-
Notifications
You must be signed in to change notification settings - Fork 15
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Ingest data from new commits in IMGTHLA repository #102
Open
chrisammon3000
wants to merge
460
commits into
nmdp-bioinformatics:main
Choose a base branch
from
chrisammon3000:conditional-deployment/merge-process-updated-releases
base: main
Could not load branches
Branch not found: {{ refName }}
Loading
Could not load tags
Nothing to show
Loading
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
Open
Ingest data from new commits in IMGTHLA repository #102
chrisammon3000
wants to merge
460
commits into
nmdp-bioinformatics:main
from
chrisammon3000:conditional-deployment/merge-process-updated-releases
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This is behind the most recent PR for Amazon Linux 2, but I'll update once it's caught up. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
New Commits
The CheckSourceUpdate Lambda function monitors the IMGTHLA source repository for new commits daily. If one or more new commits are found, the service resolves the release version number and creates new rows in the Execution State table (DynamoDB) and processes only the most recent commit for any given release. The commit's execution status is updated throughout pipeline execution using an enum class:
Execution State
A DynamoDB table is deployed to store state for pipeline executions. For new deployments, the repository's state is built using the GitHub REST API and loaded into the table.
Pipeline Request Idempotency
Idempotency is acheived by using SQS FIFO queues, where the group ID is the unique deployment ID (
${STAGE}-${APP_NAME}
) and the deduplication ID is the release version. This means that when messages are in the queue, duplicate messages are not processed and that releases are loaded in chronological order.Error Handling
Errors that occur during pipeline execution are caught and the state table entry is updated to reflect failure or aborted executions.
Database Concurrency Management
Database concurrency is maintained by a state machine called the Load Concurrency Manager (LCM). The LCM runs continuously when the main pipeline is running (by monitoring a CloudWatch Alarm) and handles the pre- and post-execution backups. This is to ensure that the database is not overloaded or shut-down during the loading process. All requests for loading data to Neo4j pass through a FIFO queue to avoid duplication and maintain the order of release versions. The consumer of the FIFO queue (
Message Received?
) will only receive one message at a time, and will not be invoked again until loading has succeeded or failed. Once the queue is empty and all releases have been loaded, the LCM will stop running.Success/Failure Notifications
Notifications are sent by email including execution outcomes, validation results and error information in the event of failure.
Pydantic Models
Pydantic is a Python framework for ensuring data integrity. Every object within the pipeline now uses a Pydantic class for automatic schema and type validation. This prevents the state table from having corrupt or missing fields when reading and writing records.
Infrastructure Changes
Known Issues
Latest
), and 2) because of inconsistencies in the versioning and availability of metadata (fix in progress)hla.dat
ormsf/
since these assets contain the source data (fix in progress)Next Steps