Current Dev State

migration/admin.py

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+from django.contrib import admin
+
+# Register your models here.

migration/apps.py

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+from django.apps import AppConfig
+
+
+class MigrationConfig(AppConfig):
+    default_auto_field = 'django.db.models.BigAutoField'
+    name = 'migration'

migration/models.py

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+from django.db import models
+
+# Create your models here.

migration/tests.py

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+from django.test import TestCase
+
+# Create your tests here.

migration/urls.py

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+from django.urls import re_path
+
+from . import views as v
+
+UUID = '[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}'
+
+urlpatterns = [
+    re_path(rf'^migration$', v.migration, name='migration'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/simple-rule/(?P<rule_uuid>{UUID})$',v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+]

migration/views.py

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+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)