[Misc] Performance improvements, SMIRKS Coverage, Minor Bugfixes (#132)

Bump Python Version to 3.12
Make use of "epauth" optional
Cache `srs` property of rules to speed up apply
Adjust view names for use of `reverse()`
Fix Views for Scenario Attachments
Added Simply Compare View/Template to identify differences between rdkit and ambit
Make migrations consistent with tests + compare
Fixes #76
Set default year for Scenario Modal
Fix html tags for package description
Added Tests for Pathway / Rule
Added remove stereo for apply

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#132

.python-version

@@ -1 +1 @@
-3.10
+3.12

envipath/settings.py

@@ -47,7 +47,6 @@ INSTALLED_APPS = [
     # Custom
     'epdb',
     'migration',
-    'epauth',
 ]
 
 AUTHENTICATION_BACKENDS = [
@@ -360,6 +359,9 @@ LOGIN_EXEMPT_URLS = [
 # MS AD/Entra
 MS_ENTRA_ENABLED = os.environ.get('MS_ENTRA_ENABLED', 'False') == 'True'
 if MS_ENTRA_ENABLED:
+    # Add app to installed apps
+    INSTALLED_APPS.append('epauth')
+    # Set vars required by app
     MS_ENTRA_CLIENT_ID = os.environ['MS_CLIENT_ID']
     MS_ENTRA_CLIENT_SECRET = os.environ['MS_CLIENT_SECRET']
     MS_ENTRA_TENANT_ID = os.environ['MS_TENANT_ID']

envipath/urls.py

@@ -14,13 +14,14 @@ Including another URLconf
     1. Import the include() function: from django.urls import include, path
     2. Add a URL to urlpatterns:  path('blog/', include('blog.urls'))
 """
+from django.conf import settings as s
 from django.contrib import admin
 from django.urls import include, path
 
 from .api import api_v1, api_legacy
 
 urlpatterns = [
-    path("", include("epauth.urls")),
+
     path("", include("epdb.urls")),
     path("", include("migration.urls")),
     path("admin/", admin.site.urls),
@@ -28,3 +29,6 @@ urlpatterns = [
     path("api/legacy/", api_legacy.urls),
     path("o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
 ]
+
+if s.MS_ENTRA_ENABLED:
+    urlpatterns.append(path("", include("epauth.urls")))

epdb/models.py

@@ -1101,7 +1101,7 @@ class ParallelRule(Rule):
     def _url(self):
         return '{}/parallel-rule/{}'.format(self.package.url, self.uuid)
 
-    @property
+    @cached_property
     def srs(self) -> QuerySet:
         return self.simple_rules.all()
 

epdb/urls.py

@@ -48,10 +48,10 @@ urlpatterns = [
     # User Detail
     re_path(rf'^user/(?P<user_uuid>{UUID})', v.user, name='user'),
     # Group Detail
-    re_path(rf'^group/(?P<group_uuid>{UUID})$', v.group, name='group_detail'),
+    re_path(rf'^group/(?P<group_uuid>{UUID})$', v.group, name='group detail'),
 
     # "in package" urls
-    re_path(rf'^package/(?P<package_uuid>{UUID})$', v.package, name='package_detail'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})$', v.package, name='package detail'),
     # Compound
     re_path(rf'^package/(?P<package_uuid>{UUID})/compound$', v.package_compounds, name='package compound list'),
     re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})$', v.package_compound, name='package compound detail'),

epdb/views.py

@@ -870,7 +870,7 @@ def package(request, package_uuid):
                 object_to_copy = request.POST.get('object_to_copy')
 
                 if not object_to_copy:
-                    return error(request, 'Invalid target package.', 'Please select a target package.')
+                    return error(request, 'No object to copy', 'There was no object to copy.')
 
                 copied_object = copy_object(current_user, current_package, object_to_copy)
                 return JsonResponse({'success': copied_object.url})
@@ -1019,7 +1019,7 @@ def package_compound(request, package_uuid, compound_uuid):
 
         selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios:
+        if selected_scenarios is not None:
             set_scenarios(current_user, current_compound, selected_scenarios)
             return redirect(current_compound.url)
 
@@ -1128,7 +1128,7 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
 
         selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios:
+        if selected_scenarios is not None:
             set_scenarios(current_user, current_structure, selected_scenarios)
             return redirect(current_structure.url)
 
@@ -1255,7 +1255,7 @@ def package_rule(request, package_uuid, rule_uuid):
 
         selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios:
+        if selected_scenarios is not None:
             set_scenarios(current_user, current_rule, selected_scenarios)
             return redirect(current_rule.url)
 
@@ -1358,7 +1358,7 @@ def package_reaction(request, package_uuid, reaction_uuid):
 
         selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios:
+        if selected_scenarios is not None:
             set_scenarios(current_user, current_reaction, selected_scenarios)
             return redirect(current_reaction.url)
 
