enviPy-bayer/migration/views.py

import gzip
import json
import os.path

from django.conf import settings as s
from django.shortcuts import render

from epdb.logic import PackageManager
from epdb.models import Rule
from epdb.views import get_base_context, _anonymous_or_real
from utilities.chem import FormatConverter


def migration(request):
    if request.method == 'GET':
        context = get_base_context(request)

        if os.path.exists(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json') and request.GET.get(
                "force") is None:
            migration_status = json.load(open(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json'))
        else:
            data = json.load(gzip.open(s.BASE_DIR / 'fixtures' / 'ambit_rules.json.gz', 'rb'))

            results = []

            success = 0
            error = 0
            total = 0

            num_keys = len(data.keys())
            for i, bt_rule_name in enumerate(data.keys()):
                print(f"{i + 1}/{num_keys}")
                bt_rule = data[bt_rule_name]
                smirks = bt_rule['smirks']

                all_prods = set()

                res = True

                for comp, ambit_prod in zip(bt_rule['compounds'], bt_rule['products']):
                    # if comp['smiles'] != 'CC1=C(C(=C(C=N1)CO)C=O)O':
                    #     continue

                    products = FormatConverter.apply(comp['smiles'], smirks, preprocess_smiles=True, bracketize=False)

                    all_rdkit_prods = []
                    for ps in products:
                        for p in ps:
                            all_rdkit_prods.append(p)

                    all_rdkit_prods = list(set(all_rdkit_prods))

                    ambit_smiles, ambit_errors = FormatConverter.sanitize_smiles(ambit_prod)
                    rdkit_smiles, rdkit_errors = FormatConverter.sanitize_smiles(all_rdkit_prods)

                    for x in ambit_smiles:
                        all_prods.add(x)

                    # TODO mode "intersection"
                    # partial_res = (len(set(ambit_smiles).intersection(set(rdkit_smiles))) > 0) or (len(ambit_smiles) == 0)
                    # FAILED (failures=37)

                    # TODO mode = "full ambit"
                    # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(ambit_smiles)
                    # FAILED (failures=46)

                    # TODO mode = "equality"
                    partial_res = set(ambit_smiles) == set(rdkit_smiles)
                    # FAILED (failures=69)

                    res &= partial_res

                results.append(
                    {
                        'name': bt_rule_name,
                        'id': bt_rule['id'].split('/')[-1],
                        'url': bt_rule['id'],
                        'status': res,
                        'detail_url': s.SERVER_URL + '/migration/' + bt_rule['id'].replace('https://envipath.org/', '')
                    }
                )

                if res:
                    success += 1
                else:
                    error += 1

                total += 1

            results = sorted(results, key=lambda x: (x['status'], x['name']))

            migration_status = {
                'results': results,
                'success': success,
                'error': error,
                'total': total
            }

            json.dump(migration_status, open(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json', 'w'))

        for r in migration_status['results']:
            r['detail_url'] = r['detail_url'].replace('http://localhost:8000', s.SERVER_URL)

        context.update(**migration_status)

        return render(request, 'migration.html', context)


def migration_detail(request, package_uuid, rule_uuid):
    current_user = _anonymous_or_real(request)

    if request.method == 'GET':
        context = get_base_context(request)

        p = PackageManager.get_package_by_id(current_user, package_uuid)
        rule = Rule.objects.get(package=p, uuid=rule_uuid)
        bt_rule_name = rule.name

        data = json.load(gzip.open(s.BASE_DIR / 'fixtures' / 'ambit_rules.json.gz', 'rb'))

        bt_rule = data[bt_rule_name]
        smirks = bt_rule['smirks']

        results = []

        res = True

        all_prods = set()
        for comp, ambit_prod in zip(bt_rule['compounds'], bt_rule['products']):
            # if comp['smiles'] != 'CC1=C(C(=C(C=N1)CO)C=O)O':
            #     continue

            products = FormatConverter.apply(comp['smiles'], smirks, preprocess_smiles=True, bracketize=False)

            all_rdkit_prods = []
            for ps in products:
                for p in ps:
                    all_rdkit_prods.append(p)

            all_rdkit_prods = list(set(all_rdkit_prods))

            ambit_smiles, ambit_errors = FormatConverter.sanitize_smiles(ambit_prod)
            rdkit_smiles, rdkit_errors = FormatConverter.sanitize_smiles(all_rdkit_prods)

            for x in ambit_smiles:
                all_prods.add(x)

            # TODO mode "intersection"
            # partial_res = (len(set(ambit_smiles).intersection(set(rdkit_smiles))) > 0) or (len(ambit_smiles) == 0)
            # FAILED (failures=37)

            # TODO mode = "full ambit"
            # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(ambit_smiles)
            # FAILED (failures=46)

            # TODO mode = "equality"
            partial_res = set(ambit_smiles) == set(rdkit_smiles)
            # FAILED (failures=69)

            #
            if len(ambit_smiles) or len(rdkit_smiles):
                temp = {
                    'url': comp['id'],
                    'id': comp['id'].split('/')[-1],
                    'name': comp['name'],
                    'initial_smiles': comp['smiles'],
                    'ambit_smiles': sorted(list(ambit_smiles)),
                    'rdkit_smiles': sorted(list(rdkit_smiles)),
                    'status': set(ambit_smiles) == set(rdkit_smiles),
                }

                if set(ambit_smiles) != set(rdkit_smiles):
                    detail = f"""
                        BT: {bt_rule_name}
                        SMIRKS: {bt_rule['smirks']}
                        Compound: {comp['smiles']}
                        Compound URL: {comp['id']}
                        Num ambit: {len(set(ambit_smiles))}
                        Num rdkit: {len(set(rdkit_smiles))}
                        Num Intersection A: {len(set(ambit_smiles).intersection(set(rdkit_smiles)))}
                        Num Intersection B: {len(set(rdkit_smiles).intersection(set(ambit_smiles)))}
                        Difference A: {set(ambit_smiles).difference(set(rdkit_smiles))}
                        Difference B: {set(rdkit_smiles).difference(set(ambit_smiles))}
                        ambit products: {ambit_smiles}
                        rdkit products: {rdkit_smiles}
                        ambit_errors: {ambit_errors}
                        rdkit_errors: {rdkit_errors}
                    """

                    temp['detail'] = '\n'.join([x.strip() for x in detail.split('\n')])
                    # print(detail.strip())

                results.append(temp)

            res &= partial_res

        results = sorted(results, key=lambda x: x['status'])
        context['results'] = results
        context['res'] = res
        context['bt_rule_name'] = bt_rule_name
        return render(request, 'migration_detail.html', context)