Skip to content

Latest commit

 

History

History
198 lines (167 loc) · 7.53 KB

INDEXING.md

File metadata and controls

198 lines (167 loc) · 7.53 KB
Raw

Indexing

Tanagra can query the source data directly, but for improved performance, Tanagra generates indexed tables and queries them instead. The indexer config specifies where Tanagra can write generated index tables.

Generating index tables is part of the deployment process; It is not managed by the service. There is a basic command line interface to run the indexing jobs. Currently, this CLI just uses Gradle's application plugin, so the commands are actually Gradle commands.

Running Indexing Jobs

Before running the indexing jobs, you need to specify the data mapping and indexer config files.

There are 4 steps to generating the index tables:

  1. Setup credentials with read permissions on the source data, and read-write permissions on the index data.
  2. Create the index dataset.
  3. Build the indexer code.
  4. Run the jobs.

Below you can see an example of the commands for an OMOP dataset.

Setup Credentials

You need to set up 2 types of credentials to run all parts of indexing:

  1. Default application credentials to allow Tanagra to talk to BigQuery.
  2. gcloud credentials to allow you to create a new BigQuery dataset using the bq CLI.

Default Application Credentials

Set the default application credentials to an account that has read permissions on the source data, and read-write permissions on the index data. Best practice is to use a service account that has indexing-specific permissions, but for debugging, end-user credentials can be very useful.

To use a service account key file, you can set an environment variable:

export GOOGLE_APPLICATION_CREDENTIALS=$(PWD)/rendered/tanagra_sa.json

To use end-user credentials, you can run:

gcloud auth application-default login

More information and ways to set up application default credentials in the GCP docs.

gcloud Credentials

To use a service account key file:

gcloud auth activate-service-account --key-file=$GOOGLE_APPLICATION_CREDENTIALS

To use end-user credentials:

gcloud auth login

Create Index Dataset

Create a new BigQuery dataset to hold the indexed tables. Change the location, project, and dataset name below to your own.

bq mk --location=location project_id:dataset_id

Build Code

Build the indexer code once.

source indexer/tools/local-dev.sh

If you make a change to any config file, no need to re-build. If you make a change to any Java code, you should re-build.

Run Jobs

Available Commands

Documentation for the indexing commands is generated from annotations in the Java classes as a manpage. You can also see usage help for the commands by omitting arguments. e.g.

> tanagra
Tanagra command-line interface.
Usage: tanagra [COMMAND]
Commands:
  index  Commands to run indexing.
  clean  Commands to clean up indexing outputs.
Exit codes:
  0     Successful program execution
  1     User-actionable error (e.g. missing parameter)
  2     System or internal error (e.g. validation error from within the Tanagra
         code)
  3     Unexpected error (e.g. Java exception)

Dry Run

Do a dry run first for validation. This provides a sanity check that the indexing jobs inputs, especially the SQL query inputs, are valid. This step is not required, but highly recommended to help catch errors/bugs sooner and without running a bunch of computation first. Dry run includes validating that the attribute data types specified match those returned by running the SQL query.

tanagra index underlay --indexer-config=cmssynpuf_verily --dry-run

All Jobs

Kick off all jobs for the underlay.

tanagra index underlay --indexer-config=cmssynpuf_verily

This can take a long time to complete. If e.g. your computer falls asleep, or you need to kill the process on your computer, you can re-run the same command again. You need to check that there are no in-progress Dataflow jobs in the project before kicking it off again, because the jobs check for the existence of the output BQ table (not whether there are any in-progress Dataflow jobs) to tell if they need to run.

Jobs for Entity/Group

You can also kick off the jobs for a single entity or entity group. This is helpful for testing and debugging. To kick off all the jobs for a single entity:

tanagra index entity --names=person --indexer-config=cmssynpuf_verily --dry-run
tanagra index entity --names=person --indexer-config=cmssynpuf_verily

all entities:

tanagra index entity --all --indexer-config=cmssynpuf_verily --dry-run
tanagra index entity --all --indexer-config=cmssynpuf_verily

a single entity group:

tanagra index group --names=conditionPerson --indexer-config=cmssynpuf_verily --dry-run
tanagra index group --names=conditionPerson --indexer-config=cmssynpuf_verily

all entity groups:

tanagra index group --all --indexer-config=cmssynpuf_verily --dry-run
tanagra index group --all --indexer-config=cmssynpuf_verily

All the entities in a group must be indexed before the group. The tanagra index underlay command ensures this ordering, but keep this in mind if you're running the jobs for each entity or entity group separately.

Troubleshooting

Concurrency

By default, the indexing jobs are run concurrently as much as possible. You can force it to run jobs serially by overriding the default job executor:

tanagra index underlay --indexer-config=cmssynpuf_verily --job-executor=SERIAL

Re-Run Jobs

Indexing jobs will not overwrite existing index tables. If you want to re-run indexing, either for a single entity/group or for everything, you need to delete any existing index tables. You can either do that manually or using the clean commands below. Similar to the indexing commands, the clean commands also allow dry runs.

To clean the generated index tables for everything:

tanagra clean underlay --indexer-config=cmssynpuf_verily --dry-run
tanagra clean underlay --indexer-config=cmssynpuf_verily

a single entity:

tanagra clean entity --names=person --indexer-config=cmssynpuf_verily --dry-run
tanagra clean entity --names=person --indexer-config=cmssynpuf_verily

a single entity group:

tanagra clean group --names=conditionPerson --indexer-config=cmssynpuf_verily --dry-run
tanagra clean group --names=conditionPerson --indexer-config=cmssynpuf_verily

Run Dataflow Locally

While developing a job, running locally is faster. Also, you can use Intellij debugger.

Add to BigQueryIndexingJob.buildDataflowPipelineOptions():

import org.apache.beam.runners.direct.DirectRunner;

dataflowOptions.setRunner(DirectRunner.class);
dataflowOptions.setTempLocation("gs://dataflow-staging-us-central1-694046000181/temp");

Filter On One Person

Filter your queries on one person, eg:

.where(
    new BinaryFilterVariable(
        idFieldVar,
        BinaryOperator.EQUALS,
        new Literal.Builder().dataType(DataType.INT64).int64Val(1107050).build()))

OMOP Example

The cmssynpuf underlay is a data mapping for a public dataset that uses the OMOP schema.

You can see the top-level underlay config file for this dataset here.

bq mk --location=US verily-tanagra-dev:cmssynpuf_index

tanagra index underlay --indexer-config=cmssynpuf_verily --dry-run
tanagra index underlay --indexer-config=cmssynpuf_verily