https://github.com/sing-group/evoppi-backend
Backend for the EvoPPI application
https://github.com/sing-group/evoppi-backend
comparative-analysis interactome protein-protein protein-protein-interaction web-application
Last synced: 3 months ago
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Backend for the EvoPPI application
- Host: GitHub
- URL: https://github.com/sing-group/evoppi-backend
- Owner: sing-group
- License: gpl-3.0
- Created: 2018-02-19T16:18:44.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2023-02-22T08:02:18.000Z (over 2 years ago)
- Last Synced: 2023-10-20T23:08:42.709Z (almost 2 years ago)
- Topics: comparative-analysis, interactome, protein-protein, protein-protein-interaction, web-application
- Language: Java
- Homepage: http://evoppi.i3s.up.pt/
- Size: 1.15 MB
- Stars: 0
- Watchers: 6
- Forks: 2
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# EvoPPI Backend
EvoPPI allows the easy comparison of publicly available data from the main Protein-Protein Interaction (PPI) databases for distinct species. EvoPPI allows two types of queries: (i) same species comparisons, for those queries involving two or more interactomes from a single species, and (ii) distinct species comparisons, for those queries involving two or more interactomes from two distinct species.
## Development
### Running the application
The application has been configured to be easily run locally, by just invoking
a Maven command.
To do so, Maven will download (if it is not already) a clean WildFly
distribution to the `target` folder, configure it, start it and deploy the
application on it.
This makes very easy and straightforward to manually test the application.
#### Configure a local MySQL
To execute the application you need a MySQL server running in `localhost` and
using the default port (3306).
In this server you have to create a database named `evoppi` accessible for the
`evoppi` user using the `evoppipass` password.
This can be configured executing the follow SQL sentences in your MySQL:
```SQL
CREATE DATABASE evoppi;
GRANT ALL ON evoppi.* TO evoppi@localhost IDENTIFIED BY 'evoppipass';
FLUSH PRIVILEGES;
```
Of course, this configuration can be changed in the POM file.
#### Building the application
The application can be built with the following Maven command:
```
mvn clean install
```
This will build the application launching the tests on a **Wildfly 10.1.0**
server.
#### Starting the application
The application can be started with the following Maven command:
```
mvn package wildfly:start wildfly:deploy-only -P wildfly-mysql-run
```
This will start a **WildFly 10.1.0**.
#### Redeploying the application
Once it is running, the application can be re-deployed with the following Maven
command:
```
mvn package wildfly:deploy-only -P wildfly-mysql-run
```
#### Stopping the application
The application can be stopped with the following Maven command:
```
mvn wildfly:shutdown
```
### REST API documentation
The REST API is documented using the [Swagger](https://swagger.io/) framework.
It can be browsed using the [Swagger UI](http://petstore.swagger.io/)
application to access the following URL:
```
http://localhost:8080/evoppi/rest/api/swagger.json
```
## Server configuration
EvoPPI can be installed in your own server. We recommend using a WildFly 10+
server. In addition, a Docker installation listening in a TCP port is required.
To install your own EvoPPI instance you should follow these steps.
### 1. Configure your WildFly
In the `additional-material/wildfly10/standalone.xml` file you can see a sample
configuration. This file includes the security, email and naming bindings
required by the application.
### 2. Create the database
A SQL script for MySQL to create the structure of the database required can be is
available at `additional-material/db/evoppi-mysql.sql`.
### 3. Populate database (optional)
The `additional-material/db/` directory contains several files to test EvoPPI:
- `evoppi-mysql-data.sql`: users and database version.
- `evoppi-mysql-data-genes.sql`: species, genes, interactomes, and predicted interactomes.
Alternatively, if you want to add the data of all the species currently supported by EvoPPI,
you can also download and import
[this SQL file](http://static.sing-group.org/EvoPPI/db/sql/2022.04/evoppi.sql.gz).
### 4. Deploy the application
The last step is to deploy the EvoPPI application in the WildFly server.
Packaged application can be downloaded from
[here](https://maven.sing-group.org/repository/maven-releases/org/sing_group/evoppi-ear/2.1.0/evoppi-ear-2.1.ear).
This file can be directly deployed in the WildFly server, for example, using the
administration web interface.
## Source code
Source code of this and **EvoPPI Frontend** projects can be found at:
* [EvoPPI Frontend](https://github.com/sing-group/evoppi-frontend)
* [EvoPPI Backend](https://github.com/sing-group/evoppi-backend)
## Troubleshooting and debugging
Some tips for troubleshooting and debugging issues with the database:
1. [This post](https://stackoverflow.com/a/678310/1821422) shows how to set MySQL to show the last queries being executed.
2. When loading the complete DB, the following error may arise: `The total number of locks exceeds the lock table size`. Following some of the suggestions of [this post](https://stackoverflow.com/questions/6901108/the-total-number-of-locks-exceeds-the-lock-table-size), it usually works editing the `my.cnf` file to set the following settings:
```[mysqld]
wait_timeout = 31536000
interactive_timeout = 31536000
max_allowed_packet = 1G
innodb_buffer_pool_size = 1G