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VIP Data Processor

The VIP Data Processor listens to an AWS SQS queue for messages about new data uploads to an AWS S3 bucket. It downloads the data and validates it. Results are stored and able to distribute or be reported upon.

Running

Setup

  1. Install postgres 11 (brew install postgresql11)
  2. Install pgadmin 4 (handy GUI to administer postgres): brew cask install pgadmin4
  3. Once both are installed, make sure postgres is running; If it is not, you can run brew services start postgresql@11
  4. Bring up pgadmin4 via MacOS Applications
    1. You will need to create a Master Password
    2. You will then create a new Server that connects to localhost
  5. Within Login/Group Roles in pgadmin4, Create a role called dataprocessor; Use the below SQL for guidance 
    CREATE ROLE dataprocessor LOGIN
ENCRYPTED PASSWORD 'vip2016' SUPERUSER INHERIT CREATEDB CREATEROLE NOREPLICATION;
  6. Within Databases in pgadmin4, Create a database called dataprocessor. Use the below SQL for guidance 
    CREATE DATABASE dataprocessor
WITH OWNER = dataprocessor
ENCODING = 'UTF8'
TABLESPACE = pg_default
LC_COLLATE = 'en_US.UTF-8'
LC_CTYPE = 'en_US.UTF-8'
CONNECTION LIMIT = -1;

lein

To run the processor against a local .zip, you'll need to have followed the above Postgres steps and have it running and a minimal conifguration file.

Create dev-resources/config.edn with a map that looks like the following (using values for your Postgres server):

{:postgres {:database "dataprocessor"
            :host "localhost"
            :port 5432
            :user "dataprocessor"
            :password nil}}

Then use lein run to process a zip file:

$ lein run ~/path/to/upload.zip

This will validate the data, import it into Postgres, and generate an XML feed.

The last line logged will be a Clojure map with information about the run, including:

  • its import-id which is used pervasively in the Postgres database as the results_id column in almost every table
  • the location of the SQLite scratch database used during processing
  • the location of the XML file generated

When diagnosing problems with processing, those can help you get started.

Docker

If you'd like to run data-processor locally exactly as it's run in production, you will need Docker.

Configuration in Docker is set via the .env file in the root of the project. Create that file, copy the following into it and provide values for each environment variable.

DB_PORT_5432_TCP_ADDR=
DB_ENV_POSTGRES_USER=
DB_ENV_POSTGRES_PASSWORD=
DB_ENV_POSTGRES_DATABASE=
POSTGRES_USER=
POSTGRES_PASSWORD=
VIP_DP_AWS_ACCESS_KEY=
VIP_DP_AWS_SECRET_KEY=
VIP_DP_AWS_REGION=
VIP_DP_S3_UNPROCESSED_BUCKET=
VIP_DP_S3_PROCESSED_BUCKET=
VIP_DP_SQS_QUEUE=
VIP_DP_SQS_FAIL_QUEUE=
VIP_DP_SNS_SUCCESS_TOPIC=
VIP_DP_SNS_FAILURE_TOPIC=
VIP_DP_MAX_ZIPFILE_SIZE=(3221225472 = 3GB by default)

As you can see, you'll need to have set up an S3 bucket and two SQS queues and two SNS topics.

The S3 bucket is where the processed results file ends up (if applicable).

The SQS queues are for initiating feed processing with a message structured like: {:filename "path/to/file.zip" :bucket "source-s3-bucket"}. Sending this to the queue configured as VIP_DP_SQS_QUEUE will kick off processing of the file located in source-s3-bucket/path/to/file.zip. If, for some reason, processing fails, a copy of the message is sent to the VIP_DP_SQS_FAIL_QUEUE, wrapped with some extra info about the attempt and the cause of the failure.

The SNS topics are for broadcasting the results of feed processing, one for successful outcomes and the other for failures. Interested applications will subscribe an SQS queue to the topic and get a copy of the message.

The format for the VIP_DP_AWS_REGION should be like us-east-1.

Running it is as per usual for docker-compose:

$ docker-compose build
$ docker-compose up

While it's running, you can place messages on the SQS queue specified by VIP_DP_SQS_QUEUE and it will be picked up by the processor, downloading the file in the message, the file will be processed, the database populated, the XML output zipped up and placed in the bucket specified by VIP_DP_S3_PROCESSED_BUCKET, and a message sent the appropriate SNS topic depending on success/failure. While it's running, you can access the PostgreSQL server running within Docker on port 55432.

The message you send on the SQS queue must look like the following:

{:filename "some-feed.xml"
 :bucket "some-s3-bucket-name"}

These two values let data-processor know where to find the file and what name it has.

Testing

Non-Postgres tests

lein test

Postgres tests

There are two ways you can do this.

