Notifications

Notifications (Projects > your_project > Project Settings > Notifications ) are events to which you can subscribe. When they are triggered, they deliver a message to an external target system such as emails, Amazon SQS or SNS systems or HTTP post requests. The following table describes available system events to subscribe to:

Description	Code	Details	Payload
Analysis failure	ICA_EXEC_001	Emitted when an analysis fails	Analysis
Analysis success	ICA_EXEC_002	Emitted when an analysis succeeds	Analysis
Analysis aborted	ICA_EXEC_027	Emitted when an analysis is aborted either by the system or the user	Analysis
Analysis status change	ICA_EXEC_028	Emitted when an state transition on an analysis occurs	Analysis
Base Job failure	ICA_BASE_001	Emitted when a Base job fails	BaseJob
Base Job success	ICA_BASE_002	Emitted when a Base job succeeds	BaseJob
Data transfer success	ICA_DATA_002	Emitted when a data transfer is marked as Succeeded	DataTransfer
Data transfer stalled	ICA_DATA_025	Emitted when data transfer hasn't progressed in the past 2 minutes	DataTransfer
Data <action>	ICA_DATA_100	Subscribing to this serves as a wildcard for all project data status changes and covers those changes that have no separate code. This does not include DataTransfer events or changes that trigger no data status changes such as adding tags to data.	ProjectData
Data linked to project	ICA_DATA_104	Emitted when a file is linked to a project	ProjectData
Data can not be created in non-indexed folder	ICA_DATA_105	Emitted when attempting to create data in a non-indexed folder	ProjectData
Data deleted	ICA_DATA_106	Emitted when data is deleted	ProjectData
Data created	ICA_DATA_107	Emitted when data is created	ProjectData
Data uploaded	ICA_DATA_108	Emitted when data is uploaded	ProjectData
Data updated	ICA_DATA_109	Emitted when data is updated	ProjectData
Data archived	ICA_DATA_110	Emitted when data is archived	ProjectData
Data unarchived	ICA_DATA_114	Emitted when data is unarchived	ProjectData
Job status changed	ICA_JOB_001	Emitted when a job changes status (INITIALIZED, WAITING_FOR_RESOURCES, RUNNING, STOPPED, SUCCEEDED, PARTIALLY_SUCCEEDED, FAILED)	JobId
Sample completed	ICA_SMP_002	Emitted when a sample is marked as completed	ProjectSample
Sample linked to a project	ICA_SMP_003	Emitted when a sample is linked to a project	ProjectSample
Workflow session start	ICA_WFS_001	Emitted when workflow is started	WorkflowSession
Workflow session failure	ICA_WFS_002	Emitted when workflow fails	WorkflowSession
Workflow session success	ICA_WFS_003	Emitted when workflow succeeds	WorkflowSession
Workflow session aborted	ICA_WFS_004	Emitted when workflow is aborted	WorkflowSession

When you subscribe to overlapping event codes such as ICA_EXEC_002 (analysis success) and ICA_EXEC_028 (analysis status change) you will get both notifications when analysis success occurs.

When integrating with external systems, it is advised to not solely rely on ICA notifications, but to also add a polling system to check the status of long-running tasks. For example verifying the status of long-running (>24h) analyses with a 12 hour interval.

Delivery Targets

Event notifications can be delivered to the following delivery targets:

Delivery Target	Description	Value
Mail	E-mail delivery	E-mail Address
Sqs	AWS SQS Queue	AWS SQS Queue URL
Sns	AWS SNS Topic	AWS SNS Topic ARN
Http	Webhook (POST request)	URL

Amazon Resource Policy Settings

In order to allow the platform to deliver events to Amazon SQS or SNS delivery targets, a cross-account policy needs to be added to the target Amazon service.

{
   "Version":"2012-10-17",
   "Statement":[
      {
         "Effect":"Allow",
         "Principal":{
            "AWS":"arn:aws:iam::<platform_aws_account>:root"
         },
         "Action":"<action>",
         "Resource": "<arn>"
      }
   ]
}

Substitute the variables in the example above according to the table below.