@@ -1545,7 +1545,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
 
         selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios:
+        if selected_scenarios is not None:
             set_scenarios(current_user, current_pathway, selected_scenarios)
             return redirect(current_pathway.url)
 
@@ -1691,7 +1691,7 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
         selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios:
+        if selected_scenarios is not None:
             set_scenarios(current_user, current_node, selected_scenarios)
             return redirect(current_node.url)
 
@@ -1800,7 +1800,7 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
 
         selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios:
+        if selected_scenarios is not None:
             set_scenarios(current_user, current_edge, selected_scenarios)
             return redirect(current_edge.url)
 

migration/urls.py

@@ -12,4 +12,5 @@ urlpatterns = [
     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})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/compare$', v.compare, name='compare'),
 ]

migration/views.py

@@ -1,15 +1,55 @@
 import gzip
 import json
+import logging
 import os.path
+from datetime import datetime
 
 from django.conf import settings as s
+from django.http import HttpResponseNotAllowed
 from django.shortcuts import render
 
 from epdb.logic import PackageManager
-from epdb.models import Rule
+from epdb.models import Rule, SimpleAmbitRule, Package, CompoundStructure
 from epdb.views import get_base_context, _anonymous_or_real
 from utilities.chem import FormatConverter
+from envipy_ambit import apply
+from rdkit import Chem
+from rdkit.Chem.MolStandardize import rdMolStandardize
 
+logger = logging.getLogger(__name__)
+
+
+def normalize_smiles(smiles):
+    m1 = Chem.MolFromSmiles(smiles)
+    if m1 is None:
+        print("Couldnt read smi: ", smiles)
+        return smiles
+    Chem.RemoveStereochemistry(m1)
+    # Normalizer takes care of charge/tautomer/resonance standardization
+    normalizer = rdMolStandardize.Normalizer()
+    return Chem.MolToSmiles(normalizer.normalize(m1), canonical=True)
+
+
+def run_both_engines(SMILES, SMIRKS):
+    ambit_res = apply(SMIRKS, SMILES)
+    # ambit_res, ambit_errors = FormatConverter.sanitize_smiles([str(s) for s in ambit_res])
+
+    ambit_res = list(set([normalize_smiles(str(x)) for x in
+                          FormatConverter.sanitize_smiles([str(s) for s in ambit_res])[0]]))
+
+    products = FormatConverter.apply(SMILES, SMIRKS)
+
+    all_rdkit_prods = []
+    for ps in products:
+        for p in ps:
+            all_rdkit_prods.append(p)
+
+    all_rdkit_prods = list(set(all_rdkit_prods))
+    # all_rdkit_res, rdkit_errors = FormatConverter.sanitize_smiles(all_rdkit_prods)
+    all_rdkit_res = list(set([normalize_smiles(str(x)) for x in
+                              FormatConverter.sanitize_smiles([str(s) for s in all_rdkit_prods])[0]]))
+    # return ambit_res, ambit_errors, all_rdkit_res, rdkit_errors
+    return ambit_res, 0, all_rdkit_res, 0
 
 def migration(request):
     if request.method == 'GET':
@@ -19,64 +59,35 @@ def migration(request):
                 "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 = []
+            BBD = Package.objects.get(url='http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1')
+            ALL_SMILES = [cs.smiles for cs in CompoundStructure.objects.filter(compound__package=BBD)]
+            RULES = SimpleAmbitRule.objects.filter(package=BBD)
 
+            results = list()
+            num_rules = len(RULES)
             success = 0
             error = 0
             total = 0
 
-            num_keys = len(data.keys())
+            for i, r in enumerate(RULES):
-            for i, bt_rule_name in enumerate(data.keys()):
+                logger.debug(f'\r{i + 1:03d}/{num_rules}')
-                print(f"{i + 1}/{num_keys}")
-                bt_rule = data[bt_rule_name]
-                smirks = bt_rule['smirks']
-
-                all_prods = set()
-
                 res = True
+                for smiles in ALL_SMILES:
+                    try:
+                        ambit_res, _, rdkit_res, _ = run_both_engines(smiles, r.smirks)
 
-                for comp, ambit_prod in zip(bt_rule['compounds'], bt_rule['products']):
+                        res &= set(ambit_res) == set(rdkit_res)
+                    except Exception as e:
+                        logger.error(e)
 
