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Use Krini

Krini is the web portal of ELIXIR On-Cloud. It replaces the TES Dashboard. In your browser, you log in with LS Login, choose services from the Cloud Registry, run GA4GH TES tasks and GA4GH WES workflows on them, and follow your runs. This page shows how, and says what doesn't work yet.

Krini has no user guide of its own; its README and deployment guide are for developers and operators.

The new Krini

This page describes the new Krini (branch staging of the Krini repository, commit c81a259). Parts of it are still in progress; see What's coming.

What works now

You want to In Krini Limits
Log in and out LS Login, in the sidebar or the top bar No other login provider.
Find services A list of the TES and WES services in the Cloud Registry Only TES and WES services, no search.
Run a task A form for TES tasks Krini doesn't send your token to TES services yet, and drops the outputs that you enter.
Follow your tasks A list of tasks, with their details No search or filter yet.
Run a workflow A form for WES runs You give the workflow by its URL or as attached files.
Follow your workflow runs A list of runs, with their states No details and no outputs in Krini yet; read them through the API.
Use your token elsewhere Copy your access token Only while you are logged in.

Before you start

  1. Get an LS Login account. See the LS Login and registration guide. Krini has no sign-up page of its own.
  2. Get access to services. Each service decides whom it lets in. Krini shows the services of the Cloud Registry, but doesn't give you access to them, and has no form to ask for it yet. To ask for services that you can use, write to cloud-service@elixir-europe.org.

Synthetic or public data only

The deployment is a sandbox for demos and tests (see Researchers: Start Here). Don't use Krini with personal or other sensitive data.

Find your way

The sidebar on the left has two pages, under Services:

  • Tasks: TES tasks, at /dashboard/tasks.
  • Workflows: WES runs, at /dashboard/workflows.

The menu at the bottom of the sidebar shows who is logged in and has the commands Login, Copy token to Dashboard and Logout. The top bar switches between light and dark mode. The button at the top left of the page hides and shows the sidebar.

The start page, Dashboard, has no content yet; open Tasks or Workflows instead. The TEST SERVER entry in the list of TES services and the info icon in the top bar don't work yet (krini#67).

Log in

  1. Select the LS Login button in the top bar, or Login in the menu at the bottom of the sidebar.
  2. Log in at LS Login with an identity provider of your choice, e.g., your home organisation, and agree to share your profile with Krini if LS Login asks.
  3. LS Login sends you back to Krini. The sidebar shows your name and email address.

Krini keeps you logged in, and renews your access token in the background while the page is open. If Krini can't renew it, it sends you to LS Login again.

To log out, select Logout in the menu at the bottom of the sidebar. This ends your session in Krini, not at LS Login: if you log in again in the same browser, LS Login may not ask for your password.

Choose a service

On Tasks and on Workflows, choose a service in the list at the top right (Select TES Instance or Select WES Instance). Krini fills the lists from the Cloud Registry:

  • TES: services of the types tes and tes-gateway, e.g., TESK, Funnel and the proTES gateway.
  • WES: services of the types wes and wes-gateway with an https address. Krini checks each one: it shows its health and the number of workflow types that it supports. You can't select a service that is unreachable, and Krini leaves out services that answer with an error. Refresh, at the top of the list, checks them again.

Krini sends your token to the WES service that you choose

Krini lists every TES and WES service in the Cloud Registry, whether you can trust it or not, and doesn't show whether a service is verified. Choose only services that you trust: anyone who runs a service that gets your token can act as you until the token expires. Check a service in the Cloud Registry first: on the safe side, use only services that are both verified and synced (see Using the Cloud Registry).

To see more about a WES service, point at the info icon next to it, which lists the workflow types and versions that it supports, or select the icon to open its service info: the service, its organisation, its workflow types, engines and file systems, the number of runs in each state, its tags and its API endpoint.

Not in the list?

Krini shows only the services that are registered in the Cloud Registry. To find services and their addresses, see Using the APIs.

Run a task

A TES task runs one or more container images, one after the other. See GA4GH TES for its parts.

Krini doesn't send your token to TES services yet

Krini calls TES services without your access token (krini#41, krini#44). Tasks work only on TES services that accept requests without a token. For the others, send your requests to the API with your token (see Using the APIs).

  1. Open Tasks and select Create Task.
  2. Choose a TES service in Select TES Instance.

  3. Fill in the form. Only the image and the command of an executor are required:

    Field What to enter
    Name, Description Free text that helps you find the task later.
    Executors One or more containers. For each: the Image (e.g., alpine:3.20), the Commands, one part per field (e.g., echo and Hello), and optionally environment variables (Env), the files for standard input and output (Stdin, Stdout, Stderr) and the working directory (Workdir).
    Inputs Files that the service copies into the container before the task starts: the URL of each file and the Path in the container.
    Outputs See the warning below.
    Resources section CPU cores, RAM and disk in GB, zones, and whether the task may run on preemptible machines.
    Tags Names and values, e.g., for a project.
    Volumes Paths in the container that the executors share.

  4. Submit the form. Krini shows the ID of the new task, or the error of the service.

Outputs aren't sent yet

The task form of Krini doesn't pass the Outputs that you enter on to the TES service, so the service doesn't copy any result files out of the container (cloud-components#574). To keep results for now, write them to a place that the container can reach, e.g., from the command, or create the task through the API.

