From d9794a1eea2b02d9bdfb446d016319b328bd70bc Mon Sep 17 00:00:00 2001 From: Croft Date: Fri, 20 Oct 2023 10:21:52 +0200 Subject: [PATCH 1/3] Information about loading data into the Bridgehead's FHIR store Added this information because many sites have asked about it. --- README.md | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/README.md b/README.md index 9d50c8a..535eb4b 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) @@ -311,6 +312,29 @@ 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/bbmri.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 are two cases where a short cut might be available: +- If you are a German biobank and you already feed your data into a Data Integration Center (DIZ). In this case, you can use the [TransFAIR tool](https://github.com/samply/transFAIR) with the `bbmri2mii` profile to pull data from the DIZ and load it into the Bridgehead's FHIR store. You will need to discuss this with your local DIZ management before proceeding with this approach. +- 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 From 096225a77d9413d82f90d46f7fc802ffe6d61e5e Mon Sep 17 00:00:00 2001 From: Croft Date: Mon, 6 Nov 2023 09:28:43 +0100 Subject: [PATCH 2/3] Incorporated Patrick's comments for PR 130 --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 535eb4b..79920a8 100644 --- a/README.md +++ b/README.md @@ -323,14 +323,13 @@ 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/bbmri.local.conf`. +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 are two cases where a short cut might be available: -- If you are a German biobank and you already feed your data into a Data Integration Center (DIZ). In this case, you can use the [TransFAIR tool](https://github.com/samply/transFAIR) with the `bbmri2mii` profile to pull data from the DIZ and load it into the Bridgehead's FHIR store. You will need to discuss this with your local DIZ management before proceeding with this approach. +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). From 545c6175f5acae9971110372f4e475287d0332a8 Mon Sep 17 00:00:00 2001 From: Croft Date: Wed, 8 Nov 2023 09:55:21 +0100 Subject: [PATCH 3/3] Replaced reference to "bbmri" with more generic "project". --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 79920a8..3b692c0 100644 --- a/README.md +++ b/README.md @@ -119,7 +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.