-                    products = FormatConverter.apply(comp['smiles'], smirks)
+                results.append({
-
+                    'name': r.name,
-                    all_rdkit_prods = []
+                    'detail_url': s.SERVER_URL + '/migration/' + r.url.replace('https://envipath.org/', '').replace('http://localhost:8000/', ''),
-                    for ps in products:
+                    'id': str(r.uuid),
-                        for p in ps:
+                    'url': r.url,
-                            all_rdkit_prods.append(p)
+                    'status': res,
-
+                })
-                    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
@@ -84,7 +95,6 @@ def migration(request):
                     error += 1
 
                 total += 1
-
             results = sorted(results, key=lambda x: (x['status'], x['name']))
 
             migration_status = {
@@ -110,69 +120,51 @@ def migration_detail(request, package_uuid, rule_uuid):
     if request.method == 'GET':
         context = get_base_context(request)
 
-        p = PackageManager.get_package_by_id(current_user, package_uuid)
+        BBD = Package.objects.get(name='EAWAG-BBD')
-        rule = Rule.objects.get(package=p, uuid=rule_uuid)
+        STRUCTURES = CompoundStructure.objects.filter(compound__package=BBD)
+        rule = Rule.objects.get(package=BBD, uuid=rule_uuid)
+
         bt_rule_name = rule.name
-
+        smirks = rule.smirks
-        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
+        results = []
 
         all_prods = set()
-        for comp, ambit_prod in zip(bt_rule['compounds'], bt_rule['products']):
+        for structure in STRUCTURES:
-            # if comp['smiles'] != 'CC1=C(C(=C(C=N1)CO)C=O)O':
-            #     continue
 
-            products = FormatConverter.apply(comp['smiles'], smirks)
+            ambit_smiles, ambit_errors, rdkit_smiles, rdkit_errors = run_both_engines(structure.smiles, smirks)
-
-            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)
+            # FAILED (failures=18)
 
             # TODO mode = "full ambit"
-            # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(ambit_smiles)
+            # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(set(ambit_smiles))
-            # FAILED (failures=46)
+            # FAILED (failures=34)
 
             # TODO mode = "equality"
             partial_res = set(ambit_smiles) == set(rdkit_smiles)
-            # FAILED (failures=69)
+            # FAILED (failures=30)
 
-            #
             if len(ambit_smiles) or len(rdkit_smiles):
                 temp = {
-                    'url': comp['id'],
+                    'url': structure.url,
-                    'id': comp['id'].split('/')[-1],
+                    'id': str(structure.uuid),
-                    'name': comp['name'],
+                    'name': structure.name,
-                    'initial_smiles': comp['smiles'],
+                    'initial_smiles': structure.smiles,
                     'ambit_smiles': sorted(list(ambit_smiles)),
                     'rdkit_smiles': sorted(list(rdkit_smiles)),
                     'status': set(ambit_smiles) == set(rdkit_smiles),
                 }
-
+                detail = f"""
-                if set(ambit_smiles) != set(rdkit_smiles):
-                    detail = f"""
                         BT: {bt_rule_name}
-                        SMIRKS: {bt_rule['smirks']}
+                        SMIRKS: {smirks}
-                        Compound: {comp['smiles']}
+                        Compound: {structure.smiles}
-                        Compound URL: {comp['id']}
+                        Compound URL: {structure.url}
                         Num ambit: {len(set(ambit_smiles))}
                         Num rdkit: {len(set(rdkit_smiles))}
                         Num Intersection A: {len(set(ambit_smiles).intersection(set(rdkit_smiles)))}
@@ -185,8 +177,7 @@ def migration_detail(request, package_uuid, rule_uuid):
                         rdkit_errors: {rdkit_errors}
                     """
 
-                    temp['detail'] = '\n'.join([x.strip() for x in detail.split('\n')])
+                temp['detail'] = '\n'.join([x.strip() for x in detail.split('\n')])
-                    # print(detail.strip())
 
                 results.append(temp)
 
@@ -197,3 +188,49 @@ def migration_detail(request, package_uuid, rule_uuid):
         context['res'] = res
         context['bt_rule_name'] = bt_rule_name
         return render(request, 'migration_detail.html', context)
+
+
+def compare(request):
+    context = get_base_context(request)
+
+    if request.method == 'GET':
+        context[
+            "smirks"] = "[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([#1,#6:7])[H:3].[#6;A:2]=O"
+        context["smiles"] = "C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
+        return render(request, 'compare.html', context)
+
+    elif request.method == 'POST':
+        smiles = request.POST.get("smiles")
+        smirks = request.POST.get("smirks")
+
+        from envipy_ambit import apply
+
+        ambit_res = apply(smirks, smiles)
+        ambit_res, _ = FormatConverter.sanitize_smiles([str(x) for x in ambit_res])
+
+        products = FormatConverter.apply(smiles, smirks)
+
+        all_rdkit_prods = []
+        for ps in products:
+            for p in ps:
+                all_rdkit_prods.append(p)
+
+        all_rdkit_prods = list(set(all_rdkit_prods))
+
+        rdkit_res, _ = FormatConverter.sanitize_smiles(all_rdkit_prods)
+        context["result"] = True
+        context['ambit_res'] = sorted(set(ambit_res))
+        context['rdkit_res'] = sorted(set(rdkit_res))
+        context['diff'] = sorted(set(ambit_res).difference(set(rdkit_res)))
+        context["smirks"] = smirks
+        context["smiles"] = smiles
+
+        r = SimpleAmbitRule.objects.filter(smirks=smirks)
+
+        if r.exists():
+            context["rule"] = r.first()
+
+        return render(request, 'compare.html', context)
+
+    else:
+        return HttpResponseNotAllowed(['GET', 'POST'])

