Accessing the server

You will be given an ip-address and a private key of an AWS instance to access. Go to the directory where you have put the training.pem file and run:

chmod 700 training.pem
ssh -i training.pem ubuntu@<ip-address>

On the server you will find:

• /opt/releases - containing the following:
  • SnomedCT_InternationalRF2_PRODUCTION_20200309T120000Z.zip (March 2020 International Edition)
  • SnomedCT_ManagedServiceDK_PRODUCTION_DK1000005_20200331T120000Z.zip (March 2020 Danish Extension)

  • SnomedCT_InternationalRF2_PRODUCTION_20200731T120000Z.zip (July 2020 International Edition)

  • SnomedCT_ManagedServiceDK_PRODUCTION_DK1000005_20200930T120000Z.zip (September 2020 Danish Extension)

• /opt/snowstorm - currently empty

• /opt/Frontend-Interaction-Demonstration - containing the following:
  
  • demo front end HTML for some exercises

Elasticsearch v7.9.2 has already been installed on the server. You can check that Elasticsearch is running with the following command:

curl localhost:9200

You will need to download the most recent release of Snowstorm (currently v5.0.6) into the /opt/snowstorm folder:

cd /opt/snowstorm
sudo wget https://github.com/IHTSDO/snowstorm/releases/download/5.0.6/snowstorm-5.0.6.jar

Starting Snowstorm

To start snowstorm you will need to run the following commands.
(Documentation available starting-snowstorm)

The simplest thing is to leave an SSH window open with this command running so you can easily access the log output. Advanced linux users feel free to use tmux or similar instead to simulate multiple sessions.

cd /opt/snowstorm
sudo java -Xms4g -Xmx4g -jar snowstorm*.jar | sudo tee -a snowstorm.log

We are using tee to see the output in the window and copy it to a snowstorm.log file in the same directory.

Loading the initial data

Next load the SNAPSHOT of the March 2020 International Edition. 
(Documentation available loading-snomed)

We will use the REST API to run the imports. Access the Snowstorm swagger interface using the AWS instance ip-address and port 8080, for example - http://<ip-address>:8080/

First we need to start the import process by creating a new import job. Look for the Import endpoint and then create a new import using

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

... and click on 'Try it now'.

The Response Headers will contain the location of the newly created job. Note the id of the import job as you will need it for the next step, this is a UUID it will look something like "d0b30d96-3714-443e-99a5-2f282b1f1b0".

We now need to upload the SNOMED CT release file. Normally, you would do this through the swagger interface but to reduce network load will use curl to upload the file from disk on the server directly.

Edit the command below replacing <import id> and then run on the server. We've also created a handy text file that you can use to easily edit the command - import.http - in a text editor.

curl -i -X POST \
--header 'Content-Type: multipart/form-data' \
--header 'Accept: application/json' \
-F file=@/opt/releases/SnomedCT_InternationalRF2_PRODUCTION_20200309T120000Z.zip \
'http://localhost:8080/imports/<import-id>/archive'

You can watch the Snowstorm log to see how this is progressing or fetch the job status from the import job URL - http://<ip-address>:8080/imports/<import_id> .

This should take no more than 30 minutes.

If you want to check that you have imported successfully, you can do this by seeing how many SNOMED CT concepts there are on the MAIN branch with the following URL - http://<ip-address>:8080/MAIN/concepts?offset=0&limit=1  - which show that there are a total of 481,044 active and inactive concepts.

Code System Registry

The Snowstorm Code System Registry should now have a single code system listed here: http://<ip-address>:8080/codesystems
And a single SNOMEDCT version listed here: http://<ip-address>:8080/codesystems/SNOMEDCT/versions

Check the registry throughout this exercise to see your changes reflected.

Loading the local edition or extension

As this is the first time we will be importing the local edition or extension (IE in this instance), we will need to create a CodeSystem on the server.
On the swagger interface in the ‘Code Systems’ section look for the ‘Create a code system’ endpoint. 
Use the following in the request to create the CodeSystem. Note the dependantVersionEffectiveTime allows you to create a CodeSystem dependent on a specific International Edition version.

{
  "branchPath": "MAIN/SNOMEDCT-DK",
  "shortName": "SNOMEDCT-DK",
  "countryCode": "dk",
  "defaultLanguageCode": "da",
  "dependantVersionEffectiveTime": 20200309,
  "defaultLanguageReferenceSets": [
        "554461000005103"
  ],
  "name": "Danish Extension"
}

click 'Try it now'.

You now need to import the local extension or edition. Like last time we start the import process by creating a new import job. Look for the Import endpoint and then create a new import using:

{
  "branchPath": "MAIN/SNOMEDCT-DK",
  "createCodeSystemVersion": true,
  "type": "SNAPSHOT"
}

click 'Try it now'.

Copy the "location" from the Response Headers and open this in a new browser tab. The status will be WAITING_FOR_FILE.

We now upload the SE release file. Normally, you would do this through the swagger interface but to reduce network load will use curl to upload the file from disk on the server directly.

Edit the command below replacing <import id> with the UUID from the import location URL and then run on the server.

curl -X POST \
--header 'Content-Type: multipart/form-data' \
--header 'Accept: application/json' \
-F file=@/opt/releases/SnomedCT_ManagedServiceDK_PRODUCTION_DK1000005_20200331T120000Z.zip \
'http://localhost:8080/imports/<import-id>/archive'

Refresh the import job in your browser to see the status change from WAITING_FOR_FILE to RUNNING and then COMPLETED. You can also see how this is progressing in the Snowstorm log.

This should take no more than a few minutes.

Upgrading MAIN to a new International Edition

Every 6 months there is a new International Edition and it is important to keep your terminology server up to date. The International Edition can be upgraded by importing a DELTA of the new changes onto the MAIN branch.

First, we need to create an import job using this configuration:

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

click 'Try it now' and note the id of the import as before. Use the Response Header location to open a new browser tab. Refresh the page to monitor the import status.

Then give the server the file as before. Replace the <import id>.

curl -X POST \
--header 'Content-Type: multipart/form-data' \
--header 'Accept: application/json' \
-F file=@/opt/releases/SnomedCT_InternationalRF2_PRODUCTION_20200731T120000Z.zip \
'http://localhost:8080/imports/<import-id>/archive'

Upgrading the extension/edition branch to the new International Edition (merging the branch)

We now need to upgrade the local extension/edition branch to use the newly imported International Edition release content.

In our example, we will now rebase the SNOMEDCT-SE branch using the CodeSystem upgrade endpoint giving the shortname, SNOMEDCT-SE:

{
  "newDependantVersion": 20200731
}

You can check this has been successful by checking the status of the branch and seeing if it is FORWARD.

Upgrading to a new extension or edition

Using what you have already done, see if you can do this making note the type and the branch that you will import into.