Local DB

Using a locally running postgres db lein test :postgres

Docker

Will create a DB as part of the docker-compose stack script/postgres-tests

Developing

The processing pipeline is defined as a sequence of functions that take and return a processing context. The processing context is a map containing an :input, processing functions in :pipeline, and validation failures in :warnings, :errors, :critical, and :fatal.

The Processing Pipeline

run-pipeline function in the vip.data-processor.pipeline namespace takes a context and will thread that context through each function in its :pipeline. Those processing functions may alter the :pipeline (for example, to alter how uploads are loaded into the database based on file type, or to add extra processing functions only if all validations are successful).

Any processing function may add a :stop key to the processing context which will halt the processing pipeline, returning the current context as the final result.

Uncaught exceptions in a processing function will result in a :stop key on the processing context and the exception being added as the :exception.

Processing Functions

Transforms

A processing function may alter the :input key for further processing functions (e.g., validation.transforms/download-from-s3, which takes the :input of an incoming context describing the location of a file on S3, downloads that file, and associates that file object to the :input key of the outgoing context). Such functions can be called transforms.

Branches

A processing function may alter the :pipeline key, as well, allowing for branching within a processing pipeline (e.g., XML and CSV files will need to be transformed differently into a database representation). Such functions can be called branches.

Validations

Validation functions check something about the context, reporting any failures in the :warnings, :errors, :critical or :fatal keys of the processing context depending on the severity of the failure.

The structure of those failure maps is the following: At the top level is the severity. Next is the scope of the failure (e.g., the filename or the XML node where the problem lies). Then the kind of problem (e.g., :duplicate-rows or :missing-headers). And finally, a message or sequence of bad data some further error message UI may use to provide feedback to the use.

For example:

{:critical
  {"contest.txt"
    {:missing-headers ["election_id", "type"]
     :reference-error {"ballot_id" [{:line 4 "ballot_id" 108}
                                    {:line 6 "ballot_id" 109}]
                       "election_id" [{:line 2 "election_id" 210}]}}}}

Validation function are simply functions that accept a processing context and return one, optionally adding failure report as above. Typically, they'll look something like the following:

(defn validate-source-cromulence [ctx]
  (let [source-table (get-in ctx [:tables :sources])]
    (if (cromulent? source-table)
      ctx  ;; everything is okay, just return the context as-is
      (assoc-in ctx [:errors :source :cromulence]  ;; otherwise add error
                "Source is not cromulent"))))

To add a validation to all processing, it should be added to the pipeline list in the vip.data-processor namespace. If it's only required for XML or CSV processing, it should be added to the xml-validations or csv-validations lists respectively in the vip.data-processor.validation.transforms namespace.

Separated Pipelines

Prior versions of the codebase had one basic pipeline that jumped around from namespace to namespace and sometimes branched based on feed format (xml/csv) and/or spec version, with the branches then concatenating new steps into the pipeline. This was often confusing to follow, and it also encouraged some aspects of the context to pull double duty, being treated differently based on which format and spec version was currently being processed. The prime example of this is the :input keyword, which at first held the EDN message that kicks off processing, then the zip/xml file, then the extracted file contents (or if it was a plain XML file, it got wrapped into a vector so that it had the same collection mechanics that the collection of CSV files does).

The new pipelines are more explicit. There's a common section that all of the pipelines run to process the EDN message, download the file from S3, validate some file aspects (like maximum uncompressed size, weeding out files with irrelevant extensions), and lastly determining which format and spec the feed is in, and then placing the files in a format appropriate location in the context (:xml-source-file-path and :csv-source-file-paths). No more is the XML file the first in a collection of files, which presumably only holds the one file. It's now the only file path at :xml-source-file-path. And rather than :input being mutated over and over again from step to step in the common pipeline, there are separate keywords in the context for holding :filename, :file, :extracted-file-paths, :valid-file-paths, and then lastly the source file paths mentioned above. Soon we'll add some specs to pre-validate calls to the pipeline functions that expect the context to have a certain shape on entry and post-validate additions to the context.

Once the feed format and spec have been determined and the source files put into their appropriate places in the context, then there's one jump to the pipeline for that particular combination of format and spec. You can find these pipelines under the namespaces vip.data-processor.pipelines.xml and vip.data-processor.pipelines.csv, both of which then have namespaces v3 and v5. In these namespace you can see all/most of the steps for that particular flavor of pipeline laid out, rather than needing to trace execution from namespace to namespace. There are still a few sub-pipelines that collect a lot of the validations out there that are concatenated in, but in general it should be much easier to follow, and to make changes to a specific pipeline.

Deploying

data-processor is currently deployed as a CoreOS cluster running atop AWS EC2 instances. There are two ways code can be deployed.

Automatic Deploys

The most common way of deploying new code is by merging an approved PR into the master branch. Buildkite, a continuous integration services, monitors this repository and triggers a build when code is pushed. For most branches, the build consists of running a test suite. Code pushed to the master branch - usually by merging an approved pull request - runs the test suite, and if that is successful, builds a Docker image and deploys it to the production CoreOS cluster.