Variable	Description
platform_aws_account	The platform AWS account ID: 079623148045
action	For SNS use SNS:Publish. For SQS, use SQS:SendMessage
arn	The Amazon Resource Name (ARN) of the target SNS topic or SQS queue

See examples for setting policies in Amazon SQS and Amazon SNS

Amazon SNS Topic

To create a subscription to deliver events to an Amazon SNS topic, one can use either GUI or API endpoints.

To create a subscription via GUI, select Projects > your_project > Project Settings > Notifications > +Create > ICA event. Select an event from the dropdown menu, insert optional filter, select the channel type (SNS), and then insert the ARN from the target SNS topic and the AWS region.

Settings for SNS subscription

To create a subscription via API, use the endpoint /api/notificationChannel to create a channel and then /api/projects/{projectId}/notificationSubscriptions to create a notification subscription.

Amazon SQS Queue

To create a subscription to deliver events to an Amazon SQS queue, you can use either GUI or API endpoints.

To create a subscription via the GUI, select Projects > your_project > Project Settings > Notifications > +Create > ICA event. Next, select an event from the dropdown menu, choose SQS as the way to receive the notifications, enter your SQS URL, and if applicable for that event, choose a payload version. Not all payload versions are applicable for all events and targets, so the system will filter the options out for you. Finally, you can enter a filter expression to filter which events are relevant for you. Only those events matching the expression will be received.

To create a subscription via API, use the endpoint /api/notificationChannel to create a channel and then /api/projects/{projectId}/notificationSubscriptions to create a notification subscription.

Messages delivered to AWS SQS contain the following event body attributes:

Attribute	Description
correlationId	GUID used to identify the event
timestamp	Date when the event was sent
eventCode	Event code of the event
description	Description of the event
payload	Event payload

The following example is a Data Updated event payload sent to an AWS SQS delivery target (condensed for readability):

{
    "correlationId": "2471d3e2-f3b9-434c-ae83-c7c7d3dcb4e0",
    "timestamp": "2022-10-06T07:51:09.128Z",
    "eventCode": "ICA_DATA_100",
    "description": "Data updates",
    "payload": {
        "id": "fil.8f6f9511d70e4036c60908daa70ea21c",
        ...
    }
}

Filtering

Notification subscriptions will trigger for all events matching the configured event type. A filter may be configured on a subscription to limit the matching strategy to only those event payloads which match the filter.

The filter expressions leverage the JsonPath library for describing the matching pattern to be applied to event payloads. The filter must be in the format [?(<expression>)].

Examples

The Analysis Success event delivers a JSON event payload matching the Analysis data model (as output from the API to retrieve a project analysis).

{
  "id": "0c2ed19d-9452-4258-809b-0d676EXAMPLE",
  "timeCreated": "2021-09-20T12:23:18Z",
  "timeModified": "2021-09-20T12:43:02Z",
  "ownerId": "15d51d71-b8a1-4b38-9e3d-74cdfEXAMPLE",
  "tenantId": "022c9367-8fde-48fe-b129-741a4EXAMPLE",
  "reference": "210920-1-CopyToolDev-9d78096d-35f4-47c9-b9b6-e0cbcEXAMPLE",
  "userReference": "210920-1",
  "pipeline": {
    "id": "20261676-59ac-4ea0-97bd-8a684EXAMPLE",
    "timeCreated": "2021-08-25T01:49:41Z",
    "timeModified": "2021-08-25T01:49:41Z",
    "ownerId": "15d51d71-b8a1-4b38-9e3d-74cdfEXAMPLE",
    "tenantId": "022c9367-8fde-48fe-b129-741a4EXAMPLE",
    "code": "CopyToolDev",
    "description": "CopyToolDev",
    "language": "CWL",
    "pipelineTags": {
      "technicalTags": ["Demo"]
    }
  },
  "status": "SUCCEEDED",
  "startDate": "2021-09-20T12:23:21Z",
  "endDate": "2021-09-20T12:43:00Z",
  "summary": "",
  "finishedSteps": 0,
  "totalSteps": 1,
  "tags": {
    "technicalTags": [],
    "userTags": [],
    "referenceTags": []
  }
}

