl_demo
```

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

### Install unbuffer with Miniconda

Source: https://docs.isabl.io/llms-full.txt

Commands to create a conda environment and install the expect package to provide the unbuffer utility.

```bash
conda create -n myenv
conda activate myenv
conda install -c conda-forge expect
```

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

### Configure Experiment Metadata and Create Instance

Source: https://docs.isabl.io/writing-applications

Sets up experiment metadata fields and initializes an instance using the Isabl API.

```python
 meta_data["sample"]["individual"]["species"] = "HUMAN"
 meta_data["storage_url"] = hello_world_datadir
 experiment = api.create_instance("experiments", identifier="a", **meta_data)
```

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

### Import Reference Data Help Command

Source: https://docs.isabl.io/llms-full.txt

Run this command to view detailed help and options for importing arbitrary reference data for assemblies and techniques.

```bash
isabl import-reference-data --help
```

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

### Create and Inspect CLI Client

Source: https://docs.isabl.io/quick-start

Create the client object and inspect the source script.

```bash
# create and update the client object
demo-cli python3.6 ./assets/metadata/create_cli_client.py

# check the file used to create the client
cat ./assets/metadata/create_cli_client.py
```

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

### Define CLI Options for Applications

Source: https://docs.isabl.io/writing-applications

Shows how to define CLI help text and options for an Isabl application.

```python
from isabl_cli import options

class HelloWorldApp(AbstractApplication):

 cli_help = "This is the Hello World App - a way to learn Isabl applications."
 cli_options = [options.TARGETS]
```

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

### Filtering by Name Starts With

Source: https://docs.isabl.io/retrieve-data

This endpoint allows you to filter results where the 'name' field starts with a specific query string, case-sensitively or case-insensitively.

```APIDOC
## GET /api/search

### Description
Filters results where the 'name' field starts with the specified query string.

### Method
GET

### Endpoint
/api/search

### Query Parameters
- **name__startswith** (string) - Required - The string to search for at the beginning of the 'name' field (case-sensitive).
- **name__istartswith** (string) - Required - The string to search for at the beginning of the 'name' field (case-insensitive).

### Request Example
```json
{
  "example": "/api/search?name__startswith=isa"
}
```

### Response
#### Success Response (200)
- **results** (array) - A list of matching records.

#### Response Example
```json
{
  "example": "{\"results\": [ { \"id\": 1, \"name\": \"isabelle\" } ]}"
}
```
```

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

### Create Isabl CLI Client

Source: https://docs.isabl.io/quick-start

Initializes and creates a client for the isabl-cli.

```bash
isabl-cli client create
```

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

### Import and Initialize Isabl CLI

Source: https://docs.isabl.io/retrieve-data

Import the isabl_cli library and initialize the samples object.

```python
import isabl_cli as ii
samples = ii
```

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

### Source Demo Profile

Source: https://docs.isabl.io/llms-full.txt

Source the demo profile script to set up environment variables for the demo.

```bash
source .demo-profile
```

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

### Retrieve analysis output directories

Source: https://docs.isabl.io/llms-full.txt

Get the storage paths for analysis instances.

```bash
isabl get-outdirs -fi name STRELKA
```

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

### Filter by date parameter

Source: https://docs.isabl.io/retrieve-data

Example of applying a date filter to a query parameter.

```text
created__date=2016-06-04
```

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

### Initialize Isabl Data Lake

Source: https://docs.isabl.io/production-deployment

Run this snippet as the admin user to initialize the data lake. Ensure the BASE_STORAGE_URL is correctly configured in your Isabl CLI settings.

```bash
python manage.py init_data_lake --base-storage-url $BASE_STORAGE_URL
```

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

### CLI Execution: isabl apps hello-world-1.0.0

Source: https://docs.isabl.io/writing-applications

Describes the command line interface for the Hello World application, including required filters and execution flags.

```APIDOC
## CLI Command: isabl apps hello-world-1.0.0

### Description
Executes the Hello World application within the Isabl environment. This command requires specific target filters to identify the experiments to process.

### Usage
`isabl apps hello-world-1.0.0 [OPTIONS]`

### Options
- **--targets-filters** (TEXT) - Required - API filters for target experiments.
- **--commit** (BOOLEAN) - Optional - Submit application analyses. Default: False.
- **--force** (BOOLEAN) - Optional - Wipe unfinished analyses and start from scratch.
```

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

### Custom Application Validation

Source: https://docs.isabl.io/writing-applications

Example of implementing an application class with experiment validation logic.

