quilt

Troubleshooting

For Catalog-specific issues, see Catalog Troubleshooting.

Missing metadata when working with Quilt packages via the API

Package.set_dir() on the package root (“.”) overrides package-level metadata. If you do not provide set_dir(".", foo, meta=baz) with a value for meta=, set_dir will set package-level metadata to None.

A common pattern is to Package.browse() to get the most recent version of a package, and then Package.push() updates. You can preserve package-level metadata when calling set_dir(".", ...) as follows:

import quilt3

p = quilt3.Package.browse(
    "user-packages/geodata", 
    registry="s3://bucket_1"
)

p.set_dir(
    ".",
    "s3://bucket_2/path/to/new/geofiles",
    meta=p.meta
)

# Push changes to the S3 registry
p.push(
    "user-packages/geodata",
    registry="s3://bucket_1",
    message="Updating package geodata source data"
)

• Reference.

QuiltConflictException when pushing a package

Package.push refuses to overwrite a package revision that the package being pushed does not descend from. A push succeeds only if the destination’s latest revision is one the local package “knows about” — i.e. it was obtained via Package.browse() (CLI: quilt3 install) or returned by a previous push. Otherwise push raises QuiltConflictException.

To resolve:

• Browse the latest revision, apply your changes to it, and push that; or
• pass force=True (CLI: --force) to overwrite the latest revision anyway; or
• pass dedupe=True to skip the push silently when the content is identical to the latest revision.

User creation and log in

Users can either be invited directly or are just-in-time provisioned (JIP) when they sign in via SSO and receive the “default role.”

Important conditions and pre-requisites

• If an admin (or any user) is created by JIP, or created through CloudFormation with an SSO Provider set to anything other than Disabled, then setting the password for that user has no effect and password login will never succeed for that user. Said another way, users created through SSO can only log in through SSO.

• You must disable SSO and enable PasswordAuth if you wish to log in as an admin using a password (as opposed to SSO).

Unable to log in

The following are common causes of failed logins. In most cases we recommend that you check the browser’s network panel for details.

1. SSO connector misconfigured. See Single sign-on (SSO) for details.
2. SSL errors are often caused by misspelled names, or incomplete Subject Alternate Names. The ACM certificate for CertificateArnELB must cover all three Quilt hostnames (plus the Connect host if Connect is enabled and CertificateArnConnect is empty) either via a suitable * or explicit Subject Alternate Names.

Changing the admin email or password

Changing the admin password is only possible with PasswordAuth=Enabled in CloudFormation and is subject to the following limitations for security reasons:

• Has no effect if SSO is in use, or was in use when the admin was first created.
• Has no effect on pre-existing admin username/password pairs.

You can click “reset password” on the login page.

To change the admin email (e.g. you have accidentally broken your admin user) try the following:

1. Change the value of the AdminEmail CloudFormation parameter to a net new email.
2. Apply the change as a stack Update.
3. Once the update is successful, the new admin can log in, set roles, and nominate other admins as needed.

General stack update failure steps

On rare occasions, Quilt stack deployment updates might fail. This can happen for several reasons. To expedite resolution of stack deployment issues, it’s helpful to have the following data and output from the following AWS CLI commands when contacting support@quilt.bio.

1. Quilt stack outputs:

    STACK_NAME="YOUR_QUILT_STACK"
    aws cloudformation describe-stacks \
        --stack-name "$STACK_NAME" \
        --query 'Stacks[].Outputs'
   

2. Initiate drift detection:

    aws cloudformation detect-stack-drift \
        --stack-name "$STACK_NAME"
   

3. After drift detection is complete:

    aws cloudformation describe-stack-resource-drifts \
        --stack-name "$STACK_NAME"
   

4. Quilt stack events:

    aws cloudformation describe-stack-events \
        --stack-name "$STACK_NAME"
   

Collect logs to diagnose

To expedite the resolution of any errors encountered while using Quilt, please capture the following logs and share them with Quilt support:

Elastic Container Service (ECS)

1. Find the name of your Quilt stack:

    aws cloudformation list-stacks
   

2. Capture Quilt log events for the last 30 minutes as follows:

    STACK_NAME="YOUR_QUILT_STACK"
    aws logs filter-log-events \
        --log-group-name "$STACK_NAME" \
        --start-time "$(( ($(date +%s) - 1800) * 1000 ))" \
        --end-time "$(( $(date +%s) * 1000 ))" > log-quilt-ecs-events.json
   

IAM permissions

Determine which principal you’re using as follows:

aws sts get-caller-identity

S3 objects

Inspect problematic objects with the following commands:

BUCKET="YOUR_BUCKET"
PREFIX="YOUR_PREFIX"
aws s3api list-object-versions --bucket "$BUCKET" --prefix "$PREFIX"
aws s3api get-object-tagging --bucket "$BUCKET" --key "$PREFIX"

Specific logical resources

Sometimes you may wish to find an ID or other information from a logical resource in a Quilt stack. The following example is for security groups. Modify the commands as needed for other resource types.

STACK_NAME="YOUR_QUILT_STACK"
RESOURCE_ID="YOUR_LOGICAL_ID"
SG_ID=$(
  aws cloudformation describe-stack-resource \
    --stack-name "$STACK_NAME" \
    --logical-resource-id "$RESOURCE_ID" \
    --query 'StackResourceDetail.PhysicalResourceId' \
    --output text
)
aws ec2 describe-security-groups --group-ids "${SG_ID}"

Event source mapping

The event source mapping is a Lambda resource that reads from SQS.

STACK_NAME="YOUR_QUILT_STACK"
aws lambda get-event-source-mapping --uuid \
    $(aws cloudformation describe-stack-resource \
        --stack-name "$STACK_NAME" \
        --logical-resource-id LambdaFunctionEventSourceMapping \
        --query StackResourceDetail.PhysicalResourceId --output text)

Remediation

If for some reason the event source mapping is disabled, it can be enabled as follows.

STACK_NAME="YOUR_QUILT_STACK"
aws lambda update-event-source-mapping --uuid \
    $(aws cloudformation describe-stack-resource \
        --stack-name "$STACK_NAME" \
        --logical-resource-id LambdaFunctionEventSourceMapping \
        --query StackResourceDetail.PhysicalResourceId \
        --output text) \
    --enabled

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