Follow your tasks

Tasks lists the tasks of the selected service, ten per page, with their IDs and states. Expand a task to see its details: name, description, resources, tags, executors, volumes, creation time, inputs and outputs, and the logs with standard output and standard error of each executor.

What a TES service lists depends on the service: some list only your own tasks, others the tasks of all users.

To cancel a task that hasn't finished, expand it and select Delete. The button cancels the task; it doesn't remove it from the list.

The states of a task:

State Meaning
QUEUED, INITIALIZING Waiting for resources, or preparing the inputs.
RUNNING The executors run.
PAUSED Paused by the service.
COMPLETE Finished without error.
EXECUTOR_ERROR A command of the task failed; see its logs.
SYSTEM_ERROR The service failed, not the task.
CANCELING, CANCELED Being canceled, or canceled.
PREEMPTED Stopped because its machine was taken away.
UNKNOWN The service doesn't know the task's state.

Run a workflow

A WES service runs a whole workflow, e.g., in CWL, Nextflow, Snakemake or WDL, depending on the service. See GA4GH WES.

Krini sends your access token to WES services, so you need to be logged in, and to have access to the service (see Before you start).

  1. Open Workflows and select Create Workflow.
  2. Choose a WES service in Select WES Instance. Krini shows the workflow types and versions that it supports.

  3. Fill in the form:

    Field What to enter
    Workflow URL (required) The address of the workflow file, e.g., on GitHub (use the raw file), or a path within the files that you attach.
    Workflow Type, Workflow Type Version (required) One of the types and versions that the service supports.
    Workflow Parameters (JSON) (required) The inputs of the workflow as a JSON object, e.g., {"input_file": "https://example.com/input.txt"}. Use {} if it has none.
    Engine Parameters (JSON), under Advanced Configuration Settings of the workflow engine, if the service accepts them.
    Tags (Optional) Keys and values, e.g., for a project.
    Workflow Attachments (Optional) Files that the service needs next to the workflow, e.g., its other files or a configuration.

  4. Select Submit Run. Krini shows the run ID, or the error of the service. Reset clears the form.

Follow your workflow runs

Workflows lists the runs of the selected service, ten per page, with their run IDs and states. Cancel stops a run that is queued, initialising or running.

The states are those of WES: QUEUED, INITIALIZING, RUNNING, PAUSED, COMPLETE, EXECUTOR_ERROR, SYSTEM_ERROR, CANCELING, CANCELED, PREEMPTED and UNKNOWN (see Follow your tasks for what they mean).

Read the details and outputs of a run

The button View Details doesn't open anything in Krini yet (krini#66). To read the log and the outputs of a run, ask the WES service directly with your access token:

  1. In Krini, select Copy token to Dashboard (see Copy your access token).
  2. Look up the API endpoint of the service: select the info icon next to the service in Select WES Instance. API endpoint shows the address of its service info, e.g., https://wes.example.org/ga4gh/wes/v1/service-info; the API endpoint is that address without /service-info.

  3. In a terminal (Bash or Zsh), read the token, then call the service with the endpoint and the run ID:

    read -rs TOKEN   # paste the token and press Enter; it isn't shown or saved in the history
printf 'Authorization: Bearer %s\n' "$TOKEN" |
  curl -H @- "<API endpoint>/runs/<run ID>"

    curl -H @- reads the header from its input, so the token doesn't appear in the list of running processes either.

The answer has the state of the run, its request, the logs of the run and of its tasks, and, under outputs, its outputs. Where the outputs are depends on the service, e.g., in a bucket of its object storage.

Copy your access token

To use the services outside Krini, e.g., with curl (see Using the APIs), select Copy token to Dashboard in the menu at the bottom of the sidebar. Krini copies your LS Login access token to the clipboard.

Keep your token to yourself

Anyone with your token can act as you at the services until it expires. Don't share it, and don't paste it into chats, issues or files that you commit.

The token expires after a while; copy a new one when a service answers 401 Unauthorized.

Troubleshooting

Message What to do
"Login to fetch TES servers from registry." The Cloud Registry asked for a login. Log in and open the page again.
"Failed to fetch TES servers." or "Failed to load WES instances" Krini couldn't reach the Cloud Registry. Try again later; for WES, select Retry.
A WES service is greyed out in the list The service didn't answer. Select Refresh later.
"Service Information Unavailable" or "No Workflow Types Reported" The service didn't say which workflow types it supports. You can still submit, but check with its operator first.
"Identity Provider Error" in the sidebar Krini couldn't reach LS Login. Select the message to try again.
"Invalid state found. State does not match." or "Invalid request parameters found." after login The login didn't complete. Select Go to Login and log in again.
A service answers 401 or 403 You aren't logged in, your token expired, or the service doesn't give you access. Log in again, or ask for access (see Before you start).

What's coming

These are planned in the Krini repository, not available yet:

  • Run TES tasks with your token, through the Cloud Components (krini#41), and send your token to all services (krini#44).
  • Access tiers, so that Krini shows what you may use (krini#43), and a link to ask for access to compute (krini#45).
  • Forms for workflow inputs, built from the workflow's I/O schema (krini#47).
  • For tasks through the proTES gateway: where a task ran (krini#48), and which gateway plugins to use (krini#49).
  • The details, log and outputs of a workflow run in Krini (krini#66), and task outputs from the task form (cloud-components#574).
  • A prefilled demo task and workflow (krini#57).

Getting help