Isabl Settings

Each component of Isabl can be configured in multiple ways. Generally, settings are strings, numbers, objects, and many other types.

Import Strings point to an importable object, whether its a class, a function, etc. (e.g.isabl_cli.data.DataImporter)

Database Managed Settings

Some Isabl API, Isabl Web, and Isabl CLI and be configured from the admin site! To do so, go to /admin/isabl_api/client/ and update the clients called default-backend-settings for Isabl API, and default-frontend-settings for Isabl Web. You may want to create your own client for Isabl CLI (see Writing Applications).

Isabl API Settings

Here is a detailed list of available configurations for Isabl API. To configure Isabl API, add a dictionary called ISABL_SETTINGS to your Django configuration.

Setting Name	Type	Description
EXTRA_GENDERS	List	Individual genders as two-value tuples (value, verbose name).
EXTRA_STATUS	List	Analysis status as two-value tuples (value, verbose name).
EXTRA_RAW_DATA_FORMATS	List	Experiment raw_data formats as two-value tuples (value, verbose name). Learn how to support extra formats here.
EXTRA_SPECIES	List	Individual species as three-value tuples (value, verbose name, system_id modifier). For example: [("YEAST", "YEAST", "Y")]
EXTRA_SAMPLE_CATEGORIES	List	Sample categories as three-value tuples (value, verbose name, system_id modifier). For example[("UNKNOWN", "UNKNOWN", "U")]
EXTRA_TECHNIQUE_METHODS	List	Technique methodsas three-value tuples (value, verbose name, system_id modifier). For example:[("SINGLE-CELL RNA", "SINGLE-CELL RNA", "scRNA")]
API_V1_EXTRA_PATTERNS	Import String	Import path to a list of urlpatternsto append to API v1.
SYSTEM_ID_PREFIX	String	A prefix for the default sample ID generated by Isabl (with the hope to differentiate objects across Isabl instances). For example, if set to DEMO, then experiments might be named DEMO_H000002_T01_01_TD01.
SYSTEM_ID_GENERATOR	Import String	Import path to a function that takes either an Individual, Sample, Aliquot, or Experiment and returns a system identifier. This will overwrite the default generation of system ids (e.g. DEMO_H000002_T01_01_TD01).
FRONTEND_URL	String	URL where the frontend is being deployed (not required if frontend running in same host as backend).
JIRA_SETTINGS	Dictionary	Feature to integrate JIRA with Isabl projects (It can assign a different JIRA epic to each Isabl Group). See more.
REQUIRE_ACCOUNT_APPROVAL	Boolean	Disable new accounts and send out email to admins to require approval before new users can login.
S3_BASE_STORAGE_DIRECTORIES	Dictionary	Support loading analyses results from a AWS s3 based "BASE_STORAGE_DIRECTORY". Learn more here.

Learn more about production deployment:

Production Deployment

Loading results from a AWS S3 bucket

If your Isabl CLI BASE_STORAGE_DIRECTORY is located in a S3 bucket, you can enable rendering results through the website using the S3_BASE_STORAGE_DIRECTORIES setting:

"S3_BASE_STORAGE_DIRECTORIES": {
    "/base/path/in/output-file": {
        "bucket": "an-S3-bucket-name",
        "access_key": "The AWS Access Key",
        "access_key": "The AWS Access Key",
        "base_directory": "/base/path/in/s3/object",
        "prefer_original": false
    }
}

For example if an analysis output path is /mnt/data/analyses/01/01/1/head_job.log and and the s3 path to it is s3://my-bucket/data/analyses/01/01/1/head_job.log you should use this setting:

"S3_BASE_STORAGE_DIRECTORIES": {
    "/mnt/data/": {
        "bucket": "my-bucket",
        "base_directory": "/data/",
        ...
    }
}

if prefer_original is set to True (False by default), it will try to retrieve the original path first if exists (i.e. /mnt/data/analyses/01/01/1/head_job.log) , if not it will try to resolve for the file in S3 (i.e. s3://my-bucket/data/analyses/01/01/1/head_job.log)

Integrating with Jira

Isabl provides a simple integration to Jira, as it's a widely used management tool used for development and analyses. The module creates a Jira Epic for each Isabl project, and allows to create a simple list of tasks (Jira issues) from the web.