pyproject.toml

@@ -3,7 +3,7 @@ name = "envipy"
 version = "0.1.0"
 description = "Add your description here"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dependencies = [
     "celery>=5.5.2",
     "django>=5.2.1",
@@ -15,6 +15,7 @@ dependencies = [
     "django-stubs>=5.2.4",
     "enviformer",
     "envipy-additional-information",
+    "envipy-ambit>=0.1.0",
     "envipy-plugins",
     "epam-indigo>=1.30.1",
     "gunicorn>=23.0.0",
@@ -33,6 +34,7 @@ dependencies = [
 enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.0" }
 envipy-plugins = { git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git", rev = "v0.1.0" }
 envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git", rev = "v0.1.4"}
+envipy-ambit = { git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git" }
 
 [project.optional-dependencies]
 ms-login = ["msal>=1.33.0"]

templates/compare.html

@@ -0,0 +1,55 @@
+{% extends "framework.html" %}
+
+{% block content %}
+    <div>
+        <form action="" method="post">
+            {% csrf_token %}
+            <input type="text" class="form-control" id="smiles" name="smiles" placeholder="SMILES"
+                   value="{{ smiles }}"/>
+            <input type="text" class="form-control" id="smiles" name="smirks" placeholder="SMIRKS"
+                   value="{{ smirks }}"/>
+            <button type="submit" class="btn btn-primary">Test</button>
+        </form>
+    </div>
+    {% if result %}
+        {{ smiles }}<p></p>
+        <img width='400' src='{% url 'depict' %}?smiles={{ smiles|urlencode }}'><br>
+        <p></p>
+        {% if rule %}
+            {{ smirks }}
+            <p></p>
+            {{ rule.reactants_smarts }}
+            <p></p>
+            {{ rule.products_smarts }}
+            <p></p>
+            <div>
+                {{ rule.as_svg|safe }}
+            </div>
+        {% endif %}
+        <h2>Diff</h2>
+        {% if diff %}
+            {% for d in diff %}
+                {{ d }}
+            {% endfor %}
+        {% else %}
+            {{ "No diff" }}
+        {% endif %}
+        <div>
+            <div class="col-md-6">
+                <h2>Ambit</h2>
+                {% for p in ambit_res %}
+                    {{ p }}<br>
+                    <img width='400' src='{% url 'depict' %}?smiles={{ p|urlencode }}'><br>
+                {% endfor %}
+            </div>
+
+            <div class="col-md-6">
+                <h2>RDKit</h2>
+                {% for p in rdkit_res %}
+                    {{ p }}<br>
+                    <img width='400' src='{% url 'depict' %}?smiles={{ p|urlencode }}'><br>
+                {% endfor %}
+            </div>
+        </div>
+    {% endif %}
+{% endblock content %}

templates/framework.html

@@ -134,7 +134,7 @@
                     <a data-toggle="dropdown" class="dropdown-toggle" href="#">Info <b class="caret"></b></a>
                     <ul role="menu" class="dropdown-menu">
                         <!--<li><a href="{{ meta.server_url }}/funding" id="fundingLink">Funding</a></li>-->
-                        <li><a href="https://envipath.com/license/" id="licenceLink">Licences</a></li>
+                        <li><a href="https://community.envipath.org/t/envipath-license/109" id="licenceLink">Licences</a></li>
                         <li class="divider"></li>
                         <li><a target="_blank" href="https://wiki.envipath.org/" id="wikiLink">Documentation Wiki</a>
                         </li>