```python
class HelloWorldApp(AbstractApplication):

 def validate_experiments(self, targets, references):
  assert len(targets) == 1, "only one target experiment per analysis"
  assert targets[0].raw_data, "target experiment has no linked raw data"
  self.validate_dna_only(targets) # multiple validators are readily available
```

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

### Test HelloWorldApp with Sample Data

Source: https://docs.isabl.io/llms-full.txt

This Python function tests the HelloWorldApp by creating a sample experiment with FASTQ data and verifying the application's run with specific configurations. It uses temporary directories and data directories for testing.

```python
def test_hello_world_app(tmpdir, datadir, commit):
    # path to hello_world test data
    hello_world_datadir = join(datadir, "hello_world")
    raw_data = [
        dict(
            file_url=join(hello_world_datadir, "test.txt"),
            file_data=dict(extra="annotations"),
            file_type="FASTQ_R1",
        ),
    ]

    # overwrite default configuration for the default client
    meta_data = factories.ExperimentFactory(raw_data=raw_data)
    meta_data["sample"]["individual"]["species"] = "HUMAN"
    meta_data["storage_url"] = hello_world_datadir
    experiment = api.create_instance("experiments", identifier="a", **meta_data)

    # create files if you may test with real data at some point
    app = HelloWorldApp()
    app.application.settings.default_client = {
        "default_message": "Hello from Elephant Island.",
        "echo_path": tmpdir.docker("ubuntu", "echo")
    }

    # run application and make sure results are reported
    utils.assert_run(
        application=app,
        tuples=[([experiment], [])],
        commit=commit,
        results=["output", "count", "input"],
    )
```

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

### Execute HelloWorldApp with custom arguments

Source: https://docs.isabl.io/writing-applications

Run the HelloWorldApp application class with specific experiment tuples and commit settings.

```python
HelloWorldApp().run(
 tuples=([target_experiment], []),
 run_args=dict(message="custom message"),
 commit=True,
)
```

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

### Test unbuffer functionality

Source: https://docs.isabl.io/llms-full.txt

Verify that the unbuffer utility is correctly installed and functioning by echoing a string.

```bash
$ unbuffer echo "Hello World!" 
Hello World
```

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

### Create Superuser

Source: https://docs.isabl.io/quick-start

Command to initialize an administrative user account.

```bash
demo-django createsuperuser
```

```bash
username=admin password=admin email=admin@demo.io
```

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

### Initialize Isabl SDK

Source: https://docs.isabl.io/llms-full.txt

Import the Isabl CLI module to begin programmatic interaction.

```python
import isabl_cli as ii  # ii stands for `interactive isabl` 😎
```

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

### Get count of database instances

Source: https://docs.isabl.io/retrieve-data

Use this command to count instances based on specific filters.

```bash
isabl get-count analyses -fi status FAILED
```

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

### Import Reference Data Help and Structure

Source: https://docs.isabl.io/import-data

Command to view help for reference data import and the expected directory structure for assemblies.

```bash
isabl import-reference-data --help

# extra resources are included in the assembly directory
assemblies/
├── GRCh37
│   ├── chr_alias
│   │   └── hg19_alias.tab
│   ├── cytoband
│   │   └── cytoBand.txt
│   ├── genes
│   │   └── refGene.txt
│   └── genome_fasta
```

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

### Set up analysis and experiment directories

Source: https://docs.isabl.io/production-deployment

Define the directories for analyses and experiments. This script sets up environment variables for organizing your data lake.

```bash
DIRS=\"00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99\"
```

```bash
BASE=\"analyses experiments\"
```

```bash
# go to your data lake base directory (see: BASE_STORAGE_DIRECTORY)
```

```bash
cd /path/to/my/data/lake
```

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

### Get Project Instance

Source: https://docs.isabl.io/retrieve-data

Retrieve a project instance using the endpoint and identifier. The signature is (endpoint, identifier).

```python
project = ii.get_instance("projects", 100) # the signature is (endpoint, identifier)
```

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

### Initialize Data Lake Directories

Source: https://docs.isabl.io/llms-full.txt

Run this bash script as the admin user to create a hierarchical directory structure for the data lake. It sets permissions for read/write/execute for the owner and group.

```bash
DIRS="00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99"
BASE="analyses experiments"

# go to your data lake base directory (see: BASE_STORAGE_DIRECTORY)
cd /path/to/my/data/lake

for i in $BASE;
do
    for j in $DIRS;
    do
        for k in $DIRS;
        do
            DIR="$i/$j/$k"
            mkdir -p $DIR
            chmod u+wrX,g+wrX $DIR
        done;
    
    chmod g-w "$i/$j/"
    done;
done
```

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

### Get Paths for Any Instance

Source: https://docs.isabl.io/quick-start

This command allows you to retrieve paths for any registered instance in the database using its ID.

