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

Healthcare-compliant servers : documentation, warnings

Closes #4506

See merge request !813

doc/healthcare.md

+
+# 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)
+

doc/index.md

@@ -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.
   - [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
+  - [Hosting options](healthcare.md) and healthcare compliance
 
 ### Bioinformatician
   - [Vidjil-algo documentation](vidjil-algo.md), usage from the command-line

doc/server.md

@@ -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`.
     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,
     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.

docker/CHANGELOG

@@ -3,6 +3,8 @@ This CHANGELOG concerns the Docker images of vidjil.
 We publish here notes to help to update these images.
 See <http://www.vidjil.org/doc/server>
 
+next version
+   - New variable in defs.py: `HEALTHCARE_COMPLIANCE`
 vidjil/server:2020-06-22-6ec207d2
    - vidjil-algo updated to 2020.06 (from 2019.05)
 vidjil/server:2020-06-15-6ec207d2

docker/vidjil-server/conf/defs.py

@@ -11,6 +11,10 @@ FROM_EMAIL = 'notifications@vidjil.org'
 ADMIN_EMAILS = ['notifications@vidjil.org']
 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
 ### sqlite (not recommended)
 # DB_ADDRESS = 'sqlite://storage.sqlite'

docker/vidjil-server/conf/defs_http.py

@@ -10,6 +10,10 @@ SMTP_CREDENTIALS = 'vidjil:smtp_pass' # set to None if no auth required
 FROM_EMAIL = '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
 ###
 DB_ADDRESS = 'sqlite://storage.sqlite'

mkdocs.yml

@@ -16,6 +16,7 @@ nav:
         - Libraries and recombinations: locus.md
         - 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/
+        - Hosting options, healthcare compliance: healthcare.md
     - Bioinformatician:
         - vidjil-algo, command-line manual: vidjil-algo.md
         - fuse.py, converting and merging immune repertoire data: tools.md

server/web2py/applications/vidjil/modules/defs.py.sample

@@ -11,6 +11,10 @@ FROM_EMAIL = 'root@vidjil.org'
 ADMIN_EMAILS = ['notifications@vidjil.org']
 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
 LIMITED_ACCOUNTS = [ ]
 

server/web2py/applications/vidjil/views/sample_set/form.html

@@ -46,6 +46,15 @@
             <i class="icon-newspaper"></i></span>
       <div class="clear"></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 }}
     <div id="fieldset_container">
         {{ for set_type in sets: }}