templates/migration_detail.html

@@ -1,50 +1,45 @@
 {% extends "framework.html" %}
 
 {% block content %}
-<div class="panel-group" id="migration-detail">
+    <div class="panel-group" id="migration-detail">
-    <div class="panel panel-default">
+        <div class="panel panel-default">
-        <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-            Migration Status for {{ bt_rule_name }}
+                Migration Status for {{ bt_rule_name }}
-        </div>
-        <div class="panel-body">
-            <p>A package contains pathways, rules, etc. and can reflect specific experimental
-                conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
-                    more &gt;&gt;</a></p>
-        </div>
-
-        {% for obj in results %}
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            {% if obj.status %}
-            <span class="glyphicon glyphicon-ok" aria-hidden="true"
-                  style="float:right" data-toggle="tooltip"
-                  data-placement="top" title="" data-original-title="Reviewed">
-            </span>
-            {% else %}
-            <span class="glyphicon glyphicon-remove" aria-hidden="true"
-                  style="float:right" data-toggle="tooltip"
-                  data-placement="top" title="" data-original-title="Reviewed">
-            </span>
-            {% endif %}
-            <h4 class="panel-title">
-                <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
-                   href="#{{ obj.id }}">{{ obj.name }}</a>
-            </h4>
-        </div>
-        <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
-            <div class="panel-body list-group-item">
-                {% if obj.status %}
-                <p>Products generated by AMBIT: {{ obj.ambit_smiles }}</p>
-                <p>Products generated by RDKit: {{ obj.rdkit_smiles }}</p>
-                {% else %}
-                    <pre>{{ obj.detail }}</pre>
-                {% endif %}
             </div>
+            <div class="panel-body">
+                <p>A package contains pathways, rules, etc. and can reflect specific experimental
+                    conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
+                        more &gt;&gt;</a></p>
+            </div>
+
+            {% for obj in results %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    {% if obj.status %}
+                        <span class="glyphicon glyphicon-ok" aria-hidden="true"
+                              style="float:right" data-toggle="tooltip"
+                              data-placement="top" title="" data-original-title="Reviewed">
+                        </span>
+                    {% else %}
+                        <span class="glyphicon glyphicon-remove" aria-hidden="true"
+                              style="float:right" data-toggle="tooltip"
+                              data-placement="top" title="" data-original-title="Reviewed">
+                        </span>
+                    {% endif %}
+                    <h4 class="panel-title">
+                        <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
+                           href="#{{ obj.id }}">{{ obj.name }}</a>
+                    </h4>
+                </div>
+                <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
+                    <div class="panel-body list-group-item">
+                        <pre>{{ obj.detail }}</pre>
+                    </div>
+                </div>
+            {% endfor %}
         </div>
-        {% endfor %}
     </div>
-</div>
 
-<script>
+    <script>
 
-</script>
+    </script>
 {% endblock content %}

templates/modals/collections/new_scenario_modal.html

@@ -29,11 +29,11 @@
                         <tr>
                             <th>
                                 <input type="number" id="dateYear" name="scenario-date-year" class="form-control"
-                                       placeholder="YYYY">
+                                       placeholder="YYYY" max="{% now "Y" %}">
                             </th>
                             <th>
                                 <input type="number" id="dateMonth" name="scenario-date-month" min="1" max="12"
-                                       class="form-control" placeholder="MM" align="">
+                                       class="form-control" placeholder="MM" >
                             </th>
                             <th>
                                 <input type="number" id="dateDay" name="scenario-date-day" min="1" max="31" class="form-control"
@@ -88,8 +88,15 @@
             $('#new_scenario_form').submit();
         });
 
-    });
+        var dateYear = document.getElementById("dateYear");
+        dateYear.addEventListener("change", () => {
+            console.log("Final value after editing:", dateYear.value);
+            if (dateYear.value.length < 4) {
+                dateYear.value = {% now "Y" %};
+            }
+        });
 
+    });
 
 </script>
 

templates/objects/package.html

@@ -29,7 +29,7 @@
             </div>
         </div>
         <div class="panel-body">
-            <p> {{ package.description }} </p>
+            <p> {{ package.description|safe }} </p>
         </div>
         <ul class="list-group">
             <li class="list-group-item">

tests/test_ruleapplication.py

@@ -4,6 +4,9 @@ import json
 from django.conf import settings as s
 from django.test import TestCase, tag
 from utilities.chem import FormatConverter
+from envipy_ambit import apply
+from rdkit import Chem
+from rdkit.Chem.MolStandardize import rdMolStandardize
 
 @tag("slow")
 class RuleApplicationTest(TestCase):
@@ -16,17 +19,56 @@ class RuleApplicationTest(TestCase):
         super(RuleApplicationTest, cls).setUpClass()
         cls.data = json.load(gzip.open(s.BASE_DIR / 'fixtures' / 'ambit_rules.json.gz', 'rb'))
         cls.error_smiles = list()
+        from collections import defaultdict
+        cls.triggered = defaultdict(lambda: defaultdict(lambda: 0))
 
     @classmethod
     def tearDownClass(cls):
         super().tearDownClass()
         print(f"\nTotal Errors across Rules {len(cls.error_smiles)}")
         # print(cls.error_smiles)
+        from pprint import pprint
+        from collections import Counter
+        pprint(Counter(cls.error_smiles))
+        # import json
+        # pprint(json.loads(json.dumps(cls.triggered)))
 
     def tearDown(self):
         super().tearDown()
         print(f"\nTotal errors {self.total_errors}")
 