```bash
isabl get-paths --instance-id <instance_id>
```

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

### CLI Help and Restart Options

Source: https://docs.isabl.io/writing-applications

Standard command-line interface flags for managing analysis processes.

```bash
 --restart Attempt restarting failed analyses from previous checkpoint.
 --help Show this message and exit.
```

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

### GET /api/v1/

Source: https://docs.isabl.io/data-model

Access the comprehensive RESTful API reference and interactive Swagger documentation for all database resources.

```APIDOC
## GET /api/v1/

### Description
Access the interactive Swagger API documentation to explore all available endpoints for each resource in the Isabl database.

### Method
GET

### Endpoint
http://<your-isabl-host>/api/v1/

### Response
#### Success Response (200)
- **HTML/Swagger UI** - Interactive documentation interface for the API.
```

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

### Create Experiments and Test Applications

Source: https://docs.isabl.io/writing-applications

Utilities for creating database instances via factories and running application tests with mock data.

```python
from isabl_cli import api
from isabl_cli import factories


meta_data = factories.ExperimentFactory()
meta_data["sample"]["individual"]["species"] = "HUMAN"
experiment = api.create_instance("experiments", **meta_data)
assert experiment.pk > 0, "failed to create database instance"
```

```python
def test_hello_world_app(tmpdir, datadir, commit):
    # path to hello_world test data
    hello_world_datadir = join(datadir, "hello_world")
    raw_data = [
        dict(
            file_url=join(hello_world_datadir, "test.txt"),
            file_data=dict(extra="annotations"),
            file_type="FASTQ_R1",
        ),
    ]

    # overwrite default configuration for the default client
    meta_data = factories.ExperimentFactory(raw_data=raw_data)
    meta_data["sample"]["individual"]["species"] = "HUMAN"
    meta_data["storage_url"] = hello_world_datadir
    experiment = api.create_instance("experiments", identifier="a", **meta_data)

    # create files if you may test with real data at some point
    app = HelloWorldApp()
    app.application.settings.default_client = {
        "default_message": "Hello from Elephant Island.",
        "echo_path": tmpdir.docker("ubuntu", "echo")
    }

    # run application and make sure results are reported
    utils.assert_run(
        application=app,
        tuples=[([experiment], [])],
        commit=commit,
        results=["output", "count", "input"],
    )
```

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

### Serve Isabl Frontend Externally

Source: https://docs.isabl.io/llms-full.txt

Example HTML structure for serving the Isabl frontend independently of the API.

```markup
<!DOCTYPE html>
<html>
    <head>
        <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
        <meta name="viewport" content="width=device-width,initial-scale=1">
        <meta charset="UTF-8">
        <link href='https://fonts.googleapis.com/css?family=Roboto:300,400,500,700|Material+Icons' rel="stylesheet" type="text/css">
        <link rel="icon" href="favicon.ico">
        <title>My Awesome App</title>
    </head>
    <body>

 <div id="isabl-web"></div>
        <script src="https://cdn.jsdelivr.net/npm/vue"></script>
        <script src="https://cdn.jsdelivr.net/npm/isabl-web"></script>
        <script>
            window.$isabl = {
                apiHost: "http://my.isabl.api.host",
                //... other settings
            }
        </script>
    </body>
</html>
```

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

### View Isabl Application Help

Source: https://docs.isabl.io/writing-applications

Command to display help information and available options for a specific Isabl application.

```bash
$ isabl apps hello-world-1.0.0 --help

Usage: isabl apps hello-world-1.0.0 [OPTIONS]

 This is the Hello World App - a way to learn Isabl applications.

Options:
 --targets-filters API filters for target experiments [required] <TEXT TEXT>...
 --commit Submit application analyses. [default: False]
 --force Wipe unfinished analyses and start from scratch.
```

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

### Run tests with py.test

Source: https://docs.isabl.io/production-deployment

Use this command to execute tests with the py.test framework. Ensure py.test is installed in your environment.

```bash
py.test
```

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

### Get Project Analysis Results

Source: https://docs.isabl.io/writing-applications

Calculates the total number of lines in the 'merged.txt' file associated with a project analysis.

```python
def get_project_analysis_results(self, analysis):
 merged = join(analysis.storage_url, "merged.txt")

 with open(merged) as f:
 count = sum(len(i) for i in f)
```

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

### Run Hello World Application via CLI

Source: https://docs.isabl.io/writing-applications

Executes the hello-world application filtered by project ID.