Jira Integration Demo

To enable, you need to add the following settings in the web and in the api.

In the Web Settings:

index.html

window.$isabl = {
    ...
    jira: true
}

In the Api Settings:

In Jira for Epic and Issues we can create custom fields. You need to create 2 custom fields where the Project ID and the Project Link will be stored, and use their ids in the settings.

"JIRA_SETTINGS": {
    "active": True,
    "default": {
        "URL": "https://my-jira-instance",
        "AUTH": ("jira-username", "secret-jira-password"),
        "PROJECT_KEY": "ISABL",
        "URL_FIELD": "customfield_id_1",
        "PROJECT_FIELD": "customfield_id_2",
    }
},

Pro Tip: Jira Epics are created under Jira Projects. You can create different Jira Projects for each Isabl Project Group, by adding extra dictionaries that map to isabl group acronyms.

i.e. If a group in Isabl is called (name: Pathology, acronym: PATH), you can set up your settings like the example below. And all Isabl Projects that belong to the PATHOLOGY group, will have their own separate Jira Project under https://my-jira-instance/projects/PATH/issues/

"JIRA_SETTINGS": {
    "active": True,
    "default": {
        "URL": "https://my-jira-instance",
        "AUTH": ("jira-username", "secret-jira-password"),
        "PROJECT_KEY": "ISABL",
        "URL_FIELD": "customfield_id_1",
        "PROJECT_FIELD": "customfield_id_2",
    },
    "PATH": {
        "URL": "https://my-jira-instance",
        "AUTH": ("jira-username", "secret-jira-password"),
        "PROJECT_KEY": "PATH",
        "URL_FIELD": "customfield_id_1",
        "PROJECT_FIELD": "customfield_id_2",
    }
},

Isabl CLI Settings

Before anything, you must set the following environment variables:

# you need to let Isabl CLI where the API is being hosted
export ISABL_API_URL='your-isabl-instance.org/api/v1/'

# you can create a client object in from the django admin
export ISABL_CLIENT_ID=<insert-client-primary-key-or-slug>

Once this is set, you can configure your client object settings with the following configurations (see isabl_cli.settings to check default settings):

Setting Name	Type	Description
API_BASE_URL	String	url host where your isabl api is running. Needed to connect the CLI with the API.
BASE_STORAGE_DIRECTORY	String	Directory where data will be store in the file system.
TIME_ZONE	String	Current timezone used by pytz package.
INSTALLED_APPLICATIONS	Import Strings Array	Array of registered applications to be run with the cli tool. These apps can be seen and run isabl apps --help.
CUSTOM_COMMANDS	Import Strings Array	Array of custom commands to be added to the custom cli tool.
SYSTEM_COMMANDS	Import Strings Array	Array of system commands that are used in isabl-cli.
ADMIN_COMMANDS	Import Strings Array	Array of commands that are only executable by admin.
ADMIN_USER	String	Linux user for which admin operations will be limited. This user will own the data and analyses results. Nevertheless, Isabl Applications can be run by multiple unix users. Learn more about it here.
CREATE_SYMLINKS	Boolean	By default, Isabl creates a symlink farm upon data import and analyses completion. You can turn it off with this setting.
DEFAULT_LINUX_GROUP	String	Linux group for data admin_user to use.
MAKE_STORAGE_DIRECTORY	Import String	Get and create path to a data directory.
TRASH_ANALYSIS_STORAGE	Import String	Move analysis storage_url to a trash directory.
REFERENCE_DATA_IMPORTER	Import String	Register input_bed_path in technique's storage dir and update data.
DATA_IMPORTER	Import String	Import raw data for multiple experiments.
BED_IMPORTER	Import String	Register input_bed_path in technique's storage dir and update data.
ON_DATA_IMPORT	Import Strings Array	Methods triggered when data has been imported successfully.
ON_STATUS_CHANGE	Import Strings Array	Methods triggered when an analysis changes status.
ON_SIGNAL_FAILURE	Import Strings Array	Methods triggered when an signal fails.
SUBMIT_ANALYSES	Import String	A function that will take a list tuples (analysis, path to analysis script) and submits them to a given compute architecture.
SUBMIT_CONFIGURATION	Dictionary	A schema-less dictionary to set configurations that the SUBMIT_ANALYSES function may utilize. See more Batch Systems.
EXTRA_RAW_DATA_FORMATS	Tuples Array	For every new supported format a tuple of (regex validator, file_data_type) i.e. To support Illumina ORA format: ["\\.ora?$", "ORA"]

Writing Applications

Submit Configuration

Isabl Web Settings

Customization of the User Interface can be achieved by defining a global $isabl settings dictionary in the main index.html.