+    @staticmethod
+    def normalize_smiles(smiles):
+        m1 = Chem.MolFromSmiles(smiles)
+        if m1 is None:
+            print("Couldnt read smi: ", smiles)
+            return smiles
+        Chem.RemoveStereochemistry(m1)
+        # Normalizer takes care of charge/tautomer/resonance standardization
+        normalizer = rdMolStandardize.Normalizer()
+        return Chem.MolToSmiles(normalizer.normalize(m1), canonical=True)
+
+    @staticmethod
+    def run_both_engines(smiles, smirks):
+        ambit_res = apply(smirks, smiles)
+
+        ambit_res = list(
+            set([RuleApplicationTest.normalize_smiles(str(x)) for x in FormatConverter.sanitize_smiles([str(s) for s in ambit_res])[0]]))
+
+        products = FormatConverter.apply(smiles, smirks)
+
+        all_rdkit_prods = []
+        for ps in products:
+            for p in ps:
+                all_rdkit_prods.append(p)
+
+        all_rdkit_prods = list(set(all_rdkit_prods))
+
+        all_rdkit_res = list(set([RuleApplicationTest.normalize_smiles(str(x)) for x in
+                                  FormatConverter.sanitize_smiles([str(s) for s in all_rdkit_prods])[0]]))
+
+        return ambit_res, 0, all_rdkit_res, 0
+
     def run_bt_test(self, bt_rule_name):
         bt_rule = self.data[bt_rule_name]
         smirks = bt_rule['smirks']
@@ -34,35 +76,26 @@ class RuleApplicationTest(TestCase):
         res = True
 
         all_prods = set()
-        for comp, ambit_prod in zip(bt_rule['compounds'], bt_rule['products']):
+        for comp in bt_rule['compounds']:
 
             smi = comp['smiles']
-            products = FormatConverter.apply(smi, smirks)
 
-            all_rdkit_prods = []
+            ambit_smiles, ambit_errors, rdkit_smiles, rdkit_errors = self.run_both_engines(smi, smirks)
-            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=33)
+            # FAILED (failures=18)
 
             # TODO mode = "full ambit"
-            # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(ambit_smiles)
+            # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(set(ambit_smiles))
-            # FAILED (failures=44)
+            # FAILED (failures=22)
 
             # TODO mode = "equality"
             partial_res = set(ambit_smiles) == set(rdkit_smiles)
-            # FAILED (failures=64)
+            # FAILED (failures=30)
 
             if len(ambit_smiles) and not partial_res:
                 print(f"""

tests/views/test_pathway_views.py

@@ -0,0 +1,98 @@
+from django.test import TestCase, override_settings
+from django.urls import reverse
+from django.conf import settings as s
+
+from epdb.logic import UserManager, PackageManager
+from epdb.models import Pathway, Edge
+
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models")
+class PathwayViewTest(TestCase):
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
+
+    @classmethod
+    def setUpClass(cls):
+        super(PathwayViewTest, cls).setUpClass()
+        cls.user1 = UserManager.create_user("user1", "user1@envipath.com", "SuperSafe",
+                                            set_setting=True, add_to_group=True, is_active=True)
+        cls.user1_default_package = cls.user1.default_package
+        cls.package = PackageManager.create_package(cls.user1, 'Test', 'Test Pack')
+
+    def setUp(self):
+        self.client.force_login(self.user1)
+
+    def test_predict_pathway(self):
+        response = self.client.post(reverse("pathways"), {
+            'name': 'Test Pathway',
+            'description': 'Just a Description',
+            'predict': 'predict',
+            'smiles': 'CCN(CC)C(=O)C1=CC(=CC=C1)CO',
+        })
+        self.assertEqual(response.status_code, 302)
+        pathway_url = response.url
+
+        pw = Pathway.objects.get(url=pathway_url)
+        self.assertEqual(self.user1_default_package, pw.package)
+
+        self.assertEqual(pw.name, 'Test Pathway')
+        self.assertEqual(pw.description, 'Just a Description')
+        self.assertEqual(len(pw.root_nodes), 1)
+        self.assertEqual(pw.root_nodes.first().default_node_label.smiles, 'CCN(CC)C(=O)C1=CC(CO)=CC=C1')
+
+        first_level_nodes = {
+            # Edge 1
+            'CCN(CC)C(=O)C1=CC(C=O)=CC=C1',
+            # Edge 2
+            'CCNC(=O)C1=CC(CO)=CC=C1',
+            'CC=O',
+            # Edge 3
+            'CCNCC',
+            'O=C(O)C1=CC(CO)=CC=C1',
+        }
+
+        predicted_nodes = set()
+        edges = Edge.objects.filter(start_nodes__in=[pw.root_nodes.first()])
+
+        for edge in edges:
+            for n in edge.end_nodes.all():
+                predicted_nodes.add(n.default_node_label.smiles)
+
+        self.assertEqual(first_level_nodes, predicted_nodes)
+
+    def test_predict_package_pathway(self):
+        response = self.client.post(
+            reverse("package pathway list", kwargs={'package_uuid': str(self.package.uuid)}), {
+                'name': 'Test Pathway',
+                'description': 'Just a Description',
+                'predict': 'predict',
+                'smiles': 'CCN(CC)C(=O)C1=CC(=CC=C1)CO',
+            })
+        self.assertEqual(response.status_code, 302)
+        pathway_url = response.url
+
+        pw = Pathway.objects.get(url=pathway_url)
+        self.assertEqual(self.package, pw.package)
+
+        self.assertEqual(pw.name, 'Test Pathway')
+        self.assertEqual(pw.description, 'Just a Description')
+        self.assertEqual(len(pw.root_nodes), 1)
+        self.assertEqual(pw.root_nodes.first().default_node_label.smiles, 'CCN(CC)C(=O)C1=CC(CO)=CC=C1')
+
+        first_level_nodes = {
+            # Edge 1
+            'CCN(CC)C(=O)C1=CC(C=O)=CC=C1',
+            # Edge 2
+            'CCNC(=O)C1=CC(CO)=CC=C1',
+            'CC=O',
+            # Edge 3
+            'CCNCC',
+            'O=C(O)C1=CC(CO)=CC=C1',
+        }
+
+        predicted_nodes = set()
+        edges = Edge.objects.filter(start_nodes__in=[pw.root_nodes.first()])
+
+        for edge in edges:
+            for n in edge.end_nodes.all():
+                predicted_nodes.add(n.default_node_label.smiles)
+
+        self.assertEqual(first_level_nodes, predicted_nodes)

