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3 changes: 2 additions & 1 deletion .gcloudignore
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Expand Up @@ -44,4 +44,5 @@ app_*
LICENSE.md
README.md
requirements_local.txt
**/.DS_Store
**/.DS_Store
.vscode/
15 changes: 8 additions & 7 deletions README.md
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@@ -1,11 +1,12 @@
# OmicsPred backend
# OmicsPred - backend

Backend part of the OmicsPred Project

* OmicsPred website: [https://www.omicspred.org/](https://www.omicspred.org/)
* OmicsPred REST API website: [https://rest.omicspred.org/](https://rest.omicspred.org/)

## Roles

Manage import, querying and retrieval of the OmicsPred metadata:

* Scripts to import the metadata and generate the genetic scoring files (app [imports](https://github.com/OmicsPred/omicspred_backend/tree/main/imports) -> [README](https://github.com/OmicsPred/omicspred_backend/tree/main/imports/README.md))
Expand All @@ -18,10 +19,9 @@ Manage import, querying and retrieval of the OmicsPred metadata:

| Tool | Role | Version |
| ---- | ---- | ------- |
| [PostgreSQL](https://www.postgresql.org/)| Database to store and query metadata | >= 18 |
| [PostgreSQL](https://www.postgresql.org/) | Database to store and query metadata | >= 18 |
| [ElasticSearch](https://www.elastic.co/) | Server used as search engine | 8.xx (e.g. 8.19) |
| [Django ](https://www.djangoproject.com/) | Python framework to communicate with the database, the ElasticSearch indexes and build a REST API | 6.0.x (e.g. 6.0.7) |

| [Django](https://www.djangoproject.com/) | Python framework to communicate with the database, the ElasticSearch indexes and build a REST API | 6.0.x (e.g. 6.0.7) |

## Setup

Expand All @@ -47,22 +47,23 @@ Go to root of the repository (e.g. `cd .../omicspred_backend`)
python manage.py search_index --create
```

> [!WARNING]
> The indexing of the scores takes few hours (2-3h)!

To rebuild existing OmicsPred indexes:

```bash
python manage.py search_index --rebuild -f
```

> [!WARNING]
> The indexing of the scores takes few hours (2-3h)!

## Deployment

First of all, you need to rename and then update the file `app.yaml_template` to `app.yaml`.

### Local

Run the command:

```bash
python manage.py runserver
```
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2 changes: 1 addition & 1 deletion requirements_local.txt
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Expand Up @@ -6,4 +6,4 @@ openpyxl==3.1.5
PyYAML==6.0.3

# For testing only:
django-debug-toolbar==6.3.0
django-debug-toolbar==7.0.0
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