load_data.py

import pandas as pd

from annotator.models import Annotation, Drug, Person

Ani = Person.objects.get(last_name='Nguyen', first_name='Ani')
Luke = Person.objects.get(last_name='Ward', first_name='Luke')
Aimee = Person.objects.get(last_name='Deaton', first_name='Aimee')


def load_drugs(annotator):
    drug_df = pd.read_excel('data/ceased_drugs_human_targets_' + annotator.first_name + '.xlsx')

    column_to_index = dict([(c, i + 1) for i, c in enumerate(drug_df.columns)])

    for record in drug_df.itertuples():
        drug = Drug(
            key=record[column_to_index['Drug Key (Unique ID)']],
            name=record[column_to_index['Drug URL']],
            overview=record[column_to_index['Overview']],
            cl_phase_1=record[column_to_index['Key Clinical - Phase I']],
            cl_phase_2=record[column_to_index['Key Clinical - Phase II']],
            cl_phase_3=record[column_to_index['Key Clinical - Phase III']],
            annotator=annotator,
        )
        drug.save()
    print("Loaded {} drugs".format(len(drug_df)))


def load_annotations(annotator):
    annotation_df = pd.read_excel('data/all_clinical_human_target_' + annotator.first_name + '.xlsx')

    column_to_index = dict([(c, i + 1) for i, c in enumerate(annotation_df.columns)])

    for record in annotation_df.itertuples():
        mdr = record[column_to_index['mdr1']]
        if mdr == '<none>':
            mdr = record[column_to_index['mdr2']]

        annotation = Annotation(
            key=Drug.objects.get(key=record[column_to_index['Drug.Key..Unique.ID.']]),
            cui=record[column_to_index['cui']],
            mdr1=mdr,
        )
        annotation.save()
    print("Loaded {} annotations".format(len(annotation_df)))