```bash
isabl apps hello-world --filters projects 102
```

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

### Initialize Global Isabl Configuration

Source: https://docs.isabl.io/isabl-settings

Sets up the global window.$isabl object with API host, application name, branding, and feature flags.

```javascript
 window.$isabl = {
 apiHost: "http://my.isabl.api.host",
 name: "My Cool App",
 logo: "/path/to/my/awesome/logo",
 customFields,
 restartButton: true,
 jira: true,
 oncoTree: true,
 darkTheme: {
 primary: '#1dc5a7',
```

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

### Get Projects by Owner

Source: https://docs.isabl.io/retrieve-data

Retrieves projects where the current user is the owner. Use this to filter projects based on ownership.

```python
# get all the projects where I'm the owner
projects = ii.get_projects(owner__startswith="besuhof")
```

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

### Get Multiple ISABL Trees

Source: https://docs.isabl.io/retrieve-data

Retrieve a collection of ISABL 'trees' (individuals and their associated data) by filtering them by project.

```python
individuals = ii.get_trees(projects=267)
```

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

### Manage Production Docker Containers

Source: https://docs.isabl.io/production-deployment

Common Docker Compose commands for building, starting, and monitoring the production environment.

```bash
docker-compose -f production.yml build
```

```bash
docker-compose -f production.yml up
```

```bash
docker-compose -f production.yml up -d
```

```bash
docker-compose -f production.yml logs
```

```bash
docker-compose -f production.yml ps
```

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

### Example of get_or_create_analyses override

Source: https://docs.isabl.io/writing-applications

Override the get_or_create_analyses method if custom logic is needed for determining analysis uniqueness or creation.

```python
def get_or_create_analyses(self, experiments, application):
    return super().get_or_create_analyses(experiments, application)
```

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

### Filter Experiments by BAM File

Source: https://docs.isabl.io/llms-full.txt

Example of filtering experiments based on the presence of a specific BAM file reference.

```python
experiments = ii.experiments(has_bam_for="GRCh37")
```

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

### Get Output Directories with FAILED Status

Source: https://docs.isabl.io/retrieve-data

Retrieve output directories where the status is FAILED and list their contents up to level 2.

```bash
isabl get-outdirs -fi status FAILED | xargs tree -L 2
```

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

### Initialize Theme Configuration

Source: https://docs.isabl.io/master

This JavaScript snippet initializes the application theme, handling system preferences and local storage persistence.

```javascript
((a,b,c,d,e,f,g,h)=>{let i=document.documentElement,j=["light","dark"];function k(b){var c;(Array.isArray(a)?a:[a]).forEach(a=>{let c="class"===a,d=c&&f?e.map(a=>f[a]||a):e;c?(i.classList.remove(...d),i.classList.add(f&&f[b]?f[b]:b)):i.setAttribute(a,b)}),c=b,h&&j.includes(c)&&(i.style.colorScheme=c)}if(d)k(d);else try{let a=localStorage.getItem(b)||c,d=g&&"system"===a?window.matchMedia("(prefers-color-scheme: dark)").matches?"dark":"light":a;k(d)}catch(a){}})("class","theme","system",null,["light","dark"],null,true,true)
```

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

### Code Snippet Examples

Source: https://docs.isabl.io/retrieve-data

These snippets represent serialized UI components containing code-styled elements for data filtering and formatting.

```json
created__month=06
```

```json
year
```

```json
YYYY
```

```json
created__year=2016
```

```json
time
```

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

### Initialize Isabl Web Configuration

Source: https://docs.isabl.io/isabl-settings

Basic initialization script for the Isabl web frontend.

```html
<script>
        window.$isabl = { }
    </script>
```

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

### Update .eggs directory permissions

Source: https://docs.isabl.io/production-deployment

Ensure correct permissions for the .eggs directory. This is a necessary step after installation if you encounter permission issues.

```bash
chmod -R g+rwX /path/to/my/isabl/apps/.eggs
```

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

### Check Platform Architecture

Source: https://docs.isabl.io/quick-start

Command to verify the current platform architecture.

```bash
linux/amd64
```

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

### Get Output Directories with FAILED Status and Specific Pattern

Source: https://docs.isabl.io/retrieve-data

Retrieve output directories with a FAILED status that match the pattern 'head_job.*'.

```bash
isabl get-outdirs -fi status FAILED --pattern 'head_job.*'
```

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

### Build Production Containers

Source: https://docs.isabl.io/production-deployment

Build the project services defined in the production configuration file.

```bash
docker-compose -f production.yml build
```