Gap Analysis ORM

This is an ORM (Object-Relational Mapping) that uses the Mongoengine library to interact with a MongoDB database. This ORM has been designed to handle information related to accessions, crop groups, crops and countries.

Features

• Built using Mongoengine for MongoDB
• Supports Python 3.x

Getting Started

To use this ORM, it is necessary to have an instance of MongoDB running.

Prerequisites

• Python 3.x
• MongoDB

Usage

This ORM can be used as a library in other Python projects. The models are located in the my_orm/models folder, and can be imported like any other Python module. To install this orm as a library you need to execute the following command:

pip install git+https://github.com/CIAT-DAPA/spcat_orm

If you want to download a specific version of orm you can do so by indicating the version tag (@v0.0.0) at the end of the install command

pip install git+https://github.com/CIAT-DAPA/spcat_orm@v0.2.0

To interact with the database, it is necessary to connect the ORM to the MongoDB database. This can be done using the connect() function of the mongoengine library, as shown in the following example:

from mongoengine import connect
from ormgap import *

# Connect to the database
connect(host='mongodb://localhost/gap_analysis')

# Perform database queries using the models defined in ormgap/models

# Query the Accession collection
accessions = Accession.objects(species_name='Solanum lycopersicum')

# Do something with the accessions
for accession in accessions:
    print(accession.id, accession.species_name, accession.crop)

Models

Country

Represents a country in the database.

Attributes:

• iso_2: str Two-letter ISO code for the country (ISO 3166-1 alpha-2). Mandatory and unique.
• name: str Name of the country. Mandatory.

Crop

Represents a crop in the database.

Attributes:

• ext_id: str External ID of the crop. Mandatory and unique.
• name: str Name of the crop. Mandatory.
• base_name: str Base name of the crop.
• app_name: str Application name of the crop. Mandatory.

Group

Represents a group in the database.

Attributes:

• group_name: str Name of the group. Mandatory.
• crop: Crop Crop object that the group belongs to. Mandatory.
• ext_id: str External identifier for the group. Mandatory and unique.

Accession

Represents an accession in the database.

Attributes:

• species_name: str Name of the species of the accession. Optional.
• crop: Crop Crop object, Crop to which the accession belongs. Mandatory.
• landrace_group: Group Group object, Landrace group to which the accession belongs. Mandatory.
• country: Country Country object, country to which the accession belongs. Mandatory.
• institution_name: str Name of the institution that holds the accession. Optional.
• source_database: str Name of the database where the accession was originally stored. Optional.
• latitude: float Latitude of the geographical location where the accession was collected. Mandatory.
• longitude: float Longitude of the geographical location where the accession was collected. Mandatory.
• accession_id: str The identifier of the accession in source database. Optional.
• ext_id: str External identifier for the accession. Mandatory and unique.
• other_attributes: dict Additional attributes of the accession. Optional.