From a00fed7df27d266797fb837691e27da3f21eea57 Mon Sep 17 00:00:00 2001 From: Croft Date: Thu, 1 Jun 2023 10:26:14 +0200 Subject: [PATCH 1/3] Changed as result of onboarding experience on the 30th * Proxy and firewall adjustments were highlighted. * The need to register with the Directory and obtain a default Collection ID was mentioned. --- README.md | 26 ++++++++++++++++++++++++-- 1 file changed, 24 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index cc70d45..446f88f 100644 --- a/README.md +++ b/README.md @@ -8,6 +8,7 @@ This repository is the starting point for any information and tools you will nee - [Hardware](#hardware) - [Software](#software) - [Network](#network) + - [Register with a Directory](#register-with-a-directory) 2. [Deployment](#deployment) - [Site name](#site-name) - [Projects](#projects) @@ -57,10 +58,31 @@ Note for Ubuntu: Please note that snap versions of Docker are not supported. ### Network -Since it needs to carry sensitive patient data, Bridgeheads are intended to be deployed within your institution's secure network and behave well even in networks in strict security settings, e.g. firewall rules. The only connectivity required is an outgoing HTTPS proxy. TLS termination is supported, too (see [below](#tls-terminating-proxies)) +A running Bridgehead requires an outgoing HTTPS proxy to communicate with the central components. + +Additionally, your site might use its own proxy. You should discuss this with your local systems administration. If a proxy is being used, you will need to note down the URL of the proxy. If it is a secure proxy, then you will also need to make a note of its username and password. This information will be used later on during the installation process. + +Note that git and Docker may also need to be configured to use this proxy. This is a job for your systems administrators. + +If there is a site firewall, this needs to be configured so that git and Docker can reach the outside world. Another job for the systems administrators. Note for Ubuntu: Please note that the uncomplicated firewall (ufw) is known to conflict with Docker [here](https://github.com/chaifeng/ufw-docker). +### Register with a Directory + +The [Directory][https://directory.bbmri-eric.eu] is a BBMRI project that aims to catalog all biobanks in Europe and beyond. Each biobank is given its own unique ID and the Directory maintains counts of the number of donors and the number of samples held at each biobank. You are strongly encouraged to register with the Directory, because this opens the door to further services, such as the [Negotiator][https://negotiator.bbmri-eric.eu/login.xhtml]. + +Generally, you should register with the BBMRI national node for the country where your biobank is based. You can find a list of contacts for the national nodes [here](http://www.bbmri-eric.eu/national-nodes/). If your country is not in this list, or you have any questions, please contact the [BBMRI helpdesk](mailto:directory@helpdesk.bbmri-eric.eu). If your biobank is for COVID samples, you can also take advantage of an accelerated registration process [here](https://docs.google.com/forms/d/e/1FAIpQLSdIFfxADikGUf1GA0M16J0HQfc2NHJ55M_E47TXahju5BlFIQ). + +Your national node will give you detailed instructions for registering, but for your information, here are the basic steps: + +* Log in to the Directory for your country. +* Add your biobank and enter its details, including contact information for a person involved in running the biobank. +* You will need to create at least one collection. +* Note the biobank ID and the collection ID that you have created - these will be needed when you register with the Locator (see below). + +Once you have registered, you should choose one of your Collections as a default collection for your biobank. This is the Collection that will be automatically used to label any samples that have not been assigned a Collection ID in your ETL process. Make a note of this ID, you will need it later on in the installation process. + ## Deployment ### Site name @@ -140,7 +162,7 @@ cd /srv/docker/bridgehead sudo ./bridgehead enroll ``` -... and follow the instructions on the screen. You should then be prompted to do the next step: +... and follow the instructions on the screen. Please send your default Collection ID and the display name of your site together with the certificate request when you enroll. You should then be prompted to do the next step: ### Starting and stopping your Bridgehead From 906b98f26e65027559ee3a9928d2882a3b5fa774 Mon Sep 17 00:00:00 2001 From: Croft Date: Thu, 1 Jun 2023 10:40:48 +0200 Subject: [PATCH 2/3] Simplified the Directory registration section --- README.md | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 446f88f..89694d1 100644 --- a/README.md +++ b/README.md @@ -70,18 +70,11 @@ Note for Ubuntu: Please note that the uncomplicated firewall (ufw) is known to c ### Register with a Directory -The [Directory][https://directory.bbmri-eric.eu] is a BBMRI project that aims to catalog all biobanks in Europe and beyond. Each biobank is given its own unique ID and the Directory maintains counts of the number of donors and the number of samples held at each biobank. You are strongly encouraged to register with the Directory, because this opens the door to further services, such as the [Negotiator][https://negotiator.bbmri-eric.eu/login.xhtml]. +If you run a biobank, you should register with the [Directory][https://directory.bbmri-eric.eu], a BBMRI project that catalogs biobanks. -Generally, you should register with the BBMRI national node for the country where your biobank is based. You can find a list of contacts for the national nodes [here](http://www.bbmri-eric.eu/national-nodes/). If your country is not in this list, or you have any questions, please contact the [BBMRI helpdesk](mailto:directory@helpdesk.bbmri-eric.eu). If your biobank is for COVID samples, you can also take advantage of an accelerated registration process [here](https://docs.google.com/forms/d/e/1FAIpQLSdIFfxADikGUf1GA0M16J0HQfc2NHJ55M_E47TXahju5BlFIQ). +To do this, contact the BBMRI national node for the country where your biobank is based, see [the list of nodes](http://www.bbmri-eric.eu/national-nodes/). -Your national node will give you detailed instructions for registering, but for your information, here are the basic steps: - -* Log in to the Directory for your country. -* Add your biobank and enter its details, including contact information for a person involved in running the biobank. -* You will need to create at least one collection. -* Note the biobank ID and the collection ID that you have created - these will be needed when you register with the Locator (see below). - -Once you have registered, you should choose one of your Collections as a default collection for your biobank. This is the Collection that will be automatically used to label any samples that have not been assigned a Collection ID in your ETL process. Make a note of this ID, you will need it later on in the installation process. +Once you have registered, **you should choose one of your sample collections as a default collection for your biobank**. This is the collection that will be automatically used to label any samples that have not been assigned a collection ID in your ETL process. Make a note of this ID, you will need it later on in the installation process. ## Deployment From 156590724393a0cdacaff15c8fbb80608e980e25 Mon Sep 17 00:00:00 2001 From: Croft Date: Thu, 1 Jun 2023 10:47:30 +0200 Subject: [PATCH 3/3] Minor text and formatting improvements --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 89694d1..3cd198e 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ This repository is the starting point for any information and tools you will nee - [Hardware](#hardware) - [Software](#software) - [Network](#network) - - [Register with a Directory](#register-with-a-directory) + - [Register with the Directory](#register-with-the-directory) 2. [Deployment](#deployment) - [Site name](#site-name) - [Projects](#projects) @@ -68,9 +68,9 @@ If there is a site firewall, this needs to be configured so that git and Docker Note for Ubuntu: Please note that the uncomplicated firewall (ufw) is known to conflict with Docker [here](https://github.com/chaifeng/ufw-docker). -### Register with a Directory +### Register with the Directory -If you run a biobank, you should register with the [Directory][https://directory.bbmri-eric.eu], a BBMRI project that catalogs biobanks. +If you run a biobank, you should register with the [Directory](https://directory.bbmri-eric.eu), a BBMRI project that catalogs biobanks. To do this, contact the BBMRI national node for the country where your biobank is based, see [the list of nodes](http://www.bbmri-eric.eu/national-nodes/).