Commit 7b78d8c9 authored by Mikaël Salson's avatar Mikaël Salson

Merge branch 'feature-s/4506-healthcare-compliance-warning' into 'dev'

Healthcare-compliant servers : documentation, warnings

Closes #4506

See merge request !813
parents 172ac2d3 2add31e7
Pipeline #188857 failed with stages
in 10 minutes and 23 seconds
# Hosting options and healthcare compliance
The Vidjil platform is open-source.
We gladly help any people to install or use the platform.
Through the VidjilNet consortium, we also offer options for data hosting and processing.
## Public server – [app.vidjil.org](https://app.vidjil.org)
- Open and free for anyone, with basic support
- Research use only
- University data center: [Mésocentre de Calcul Scientifique Intensif de l'Université de Lille](http://hpc.univ-lille.fr/), in Lille (F)
## VidjilNet Healthcare server – [health.vidjil.org](http://health.vidjil.org)
- Available for [VidjilNet](http://www.vidjil.net) members, with dedicated support
- Suitable for production and hosting clinical data in France and some other EU countries
- Secure data center in Gravelines (F) contracted with [OVHcloud Healthcare](https://www.ovhcloud.com/en/enterprise/solutions/certified-cloud-solutions/healthcare-data-hosting-hds/)
- Data hosting: ISO 27001, compliant with healthcare data hosting regulation (GDPR, French HDS certification)
- Eligible for laboratory accreditation (through COFRAC in France or national equivalents in other EU countries)
## In-lab/in-hospital Hosting
- Installed by your local IT staff, with support from the Vidjil team
- Documentation on [installation and maintenance](server.md#docker-installation)
- Remote dedicated support and/or maintenance available for [VidjilNet](http://www.vidjil.net) members, possibly through remote SSH access
- Suitable for production and hosting clinical data, depending the regulations of your country
- Eligible for laboratory accreditation (through COFRAC in France or national equivalents in other EU countries)
...@@ -23,6 +23,7 @@ sequencing methods and software, called either Rep-Seq or AIRR-Seq. ...@@ -23,6 +23,7 @@ sequencing methods and software, called either Rep-Seq or AIRR-Seq.
- Web platform [user manual](user.md). This is the main user manual of the Vidjil platform. - Web platform [user manual](user.md). This is the main user manual of the Vidjil platform.
- [Libraries and recombinations](locus.md), documentation on library preparation and sequencing as well on detected immune recombinations - [Libraries and recombinations](locus.md), documentation on library preparation and sequencing as well on detected immune recombinations
- [Demo access](http://app.vidjil.org/) 🔗 to the patient, experiment and sample public test server - [Demo access](http://app.vidjil.org/) 🔗 to the patient, experiment and sample public test server
- [Hosting options](healthcare.md) and healthcare compliance
### Bioinformatician ### Bioinformatician
- [Vidjil-algo documentation](vidjil-algo.md), usage from the command-line - [Vidjil-algo documentation](vidjil-algo.md), usage from the command-line
......
...@@ -269,6 +269,13 @@ Here are some notable configuration changes you should consider: ...@@ -269,6 +269,13 @@ Here are some notable configuration changes you should consider:
- Change the `FROM_EMAIL` and `ADMIN_EMAILS` variables in `vidjil-server/conf/defs.py`. - Change the `FROM_EMAIL` and `ADMIN_EMAILS` variables in `vidjil-server/conf/defs.py`.
They are used for admin emails monitoring the server an reporting errors. They are used for admin emails monitoring the server an reporting errors.
- <a name='healthcare'></a>
If, according yo your local regulations, the server is suitable for hosting clinical data,
you may update the `HEALTHCARE_COMPLIANCE` variable to remove warnings related to non-healthcare compliance.
Updating this variable is the sole responsibility of the institution responsible for the server,
and should be done in accordance with the regulations that apply in your country.
See also the [hosting options](healthcare.md) offered by the VidjilNet consortium.
- To allow users to select files from a mounted volume, - To allow users to select files from a mounted volume,
set `FILE_SOURCE` and `FILE_TYPES` in `vidjil-server/conf/defs.py`. set `FILE_SOURCE` and `FILE_TYPES` in `vidjil-server/conf/defs.py`.
