1. Accessing the server

You will be given an ip-address and a you can download the training.pem private key of an to access the AWS instance to access. Go to the directory where you have put saved 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_20190731T120000Z20210731T120000Z.zip (July 2019 2021 International Edition)

  • SnomedCT_ManagedServiceSEManagedServiceDK_PRODUCTION_SE1000052DK1000005_20191130T120000Z20210930T120000Z.zip (November 2019 Swedish September 2021 Danish Extension)

  • SnomedCT_InternationalRF2_PRODUCTION_20200131T120000Z20220131T120000Z.zip (January 2020 International Edition2022 International Edition)

  • SnomedCT_InternationalRF2ManagedServiceDK_PRODUCTION_DK1000005_20200309T120000Z20220331T120000Z.zip (March 2020 International Edition)SnomedCT_ManagedServiceSE_PRODUCTION_SE1000052_20200531T120000Z.zip (May 2020 Swedish 2022 Danish Extension)

• /opt/snowstorm - currently emptycontains the most recent released Snowstorm jar file

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

Elasticsearch v6v7.89.8 2 has already been installed on the server. You can check that Elasticsearch is running with the following command:

curl localhost:9200

You When normally installing Snowstorm, you will need to download the most recent release of Snowstorm (currently v4.10.2) into the /opt/snowstorm folder:

cd /opt/snowstorm
sudo wget https://github.com/IHTSDO/snowstorm/releases/download/4.10.2/snowstorm-4.10.2.jar

from the GitHub repository releases page. However, we have put the Snowstorm executable jar file on the server already.

2. 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. 

tmux
cd /opt/snowstorm
sudo java -Xms4g -Xmx4g -jar snowstorm*.jar --elasticvc.save.batch-size=10000 | sudo tee -a snowstorm.log

We are using tmux so that if you have an internet connection issue and get disconnected Snowstorm will keep running. If this happens you can reconnect to the machine and type "tmux a" to continue where you left off.
We are using tee to  to see the output in the window and copy it to a snowstorm.log file in the same directory.

3. Loading the initial data

Next load the SNAPSHOT of the July 2019 July 2021 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 endpoints and then create a new import using the start-local-file-import endpoint with the following importRequest parameter

{
  "branchPath": "MAIN",
  "createCodeSystemVersion": true,
  "filePath": "/opt/releases/SnomedCT_InternationalRF2_PRODUCTION_20210731T120000Z.zip",
  "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.

Copy this URL into a new tab to monitor the status of the job.

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 around 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?activeFilter=true&offset=0&limit=1  - which show that there are a total of 350474,830 074 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.

4. Loading the local edition or extension

As this is the first time we will be importing the local edition or extension (SE Danish extension 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.

{
  "branchPathname": "MAIN/SNOMEDCT-SEDanish Extension",
  "shortName": "SNOMEDCT-SEDK",
  "countryCode": "sedk",
  "defaultLanguageCodebranchPath": "svMAIN/SNOMEDCT-DK",
  "dependantVersionEffectiveTime": 2019073120210731,
  "namedefaultLanguageCode": "Swedish Extensiondk"
}

click 'Try it now'.

You now need to import the local extension or edition. Like last time we , we need to start the import process by creating a new import job. Look for the Import endpoint endpoints and then create a new import using :the start-local-file-import endpoint with the following importRequest parameter

{
  "branchPath": "MAIN/SNOMEDCT-SEDK",
  "createCodeSystemVersion": true,
  "filePath": "/opt/releases/SnomedCT_ManagedServiceDK_PRODUCTION_DK1000005_20210930T120000Z.zip",
  "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_ManagedServiceSE_PRODUCTION_SE1000052_20191130T120000Z.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.

5. Upgrading MAIN to a new International Edition

Every 6 months month now, there is a new International Edition and it is important to keep your terminology server up to date. For the purpose of this exercise, we will only import the relevant International Edition release that the Danish extension depends on.

Option A

The International Edition can be upgraded by importing a DELTA SNAPSHOT of the new changes onto the MAIN branch.

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

{
  "branchPath": "MAIN",
  "createCodeSystemVersion": true,
  "typefilePath": "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_20200131T120000Z20220131T120000Z.zip \
'http://localhost:8080/imports/<import-id>/archive'

Unusually, there was an interim release of the International Edition in March 2020 before the next Swedish release to respond to this year's COVID-19 pandemic. We need to import that too before the Swedish release.

",
  "type": "SNAPSHOT"
}

Option B

The International Edition can be upgraded by importing a generated DELTA of the new changes onto the MAIN branch.

We now need to create an import job using this configuration:

/opt/releases/SnomedCT_InternationalRF2_PRODUCTION_20220131T120000Z_

Delta.zip

",
  "type": "DELTA"
}

{
  "branchPath": "MAIN",
  "createCodeSystemVersion": true,
  "

filePath": 

"

click 'Try it now'. As before use the URL in the location Response Header to open a new browser tab. Refresh the page to monitor the import status.

6.1 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 MAIN/SNOMEDCT-SE branch DK branch using the CodeSystem upgrade endpoint giving the shortname, short name SNOMEDCT-SEDK:

{
  "contentAutomations": false,
  "newDependantVersion": 2020030920220131
}

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

6.2 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. 

Do this by creating an import job as before, using this configuration:

{
  "branchPath": "MAIN/SNOMEDCT-DK",
  "createCodeSystemVersion": true,
  "filePath": "/opt/releases/SnomedCT_ManagedServiceDK_PRODUCTION_DK1000005_20220331T120000Z.zip",
  "type": "SNAPSHOT"
}

click 'Try it now' and use the location Response Header to open a new browser tab. Refresh the page to monitor the import status.