コード例 #1
0
def chembl_assay(chemblid):
    global CHEMBL
    if CHEMBL is None:
        from bioservices import ChEMBLdb

        CHEMBL = ChEMBLdb()

    data = CHEMBL.get_assay_by_chemblId(str(chemblid))['assay']

    return {FIELDS[key]: value for key, value in data.items()
            if key in FIELDS}
コード例 #2
0
def run(days=180):
    """Run as::

      $ python manage.py runscript update_activities

    By default, updates bioactivities of compounds that were never updated
    or updates 180 days ago.

    To force updating bioactivities for all compounds, give 0 days argument
    as follows::

        $ python manage.py runscript update_activities --script-args=0

    """

    try:
        days = int(days)
    except ValueError:
        days = 180

    chembl = ChEMBLdb()

    #for table, func in [
    #    (Compound, chembl.get_compounds_activities),
    #    (Target, chembl.get_target_bioactivities),
    #    (Assay, chembl.get_assay_bioactivities), ]:
    count = skip = error = ncomp = 0
    # will iterate over all compounds one-by-one
    for compound in Compound.objects.all():

        # if no updates were made, last_update is None
        if (compound.last_update is None or
            (datetime.date.today() - compound.last_update) >=
             datetime.timedelta(days)):
            ncomp += 1

            try:            
                acts = chembl.get_compounds_activities(str(compound.chemblid))
            except BioServicesError:
                continue

            for act in acts['bioactivities']:
                act = {FIELDS[key]: value for key, value in act.items()
                        if key in FIELDS}

                tid, aid, cid, pid = (act['target'], act['assay'],
                    act['compound'], act['parent_compound'])
                try:
                    parent = Compound.objects.get(chemblid=pid)
                except Compound.DoesNotExist:
                    try:
                        parent = Compound.objects.create(locked=True, **chembl_compound(pid))
                    except ValueError:
                        error += 1
                        continue

                try:
                    target = Target.objects.get(chemblid=tid)
                except Target.DoesNotExist:
                    try:
                        target = Target.objects.create(locked=True, **chembl_target(tid))
                    except ValueError:
                        error += 1
                        continue

                try:
                    assay = Assay.objects.get(chemblid=aid)
                except Assay.DoesNotExist:
                    try:
                        assay = Assay.objects.create(locked=True, **chembl_assay(aid))
                    except ValueError:
                        error += 1
                        continue

                try:
                    activity = Bioactivity.objects.get(
                        target=target, assay=assay, compound=compound)
                except Bioactivity.DoesNotExist:

                    (act['target'], act['assay'], act['compound'],
                        act['parent_compound']) = (
                        target, assay, compound, parent)

                    try:
                        ba = Bioactivity.objects.create(locked=True, **act)
                    except ValueError:
                        error += 1
                    except Exception as err:
                        for key, val in act.items():
                            if isinstance(val, str):
                                print('{}: ({}) {}'.format(key, len(val), val))
                        raise err
                    else:
                        count += 1
                else:
                    skip += 1
            compound.last_update = datetime.date.today()
            compound.save()

    print('{} bioactivities were added, {} were found in the database, and '
          '{} failed due to value errors.'.format(count, skip, error))