diff --git a/README.md b/README.md index 69f037f..2a4f851 100644 --- a/README.md +++ b/README.md @@ -22,6 +22,7 @@ This repository is the starting point for any information and tools you will nee - [TLS terminating proxies](#tls-terminating-proxies) - [File structure](#file-structure) - [BBMRI-ERIC Directory entry needed](#bbmri-eric-directory-entry-needed) + - [Loading data](#loading-data) 4. [Things you should know](#things-you-should-know) - [Auto-Updates](#auto-updates) - [Auto-Backups](#auto-backups) @@ -118,7 +119,7 @@ Mention: We will set the repository up for you. We will then send you: - A Repository Short Name (RSN). Beware: this is distinct from your site name. -- Repository URL containing the acces token eg. https://BH_Dummy:dummy_token@git.verbis.dkfz.de/bbmri-bridgehead-configs/dummy.git +- Repository URL containing the acces token eg. https://BH_Dummy:dummy_token@git.verbis.dkfz.de/-bridgehead-configs/dummy.git During the installation, your Bridgehead will download your site's configuration from GitLab and you can review the details provided to us by email. @@ -311,6 +312,28 @@ Once you edited the gitlab config, the bridgehead will autoupdate the config wit There will be a delay before the effects of Directory sync become visible. First, you will need to wait until the time you have specified in ```TIMER_CRON```. Second, the information will then be synchronized from your national node with the central European Directory. This can take up to 24 hours. +### Loading data + +The data accessed by the federated search is held in the Bridgehead in a FHIR store (we use Blaze). + +You can load data into this store by using its FHIR API: + +``` +https:///bbmri-localdatamanagement/fhir +``` +The name of your server will generally be the full name of the VM that the Bridgehead runs on. You can alternatively supply an IP address. + +The FHIR API uses basic auth. You can find the credentials in `/etc/bridgehead/.local.conf`. + +Note that if you don't have a DNS certificate for the Bridgehead, you will need to allow an insecure connection. E.g. with curl, use the `-k` flag. + +#### ETL for BBMRI and GBA + +Normally, you will need to build your own ETL to feed the Bridgehead. However, there is one case where a short cut might be available: +- If you are using CentraXX as a BIMS and you have a FHIR-Export License, then you can employ standard mapping scripts that access the CentraXX-internal data structures and map the data onto the BBMRI FHIR profile. It may be necessary to adjust a few parameters, but this is nonetheless significantly easier than writing your own ETL. + +You can find the profiles for generating FHIR in [Simplifier](https://simplifier.net/bbmri.de/~resources?category=Profile). + ## Things you should know ### Auto-Updates