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Merge pull request #25 from CBBIO/fantasia
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doc fix
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frapercan authored Dec 19, 2024
2 parents eeb7fa5 + 7adc713 commit 05781c3
Showing 1 changed file with 30 additions and 16 deletions.
46 changes: 30 additions & 16 deletions README.md
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Expand Up @@ -46,11 +46,28 @@ docker run -d --name pgvectorsql \

Once the container is running, connect to the database and enable the `vector` extension:

```sql
CREATE EXTENSION IF NOT EXISTS vector;
```bash
docker exec -it pgvectorsql psql -U usuario -d BioData -c "CREATE EXTENSION IF NOT EXISTS vector;"
```

### 3. Set Up RabbitMQ
### 3. (Optional) Connect to the Database

You can use **pgAdmin 4**, a graphical interface for managing and interacting with PostgreSQL databases, or any other SQL client. Use the connection details defined during the `docker run` command (`POSTGRES_USER`, `POSTGRES_PASSWORD`, `POSTGRES_DB`, `port`) to access the database.

For more information or to download pgAdmin 4, visit the official website: [pgAdmin 4](https://www.pgadmin.org/).

After connecting to the database, you can:

- **Verify the database status**:
Check that the database is running and accepting connections.
- **Inspect tables and schema**:
Explore the database structure, including tables, columns, and relationships.
- **Run queries**:
Perform SQL operations such as inserting, updating, or retrieving data.
- **Monitor activity**:
Trace database activity by reviewing logs and active processes.

### 4. Set Up RabbitMQ

Start a RabbitMQ container using the command below:

Expand All @@ -61,27 +78,24 @@ docker run -d --name rabbitmq \
rabbitmq:management
```

### 4. Install Poetry
### 5. (Optional) Manage RabbitMQ

Poetry is used for managing dependencies. Install it by following the official instructions [here](https://python-poetry.org/docs/#installation).
Once RabbitMQ is running, you can access its management interface to monitor and manage queues, exchanges, and messages.

### 5. Clone the Repository
Open your browser and go to: [RabbitMQ Management Interface](http://localhost:15672/#/queues).

Clone the repository and navigate into its directory:
From this interface, you can:

```bash
git clone https://github.com/CBBIO/protein-metamorphisms-is.git
cd protein-metamorphisms-is
```
- **Inspect queues**:
View the list of queues, their message rates, and other details.
- **Monitor message flow**:
Track the rate of incoming and outgoing messages in real-time.

### 6. Install Dependencies
Ensure that the RabbitMQ container is running and accessible at `localhost:15672`. Use the default credentials (`guest`/`guest`) unless you have configured different ones.

Use Poetry to install the project dependencies:

```bash
poetry install
```

--------
### Configuration Parameters and Constants

#### **Configuration Parameters (`config.yaml`)**
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