relecov-platform

THIS REPO IS IN ACTIVE DEVELOPMENT.

Web application for the RELECOV Platform.
This README focuses on RELECOV Platform setup and the integration points with iSkyLIMS.
Generic iSkyLIMS steps are referenced to its official LEAME to avoid duplication.

Component	Version	Description
Apache Tomcat	8.5+	Application server, Java Servlet container.
Red Hat Enterprise Linux	7+	Operating system (Red Hat distribution).
Microsoft SQL Server	2017	Relational database system (if used externally).
Python	3.10+	Programming language.
Django	5.1.6	Web framework.

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Table of contents

• 1. Installation flow overview
• 2. System prerequisites
  • 2.1 Base packages

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1. Installation flow overview

1. Host prerequisites (packages, basic services, users/groups, directories and permissions).
2. MySQL/MariaDB: install/start, harden, create DBs and application user.
3. Restore DB dumps (if available) or perform a clean install with migrations.
4. Clone repositories: relecov-platform and iSkyLIMS.
5. Configure install_settings.txt in each project.
6. Install (dependencies + application) using install.sh.
7. Load initial data (schema, GFF, test data, iSkyLIMS projects/ontologies).
8. Start and validate (web service, Django admin access, smoke tests).

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2. System prerequisites

2.1 Base packages

Before you start, ensure:

• You have sudo privileges to install required packages.
• Database server (MySQL/MariaDB) is running.
• A local mail server is configured to send emails.
• Apache HTTP server is running.
• System dependencies are installed.

RedHat/CentOS:

sudo yum install -y redhat-lsb-core

Ubuntu:

sudo apt update && sudo apt install -y lsb-release

pkg-config:

sudo apt install -y pkgconf

MySQL server y cliente (Ubuntu):

sudo apt install -y mysql-server mysql-client

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3. Database (MySQL)

If there is no active MySQL server, it will be necessary to create one first.

Install MySQL (Ubuntu):

sudo apt install -y mysql-server mysql-client

Start SQL server and enable at start-up:

sudo systemctl start mysql
sudo systemctl enable mysql

Check that the server is active:

systemctl status mysql

Example output:

mysql.service - MySQL Community Server
Loaded: loaded (/lib/systemd/system/mysql.service; enabled; vendor preset: enabled)
Active: active (running) since Wed 2025-01-29 08:36:16 CET; 1 month 17 days ago
Main PID: 1648 (mysqld)
Status: "Server is operational"
Tasks: 46 (limit: 38269)
Memory: 772.4M
CPU: 1d 5h 31min 6.848s
CGroup: /system.slice/mysql.service
└─1648 /usr/sbin/mysqld

Create admin credentials:

sudo mysql_secure_installation

• Delete test database (test_database)
• Disable anonymous users and remote administrator access
• Reload privilege tables to apply changes

3.1 Creating the Database (once MySQL has been initialised)

Create RELECOV database:

sudo mysql -u root -p

Within the MySQL client:

CREATE DATABASE relecov;
CREATE DATABASE relecovlims;

Check if it is created correctly:

SHOW DATABASES;

Create a non-admin user for managing the new databases:

CREATE USER 'relecov_user'@'localhost' IDENTIFIED BY 'mypassword';
GRANT ALL PRIVILEGES ON relecov.* TO 'relecov_user'@'localhost';
GRANT ALL PRIVILEGES ON relecovlims.* TO 'relecov_user'@'localhost';
FLUSH PRIVILEGES;
EXIT;

Upload database backup (if applicable):

sudo mysql -p relecov     < /path/to/relecov-platform_db.sql
sudo mysql -p relecovlims < /path/to/relecov-iskylims_db.sql

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4. Clone repositories

Now that we have MySQL ready, we can begin installing the platform.

Clone the latest version of the code:

git clone [email protected]:BU-ISCIII/relecov-platform.git
git clone [email protected]:BU-ISCIII/iskylims.git

Create deployment directories:

cd /opt
sudo mkdir relecov-platform
sudo mkdir iskylims
sudo chown -R root:www-data iskylims
sudo chown -R dadmin:apache iskylims
sudo chmod 2775 iskylims

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5. Configuration – install_settings.txt

Copy the configuration template (relecov-platform):

cp relecov_platform/conf/template_install_settings.txt relecov_platform/install_settings.txt

5.1 Edit install_settings.txt – relecov-platform

### Installation path
INSTALL_PATH='/opt/relecov-platform'
PROJECT_NAME='relecov_platform'
REQUIRED_MODULES='core dashboard docs'
MIGRATION_MODULES='core dashboard'

### (optional) Python installation path where pip and python executables are located
PYTHON_BIN_PATH='/path/to/bin/python3'  # example: /usr/bin/python3

### Settings required to access database
DB_USER='relecov_user'
DB_PASS='relecov_user-password'  ## The One defined in the ddbb creation in 3.4.3
DB_NAME='relecov'
DB_SERVER_IP='mydatabaseip.isciii.es'  # 'localhost' si fuera solo para uso local
DB_PORT='3306'                         # ejemplo

### Settings required for accessing relecov-platform
LOCAL_SERVER_IP='10.22.140.235'        # example: 172.0.0.1
DNS_URL='relecov-platform.isciiides.es' # Dejarlo vacío si fuera solo para uso local
SUPERUSER='admin'

