DatasetLoader.py

from requests.exceptions import RetryError

from drugstone import models
from python_nedrex.static import get_metadata, get_license

LICENSE_FILE = "./data/license.txt"


def get_ppi_string():
    dataset, _ = models.PPIDataset.objects.get_or_create(
        name='STRING',
        link='https://string-db.org/',
        version='11.0'
    )
    return dataset


def get_ppi_apid():
    dataset, _ = models.PPIDataset.objects.get_or_create(
        name='APID',
        link='http://cicblade.dep.usal.es:8080/APID/',
        version='January 2019'
    )
    return dataset


def get_ppi_nedrex_biogrid(url):
    version = get_today_version()
    try:
        version = get_metadata()['source_databases']['biogrid']['date']
    except RetryError:
        pass

    dataset, _ = models.PPIDataset.objects.get_or_create(
        name='BioGRID',
        link=url,
        version=version
    )
    return dataset


def get_ppi_nedrex_iid(url):
    version = get_today_version()
    try:
        version = get_metadata()['source_databases']['iid']['date']
    except RetryError:
        pass

    dataset, _ = models.PPIDataset.objects.get_or_create(
        name='IID',
        link=url,
        version=version
    )
    return dataset


def get_ppi_nedrex_intact(url):
    version = get_today_version()
    try:
        version = get_metadata()['source_databases']['intact']['date']
    except RetryError:
        pass

    dataset, _ = models.PPIDataset.objects.get_or_create(
        name='IntAct',
        link=url,
        version=version
    )
    return dataset


def get_ppi_biogrid():
    dataset, _ = models.PPIDataset.objects.get_or_create(
        name='BioGRID',
        link='https://thebiogrid.org/',
        version='4.0'
    )
    return dataset


def get_drug_target_nedrex(url):
    version = get_today_version()
    try:
        version = get_metadata()['version'],
    except RetryError:
        pass

    dataset, _ = models.PDIDataset.objects.get_or_create(
        name='NeDRex',
        link=url,
        version=version
    )
    return dataset


def get_ppi_nedrex(url):
    version = get_today_version()
    try:
        version = get_metadata()['version'],
    except RetryError:
        pass

    dataset, _ = models.PPIDataset.objects.get_or_create(
        name='NeDRex',
        link=url,
        version=version
    )
    return dataset


def get_protein_disorder_nedrex(url):
    version = get_today_version()
    try:
        version = get_metadata()['version'],
    except RetryError:
        pass

    dataset, _ = models.PDisDataset.objects.get_or_create(
        name='NeDRex',
        link=url,
        version=version
    )
    return dataset


def write_license(text):
    with open(LICENSE_FILE,'w') as fh:
        fh.write(text)


def update_license():
    try:
        license = get_license()
        write_license(license)
        return license
    except RetryError:
        print(f'License could not be retreived.')
        return ""


def import_license():
    try:
        license = ""
        with open(LICENSE_FILE, 'r') as fh:
            for line in fh:
                license += line
        return license
    except FileNotFoundError:
        print(f'No license doc there yet! Make sure to run an update first!')
    return ""


def get_drug_disorder_nedrex(url):
    version = get_today_version()
    try:
        version = get_metadata()['version'],
    except RetryError:
        pass

    dataset, _ = models.DrDiDataset.objects.get_or_create(
        name='NeDRex',
        link=url,
        version=version
    )
    return dataset


def get_drug_target_chembl():
    dataset, _ = models.PDIDataset.objects.get_or_create(
        name='ChEMBL',
        link='https://www.ebi.ac.uk/chembl/',
        version='27',
    )
    return dataset


def get_drug_target_dgidb():
    dataset, _ = models.PDIDataset.objects.get_or_create(
        name='DGIdb',
        link='https://www.dgidb.org/',
        version='4.2.0'
    )
    return dataset


def get_drug_target_drugbank():
    dataset, _ = models.PDIDataset.objects.get_or_create(
        name='DrugBank',
        link='https://go.drugbank.com/',
        version='5.1.7'
    )
    return dataset


def get_disorder_protein_disgenet():
    dataset, _ = models.PDisDataset.objects.get_or_create(
        name='DisGeNET',
        link='https://www.disgenet.org/home/',
        version='6.0',
    )
    return dataset


def get_drug_disorder_drugbank():
    dataset, _ = models.DrDiDataset.objects.get_or_create(
        name='DrugBank',
        link='https://go.drugbank.com/',
        version='5.1.8',
    )
    return dataset


def get_today_version():
    import datetime
    now = datetime.date.today()
    version = f'{now.year}-{now.month}-{now.day}_temp'
    return version


def get_dis_prot_nedrex_disgenet(url):
    version = get_today_version()
    try:
        version = get_metadata()['source_databases']['disgenet']['date']
    except RetryError:
        pass

    dataset, _ = models.PDisDataset.objects.get_or_create(
        name='DisGeNET',
        link=url,
        version=version
    )
    return dataset


def get_dis_prot_nedrex_omim(url):
    version = get_today_version()
    try:
        version = get_metadata()['source_databases']['omim']['date']
    except RetryError:
        pass

    dataset, _ = models.PDisDataset.objects.get_or_create(
        name='OMIM',
        link=url,
        version=version
    )
    return dataset


def get_drdis_nedrex_drugcentral(url):
    version = get_today_version()
    try:
        version = get_metadata()['source_databases']['drug_central']['date']
    except RetryError:
        pass

    dataset, _ = models.DrDiDataset.objects.get_or_create(
        name='Drug Central',
        link=url,
        version=version
    )
    return dataset


def get_drdis_nedrex_ctd(url):
    version = get_today_version()
    try:
        version = get_metadata()['source_databases']['ctd']['date']
    except RetryError:
        pass

    dataset, _ = models.DrDiDataset.objects.get_or_create(
        name='CTD',
        link=url,
        version=version
    )
    return dataset


def get_pdr_nedrex_drugcentral(url):
    version = get_today_version()
    try:
        version = get_metadata()['source_databases']['drug_central']['date']
    except RetryError:
        pass

    dataset, _ = models.PDIDataset.objects.get_or_create(
        name='Drug Central',
        link=url,
        version=version
    )
    return dataset


def get_pdr_nedrex_drugbank(url):
    version = get_today_version()
    try:
        version = get_metadata()['source_databases']['drugbank']['date']
    except RetryError:
        pass

    dataset, _ = models.PDIDataset.objects.get_or_create(
        name='DrugBank',
        link=url,
        version=version
    )
    return dataset


def get_pdr_nedrex_datasets(url):
    return {'drugbank': get_pdr_nedrex_drugbank(url), 'drugcentral': get_pdr_nedrex_drugcentral(url)}


def get_drdis_nedrex_datasets(url):
    return {'ctd': get_drdis_nedrex_ctd(url), 'drugcentral': get_drdis_nedrex_drugcentral(url)}


def get_ppi_nedrex_datasets(url):
    return {'biogrid': get_ppi_nedrex_biogrid(url), 'iid': get_ppi_nedrex_iid(url),
            'intact': get_ppi_nedrex_intact(url)}


def get_dis_prot_nedrex_datasets(url):
    return {'disgenet': get_dis_prot_nedrex_disgenet(url), 'omim': get_dis_prot_nedrex_omim(url)}