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

You can configure the window.$isabl with the following parameters:

Setting Name	Type	Default	Description
apiHost	String	''	Url host where your isabl api is running.
name	String	'isabl'	Custom app title that is shown in the top of the app.
logo	String		Custom image path that is shown as the main logo of the app. Use a square size image for better display.
jira	Boolean	false	Activate the jira card in the projects view. If the jira endpoint is available from the api, it will show the current tickets for each project. Learn more about jira integration.
oncoTree	Boolean	false	If it's enabled, more information about the onco tree disease is added in the Sample details.
customFields	Object	{}	Every detail info for each model shown in the frontend can be customized, by overwriting the specific key of a fields object. Available fields can be seen here. Learn more on how to create custom fields (TODO).
restartButton	Boolean	false	If enabled,FAILED analyses can send a signal to restart or force to the database. Learn more in signals (TODO).
lightTheme	Object	See defaults	Colors to customize the light theme.
darkTheme	Object	See defaults	Colors to customize the dark theme.
modelIcons	Object	{}	Material Icon names to customize panel icons.
distinctRecords	Boolean	false	By default, api queries don't remove duplicates as it impacts speed. Set true to avoid duplicate records.
treeIcons	Object	{}	Please use these if the graph icons are broken: "treeIcons": { "male": "https://isabl-web.s3.us-east-1.amazonaws.com/male.svg", "female": "https://isabl-web.s3.us-east-1.amazonaws.com/female.svg", "normal": "https://isabl-web.s3.us-east-1.amazonaws.com/normal.svg", "tumor": "https://isabl-web.s3.us-east-1.amazonaws.com/tumor.png", "aliquot": "https://isabl-web.s3.us-east-1.amazonaws.com/normal.svg", "dna": "https://isabl-web.s3.us-east-1.amazonaws.com/dna.svg", "rna": "https://isabl-web.s3.us-east-1.amazonaws.com/rna.svg", "mouse": "https://isabl-web.s3.us-east-1.amazonaws.com/mouse.svg", "image": "https://isabl-web.s3.us-east-1.amazonaws.com/image.svg", "alien": "https://isabl-web.s3.us-east-1.amazonaws.com/unknown.svg", }

Example of a custom UI configuration

<script>
    const customFields = {
        // overwrite 2 of the fields of the analysis panel
        analysisFields: {
            // Add a new formatter for status
            status: {
                section: 'Analysis Details',
                verboseName: 'Status',
                field: 'status',
                formatter: value => {
                    if (value === 'SUCEEDED') {
                        return 'DONE!'
                    } else if (value === 'FAILED') {
                        return 'OOPS...'
                    } else {
                        return value
                    }
                }
            },
            // Make notes not editable
            notes: {
                section: 'Analysis Details',
                verboseName: 'Notes',
                field: 'notes',
                editable: false
            }
        },
        // display a new custom field for project that exist in the db.
        // Use http://<api-host>/admin/ to create custom fields.
        projectFields: {
            // custom field
            irbConstent: {
              section: 'Project Details',
              verboseName: 'IRB Consent',
              field: 'custom_fields.irb_consent',
              editable: true,
              apiPermission: 'change_project'
            }
          }
        }
    }

    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',
          background: '#1a202c',
          surface: '#3a4556',
          accent: '#4a5568'
        },
        modelIcons: {
          project: 'insert_chart',
          analysis: 'bubble_chart',
          individual: 'person',
          sample: 'gesture',
          experiment: 'flash_on',
          search: 'search',
          submission: 'assignment'
        },
    }
</script>

Important: In case you're running your frontend instance in a different host that the backend, you should add this ENV variable to your django project where the isabl-api is running:

export FRONTEND_URL="http://your-frontend-host.com"

If you want to consume isabl-web and serve your own html, outside of isabl-api. You can consume the frontend just as:

index.html

<!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>