### Logs settings
LOG_TYPE='symbolic_link'                # can be symbolic_link or regular_folder
LOG_PATH='/var/log/apps/relecov-platform'  # obligatorio si LOG_TYPE='symbolic_link'

# Check whether LOG_PATH exists; if not, create it.

5.2 Edit install_settings.txt – relecov-iskylims

### Installation path and modules settings
INSTALL_PATH='/opt/iskylims'
REQUIRED_MODULES='core drylab wetlab clinic django_utils'
MIGRATION_MODULES='core drylab wetlab django_utils'
FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab'

### (optional) Python installation path where pip and python executables are located
PYTHON_BIN_PATH='python3'  # example: /opt/python/3.9.6/bin/python3

### Settings required to access database
DB_USER='relecov_user'
DB_PASS='relecov_user-password'  ## The One defined in the ddbb creation in 3.4.3
DB_NAME='relecovlims'
DB_SERVER_IP='mydatabaseip.isciii.es'   # 'localhost' si fuera solo para uso local
DB_PORT='3306'                          # ejemplo

### Settings required for sending emails
EMAIL_HOST_SERVER='localhost'
EMAIL_PORT='25'
EMAIL_HOST_USER='bioinfo'
EMAIL_HOST_PASSWORD=''
EMAIL_USE_TLS='False'

### Settings required for accessing relecov-platform
LOCAL_SERVER_IP='10.22.140.235'         # example: 172.0.0.1
DNS_URL='relecov-iskylims.isciiides.es' # '' si fuera solo para uso local
SUPERUSER='admin'                        # name of the django superuser that will be created

### Logs settings
LOG_TYPE='symbolic_link'                 # can be symbolic_link or regular_folder
LOG_PATH='/var/log/apps/relecov-iskylims'  # obligatorio si LOG_TYPE='symbolic_link'

# Check whether LOG_PATH exists; if not, create it.

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6. Installation and deployment

6.1 Instalation relecov-platform

With preloaded database:

sudo bash install.sh --upgrade dep
sudo bash install.sh --upgrade app

Full installation (without preloaded DB):

sudo bash install.sh --install full

6.2 Instalation relecov-iskylims

With preloaded database:

sudo bash install.sh --upgrade dep
sudo bash install.sh --upgrade app

Full installation (without preloaded DB):

sudo bash install.sh --install full --conf install_settings.txt

6.3 Local deployment

source activate env/bin/activate

RELECOV-PLATFORM:

./manage.py runserver 8000

RELECOV-ISKYLIMS:

./manage.py runserver 8001

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6.4 Deployment in development server

On the development server, run basic hardening and restart Apache:

# 1) Server hardening
sudo /scripts/hardening.sh

# 2) Restart the web service (apache)
sudo systemctl restart httpd

7. Post-installation data upload

Once we have both platforms deployed, we can proceed with the post-installation configuration files directly from the web.

7.1 Post-installation files – Relecov-Platform

• Loading relecov_schema.json
  In Configuration → SchemaHandling of the new deployment, it is possible to attach the latest version of relecov_schema.json.

• Loading the Annotation GFF In Configuration → Annotation of the new deployment, it is possible to attach the GFF file.

• iSkyLIMS verification In the admin panel of the new deployment, verify that ISKYLIMS_SERVER in /admin/core/configsetting/ points to relecov-lims.

7.2 Post-installation files – Relecov-Iskylims

• Create relecovbot as a user in the admin panel: /admin/auth/user/.

Configure the RELECOV scheme in iSkyLIMS (via web interface)

1. URL for accessing the WetLab module (adjust to your environment):
   http://----/wetlab (or equivalent).

2. Access
   Log in to …/wetlab with your iSkyLIMS username.

3. Navigation
   Go to: PARAMETERS SETTINGS → Define Sample projects.

4. Create (or locate) the RELECOV project

   • If it does not exist, click Add and create a project that includes ‘RELECOV’ in the name.
   • In Manager, select isabel.cuesta (or the manager defined for your installation).
   • Save the changes.

5. Cargar campos desde el esquema («Load batch»)

   • Dentro del proyecto RELECOV: Define fields → Load batch
   • Upload schema: seleccionar el archivo relecov_schema.json.
   • Property where to fetch fields: classification
   • Seleccionar los valores que se van a filtrar (deben coincidir con las Classification del esquema que quieras cargar). Marca:
     • Identificadores de la base de datos
     • Información de los archivos
     • Información del host
     • Pruebas de diagnóstico de patógenos
     • Recogida y procesamiento de muestras
     • Secuenciación
   • Confirmar y guardar.

6. Ontologymap (variable mapping)
   Configure the relationships between iSkyLIMS variables to map based on the schema ontology. Go to:
   http://…./admin/core/ontologymap/ and adjust, for example:

   • sample_type → SNOMED:703065002
   • lab_request → GENEPIO:0001159 (submitting_institution)
   • species → SNOMED:410607006 (Organism)
   • sample_name → GENEPIO:0000079 (sequencing_sample_id)
   • sample_entry_date → SNOMED:281271004 (received_date)
   • collection_sample_date → SNOMED:399445004 (sample_collection_date)

7. Define Species
   Register the different organisms in the schema at http://…./admin/core/species/:

   • Severe acute respiratory syndrome coronavirus 2
   • Respiratory syncytial virus
   • Influenza virus

8. Apply ‘wetlab’
   In the Apps name section, select wetlab.

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