In this case, the `DIR_SEQUENCES` directory will be populated with links to the selected files. In this case, the `DIR_SEQUENCES` directory will be populated with links to the selected files.
......
...@@ -3,6 +3,8 @@ This CHANGELOG concerns the Docker images of vidjil. ...@@ -3,6 +3,8 @@ This CHANGELOG concerns the Docker images of vidjil.
We publish here notes to help to update these images. We publish here notes to help to update these images.
See <http://www.vidjil.org/doc/server> See <http://www.vidjil.org/doc/server>
next version
- New variable in defs.py: `HEALTHCARE_COMPLIANCE`
vidjil/server:2020-06-22-6ec207d2 vidjil/server:2020-06-22-6ec207d2
- vidjil-algo updated to 2020.06 (from 2019.05) - vidjil-algo updated to 2020.06 (from 2019.05)
vidjil/server:2020-06-15-6ec207d2 vidjil/server:2020-06-15-6ec207d2
......
...@@ -11,6 +11,10 @@ FROM_EMAIL = 'notifications@vidjil.org' ...@@ -11,6 +11,10 @@ FROM_EMAIL = 'notifications@vidjil.org'
ADMIN_EMAILS = ['notifications@vidjil.org'] ADMIN_EMAILS = ['notifications@vidjil.org']
EMAIL_SUBJECT_START = '[Vidjil]' # Customize the start of the email subject EMAIL_SUBJECT_START = '[Vidjil]' # Customize the start of the email subject
### Server healthcare compliance
### Please see <http://www.vidjil.org/doc/server#healthcare>
HEALTHCARE_COMPLIANCE = False
### address for the sql database ### address for the sql database
### sqlite (not recommended) ### sqlite (not recommended)
# DB_ADDRESS = 'sqlite://storage.sqlite' # DB_ADDRESS = 'sqlite://storage.sqlite'
......
...@@ -10,6 +10,10 @@ SMTP_CREDENTIALS = 'vidjil:smtp_pass' # set to None if no auth required ...@@ -10,6 +10,10 @@ SMTP_CREDENTIALS = 'vidjil:smtp_pass' # set to None if no auth required
FROM_EMAIL = 'notifications@vidjil.org' FROM_EMAIL = 'notifications@vidjil.org'
ADMIN_EMAILS = ['notifications@vidjil.org'] ADMIN_EMAILS = ['notifications@vidjil.org']
### Server healthcare compliance
### Please see <http://www.vidjil.org/doc/server#healthcare>
HEALTHCARE_COMPLIANCE = False
### address for the sql database ### address for the sql database
### ###
DB_ADDRESS = 'sqlite://storage.sqlite' DB_ADDRESS = 'sqlite://storage.sqlite'
......
...@@ -16,6 +16,7 @@ nav: ...@@ -16,6 +16,7 @@ nav:
- Libraries and recombinations: locus.md - Libraries and recombinations: locus.md
- Tutorial "Mastering the Vidjil web application" 🔗: http://www.vidjil.org/doc/tutorial/mastering-vidjil.html - Tutorial "Mastering the Vidjil web application" 🔗: http://www.vidjil.org/doc/tutorial/mastering-vidjil.html
- Demo access to app.vidjil.org 🔗: http://app.vidjil.org/ - Demo access to app.vidjil.org 🔗: http://app.vidjil.org/
- Hosting options, healthcare compliance: healthcare.md
- Bioinformatician: - Bioinformatician:
- vidjil-algo, command-line manual: vidjil-algo.md - vidjil-algo, command-line manual: vidjil-algo.md
- fuse.py, converting and merging immune repertoire data: tools.md - fuse.py, converting and merging immune repertoire data: tools.md
......
...@@ -11,6 +11,10 @@ FROM_EMAIL = 'root@vidjil.org' ...@@ -11,6 +11,10 @@ FROM_EMAIL = 'root@vidjil.org'
ADMIN_EMAILS = ['notifications@vidjil.org'] ADMIN_EMAILS = ['notifications@vidjil.org']
EMAIL_SUBJECT_START = '[Vidjil]' # Customize the start of the email subject EMAIL_SUBJECT_START = '[Vidjil]' # Customize the start of the email subject
### Server healthcare compliance
### Please see <http://www.vidjil.org/doc/server#healthcare>
HEALTHCARE_COMPLIANCE = False
### Specific accounts ### Specific accounts
LIMITED_ACCOUNTS = [ ] LIMITED_ACCOUNTS = [ ]
......
...@@ -46,6 +46,15 @@ ...@@ -46,6 +46,15 @@
<i class="icon-newspaper"></i></span> <i class="icon-newspaper"></i></span>
<div class="clear"></div> <div class="clear"></div>
</div> </div>
{{ pass }}
{{ if hasattr(defs, 'HEALTHCARE_COMPLIANCE') and not defs.HEALTHCARE_COMPLIANCE: }}
<div>
<p>
<span class='warn'><b>⚠️ Research Use Only.</b></span>
This server is not compliant for clinical use.
See options for using Vidjil while <a href="http://www.vidjil.org/doc/healthcare">hosting healthcare data</a>.
</p>
</div>
{{ pass }} {{ pass }}
<div id="fieldset_container"> <div id="fieldset_container">
{{ for set_type in sets: }} {{ for set_type in sets: }}
......
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