Manual Deploys

In order to manually deploy something other than the master branch's HEAD, e.g, to test new features in a staging environment, you'll need to have a few things:

  • fleetctl installed (available in Homebrew)
  • The public IP address of an EC2 instance in your chosen cluster (aka $FLEETCTL_TUNNEL), and the appropriate key for that environment added to your ssh-agent, e.g. ssh-add ~/.ssh/key.pem.
  • A quay.io account to use with Docker (run docker login quay.io if you haven't already)

Begin by checking out the code you want to deploy at a given commit, then run script/build. If the test suite passes, a Docker image is built. Push this image to Quay as directed by the output of the build script.

Setup your environment for fleet and run script/deploy. A successful deployment should look something like this.

$ export FLEETCTL_TUNNEL=an-ip-in-your-cluster
$ ./script/deploy
Agent pid 88741
Destroyed [email protected]
Unit [email protected] inactive
--- (re-)starting fleet service instances
Destroyed [email protected]
Unit [email protected] inactive
Unit [email protected] launched on 94554086.../10.0.103.12
Destroyed [email protected]
Unit [email protected] inactive
Unit [email protected] launched on 6f2818e4.../10.0.101.122
Destroyed [email protected]
Unit [email protected] inactive
Unit [email protected] launched on cea44c01.../10.0.104.31

You can verify that a node is running properly by checking its logs.

$ fleetctl journal -f data-processor@1
Feb 20 19:04:08 ip-10-0-103-12 bash[25140]: 19:04:08.339 [main] INFO  vip.data-processor - VIP Data Processor starting up. ID: #uuid "9cc1b957-eb61-4e1d-883d-39fffda98967"
Feb 20 19:04:08 ip-10-0-103-12 bash[25140]: 19:04:08.422 [main] INFO  vip.data-processor.db.postgres - Initializing Postgres
Feb 20 19:04:08 ip-10-0-103-12 bash[25140]: Migrating #ragtime.jdbc.SqlDatabase{:db-spec {:connection-uri jdbc:postgresql://your-db-host:5432/database?user=vip&password=secret-secret}, :migrations-table ragtime_migrations, :url jdbc:postgresql://your-db-host:5432/database?user=vip&password=secret-secret, :connection-uri jdbc:postgresql://your-db-host:5432/database?user=vip&password=secret-secret, :db {:type :sql, :url jdbc:postgresql://your-db-host:5432/database?user=vip&password=secret-secret}, :migrator resources/migrations}
Feb 20 19:04:09 ip-10-0-103-12 bash[25140]: 19:04:09.296 [clojure-agent-send-off-pool-0] INFO  squishy.core - Consuming SQS messages from https://sqs.us-east-1.amazonaws.com/1234/your-sqs-queue

Database Maintenance

cleanup.feeds_by_election looks at any election that has more than 5 copies in the database and returns a list of old_runs and a list of new_runs.

To delete any but the most recent 5 versions of a feed (where two feeds are considered the "same" if they have the same state, vip_id, election_date, and election_type) run

delete from results where id in (select unnest(old_runs) from cleanup.feeds_by_election);

Migrations

For development, there are a couple of options for manually running, rolling back, and creating migrations. We now have aliases setup so you can activate these from the command line, or you can also run them from a REPL in the dev.core namespace.

Command Line Migration Interactions

Running pending migrations

lein migrate

Seeing if there are pending migrations

lein pending

Creating new migration up/down files

lein create 01-my-cool-new-migration

With this one, the joplin subsystem automatically prepends the date in YYYYMMDD- format to the value you supply, and creates up/down migration files. If you have multiple migrations on the same day that you want applied in a particular order, our best practice is to start your migrations with 01-, 02-, 03-. That way when the date is prepended, the migrations lexically sort with the 01 first, then 02, 03, etc.

Rolling back migrations

Rollback the most recent migration lein rollback

Rollback N number of migrations lein rollback N (where N is some integer between 1 and the total number of migrations applied)

Rollback all migrations after a particular ID lein rollback 20210615-01-my-cool-new-migration (Note that this is the full ID including the date stamp, but minus the up/down parts)

REPL

Alternatively to the command line options above, you can call the functions in the dev.core namespace directly. The following examples assume you're in the dev.core namespace, which is the default when you fire up a REPL.

Run all pending migrations

(migrate)

List all pending migrations

(pending)

Create a new migration

See the notes about naming migrations under the command line section. (create "01-my-cool-new-migration")

Rollback migrations

Rollback the last migration (rollback)

Rollback the last N migrations (where N is an integer between 1 and the number of applied migrations) (rollback N)

Rollback all migrations applied after a specific migration ID (see notes above in command line section) (rollback "20210605-01-my-cool-new-migration")