tests/views/test_rule_views.py

@@ -0,0 +1,225 @@
+from django.test import TestCase
+from django.urls import reverse
+from envipy_additional_information import Temperature, Interval
+
+from epdb.logic import UserManager, PackageManager
+from epdb.models import Rule, Scenario
+
+
+class RuleViewTest(TestCase):
+    fixtures = ["test_fixtures.jsonl.gz"]
+
+    @classmethod
+    def setUpClass(cls):
+        super(RuleViewTest, cls).setUpClass()
+        cls.user1 = UserManager.create_user("user1", "user1@envipath.com", "SuperSafe",
+                                            set_setting=False, add_to_group=True, is_active=True)
+        cls.user1_default_package = cls.user1.default_package
+        cls.package = PackageManager.create_package(cls.user1, 'Test', 'Test Pack')
+
+    def setUp(self):
+        self.client.force_login(self.user1)
+
+    def test_create_rule(self):
+        response = self.client.post(
+            reverse("rules"), {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            }
+        )
+
+        self.assertEqual(response.status_code, 302)
+        rule_url = response.url
+
+        r = Rule.objects.get(url=rule_url)
+
+        self.assertEqual(r.package, self.user1_default_package)
+        self.assertEqual(r.name, "Test Rule")
+        self.assertEqual(r.description, "Just a Description")
+        self.assertEqual(r.smirks,
+                         "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]")
+        self.assertEqual(self.user1_default_package.rules.count(), 1)
+
+        # Adding the same rule again should return the existing one, hence not increasing the number of rules
+        response = self.client.post(
+            reverse("rules"), {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            }
+        )
+
+        self.assertEqual(response.url, rule_url)
+        self.assertEqual(response.status_code, 302)
+        self.assertEqual(self.user1_default_package.rules.count(), 1)
+
+        # Adding the same rule in a different package should create a new rule
+        response = self.client.post(
+            reverse("package rule list", kwargs={'package_uuid': self.package.uuid}), {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            }
+        )
+
+        self.assertEqual(response.status_code, 302)
+        self.assertNotEqual(rule_url, response.url)
+
+    # Edit
+    def test_edit_rule(self):
+        response = self.client.post(
+            reverse("rules"), {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            }
+        )
+
+        self.assertEqual(response.status_code, 302)
+        rule_url = response.url
+
+        r = Rule.objects.get(url=rule_url)
+
+        response = self.client.post(
+            reverse("package rule detail", kwargs={
+                'package_uuid': str(self.user1_default_package.uuid),
+                'rule_uuid': str(r.uuid)
+            }), {
+                "rule-name": "Test Rule Adjusted",
+                "rule-description": "New Description",
+            }
+        )
+
+        self.assertEqual(response.status_code, 302)
+        r = Rule.objects.get(url=rule_url)
+        self.assertEqual(r.name, "Test Rule Adjusted")
+        self.assertEqual(r.description, "New Description")
+
+    # Scenario
+    def test_set_scenario(self):
+        s1 = Scenario.create(
+            self.user1_default_package,
+            "Test Scen",
+            "Test Desc",
+            "2025-10",
+            "soil",
+            [Temperature(interval=Interval(start=20, end=30))]
+        )
+
+        s2 = Scenario.create(
+            self.user1_default_package,
+            "Test Scen2",
+            "Test Desc2",
+            "2025-10",
+            "soil",
+            [Temperature(interval=Interval(start=10, end=20))]
+        )
+
+        response = self.client.post(
+            reverse("rules"), {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            }
+        )
+
+        self.assertEqual(response.status_code, 302)
+        rule_url = response.url
+        r = Rule.objects.get(url=rule_url)
+
+        response = self.client.post(
+            reverse("package rule detail", kwargs={