The below examples demonstrate various filters operating on the above event payload:

• Filter on a pipeline, with a code that starts with ‘Copy’. You’ll need a regex expression for this:

  [?($.pipeline.code =~ /Copy.*/)]

• Filter on status (note that the Analysis success event is only emitted when the analysis is successful):

  [?($.status == 'SUCCEEDED')]

  Both payload Version V3 and V4 guarantee the presence of the final state (SUCCEEDED, FAILED, FAILED_FINAL, ABORTED) but depending on the flow (so not every intermediate state is guaranteed):

  • V3 can have REQUESTED - IN_PROGRESS - SUCCEEDED

  • V4 can have the status REQUESTED - QUEUED - INITIALIZING - PREPARING_INPUTS - IN_PROGRESS - GENERATING_OUTPUTS - SUCCEEDED

• Filter on pipeline, having a technical tag “Demo":

  [?('Demo' in $.pipeline.pipelineTags.technicalTags)]

• Combination of multiple expressions using &&. It's best practice to surround each individual expression with parentheses:

  [?(($.pipeline.code =~ /Copy.*/) && $.status == 'SUCCEEDED')]

Examples for other events

• Filtering ICA_DATA_104 on owning project name. The top level keys on which you can filter are under the payload key, so payload is not included in this filter expression.

  [?($.details.owningProjectName == 'my_project_name')]

Custom Events

Custom events enable triggering notification subscriptions using event types beyond the system-defined event types. When creating a custom subscription, a custom event code may be specified to use within the project. Events may then be sent to the specified event code using a POST API with the request body specifying the event payload.

Custom events can be defined using the API. In order to create a custom event for your project please follow the steps below:

1. Create a new custom event POST {ICA_URL}/ica/rest/api/projects/{projectId}/customEvents a. Your custom event code must be 1-20 characters long, e.g. 'ICA_CUSTOM_123'. b. That event code will be used to reference that custom event type.\

2. Create a new notification channel POST {ICA_URL}/ica/rest/api/notificationChannels a. If there is already a notification channel created with the desired configuration within the same project, it is also possible to get the existing channel ID using the call GET {ICA_URL}/ica/rest/api/notificationChannels.\

3. Create a notification subscription POST {ICA_URL}/ica/rest/api/projects/{projectId}/customNotificationSubscriptions. a. Use the event code created in step 1. b. Use the channel ID from step 2.\

To create a subscription via the GUI, select Projects > your_project > Project Settings > Notifications > +Create > Custom event.

Once the steps above have been completed successfully, the call from the first step POST {ICA_URL}/ica/rest/api/projects/{projectId}/customEvents could be reused with the same event code to continue sending events through the same channel and subscription.

Following is a sample Python function used inside an ICA pipeline to post custom events for each failed metric:

def post_custom_event(metric_name: str, metric_value: str, threshold: str, sample_name: str):
    api_url = f"{ICA_HOST}/api/projects/{PROJECT_ID}/customEvents"
    headers = {
        "Content-Type": "application/vnd.illumina.v3+json",
        "accept": "application/vnd.illumina.v3+json",
        "X-API-Key": f"{ICA_API_KEY}"
    }
    content = {\"code\": \"ICA_CUSTOM_123\", \"content\": { \"metric_name\": metric_name, \"metric_value\": metric_value,\"threshold\": threshold, \"sample_name\": sample_name}}
    json_data = json.dumps(content)
    response = requests.post(api_url, data=json_data, headers=headers)

    if response.status_code != 204:
        print(f"[EVENT-ERROR] Could not post metric failure event for the metric {metric_name} (sample {sample_name}).")