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Loading SNOMED CT into Snowstorm

Before anything, get hold of the most recent SNOMED CT International Edition RF2 release files release files.

Contents

Loading Release Snapshot

This loads the content of the current release and skips loading outdated content. This is the recommended option for development due to the speed of loading. There are two ways to do this:

Via REST

Once Snowstorm is running, you will need to start the import process by creating a new import job. Look for the Imports endpoint on Swagger, (http://localhost:8080) and then create a new import using

{
  "branchPath": "MAIN",
  "createCodeSystemVersion": true,
  "type": "SNAPSHOT"
}

and then click on 'Try it now' and then note the id of the import as you will need it for the next step (it will look something like - d0b30d96-3714-443e-99a5-2f282b1f1b0).

You now need to upload the file. You can do this through the swagger interface at the imports/archive end point, but the following will allow you to run it using curl to do this from the command line (this example uses the January 2018 release file):

curl -X POST --header 'Content-Type: multipart/form-data' --header 'Accept: application/json' -F file=@SnomedCT_InternationalRF2_PRODUCTION_20180131T120000Z.zip 'http://localhost:8080/imports/<import id>/archive'

You can watch the log to see how this is progressing, or simply to the import endpoint - http://:8080/imports/ . This can take between 20-60 minutes depending on the performance of your machine.

Via Command line

To delete any existing Snowstorm Elasticsearch indices and load the RF2 Snapshot start Snowstorm with the following arguments:

java -Xms2g -Xmx4g -jar target/snowstorm*.jar --delete-indices --import=<Absolute-path-of-SNOMED-CT-RF2-zip>

This will take between 30-60 minutes depending on the performance of your machine.

Do not use Generated Delta Files

Do not attempt to import generated delta files into Snowstorm! Since Janurary 2022 the International Edition no longer contains RF2 delta files. There is a tool to generate delta files if required but Snowstorm can not currently import these because they can contain multiple states of SNOMED CT components. When importing generated delta files the import will complete but the content will be inconsistent. Instead use the SNAPSHOT import type when importing a new version of any release that does not contain delta files. Using a Snapshot import is slightly slower than a delta but will result in the same outcome.

Loading Release Full Files

It's possible to load the RF2 Full files which gives you access to all previous releases of SNOMED CT in addition to the current content. However, this will take longer (last run took 2h15 on an m5.xlarge AWS instance with 4 vCPU and 16GB Memory), but will not have an impact to the performance.

Simply replace the --import argument above with --import-full or the type with FULL within Swagger.

Stopping After Loading

To shutdown Snowstorm after loading data automatically include the --exit flag.