+                'package_uuid': str(r.package.uuid),
+                'rule_uuid': str(r.uuid)
+            }), {
+                "selected-scenarios": [s1.url, s2.url]
+            }
+        )
+
+        self.assertEqual(len(r.scenarios.all()), 2)
+
+        response = self.client.post(
+            reverse("package rule detail", kwargs={
+                'package_uuid': str(r.package.uuid),
+                'rule_uuid': str(r.uuid)
+            }), {
+                "selected-scenarios": [s1.url]
+            }
+        )
+
+        self.assertEqual(len(r.scenarios.all()), 1)
+        self.assertEqual(r.scenarios.first().url, s1.url)
+
+        response = self.client.post(
+            reverse("package rule detail", kwargs={
+                'package_uuid': str(r.package.uuid),
+                'rule_uuid': str(r.uuid)
+            }), {
+                "selected-scenarios": []
+            }
+        )
+
+        self.assertEqual(len(r.scenarios.all()), 0)
+
+    def test_copy(self):
+        response = self.client.post(
+            reverse("rules"), {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            }
+        )
+
+        self.assertEqual(response.status_code, 302)
+        rule_url = response.url
+        r = Rule.objects.get(url=rule_url)
+
+        response = self.client.post(
+            reverse("package detail", kwargs={
+                'package_uuid': str(r.package.uuid),
+            }), {
+                "hidden": "copy",
+                "object_to_copy": r.url
+            }
+        )
+
+        self.assertEqual(response.status_code, 200)
+
+        copied_object_url = response.json()["success"]
+        copied_rule = Rule.objects.get(url=copied_object_url)
+
+        self.assertEqual(copied_rule.name, r.name)
+        self.assertEqual(copied_rule.description, r.description)
+        self.assertEqual(copied_rule.smirks, r.smirks)
+
+    def test_delete(self):
+        response = self.client.post(
+            reverse("rules"), {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            }
+        )
+        self.assertEqual(response.status_code, 302)
+
+        rule_url = response.url
+        r = Rule.objects.get(url=rule_url)
+
+        response = self.client.post(
+            reverse("package rule detail", kwargs={
+                'package_uuid': str(r.package.uuid),
+                'rule_uuid': str(r.uuid)
+            }), {
+                "hidden": "delete"
+            }
+        )
+
+        self.assertEqual(self.user1_default_package.rules.count(), 0)

utilities/chem.py

@@ -244,7 +244,7 @@ class FormatConverter(object):
 
     @staticmethod
     def apply(smiles: str, smirks: str, preprocess_smiles: bool = True, bracketize: bool = True,
-              standardize: bool = True, kekulize: bool = True) -> List['ProductSet']:
+              standardize: bool = True, kekulize: bool = True, remove_stereo: bool = True) -> List['ProductSet']:
         logger.debug(f'Applying {smirks} on {smiles}')
 
         # If explicitly wanted or rule generates multiple products add brackets around products to capture all
@@ -274,7 +274,7 @@ class FormatConverter(object):
                             Chem.SanitizeMol(product)
                             product = GetMolFrags(product, asMols=True)
                             for p in product:
-                                p = FormatConverter.standardize(Chem.MolToSmiles(p))
+                                p = FormatConverter.standardize(Chem.MolToSmiles(p), remove_stereo=remove_stereo)
                                 prods.append(p)
 
                             # if kekulize:
@@ -314,30 +314,10 @@ class FormatConverter(object):
 
         return pss
 
-    # @staticmethod
-    # def apply(reaction, smiles):
-    #     rxn = AllChem.ReactionFromSmarts(reaction)
-    #     return [Chem.MolToSmiles(x, 1) for x in rxn.RunReactants((Chem.MolFromSmiles(smiles),))[0]]
-
     @staticmethod
     def MACCS(smiles):
         return MACCSkeys.GenMACCSKeys(FormatConverter.from_smiles(smiles))
 
-    @staticmethod
-    def neutralize_atoms(mol):
-        pattern = Chem.MolFromSmarts("[+1!h0!$([*]~[-1,-2,-3,-4]),-1!$([*]~[+1,+2,+3,+4])]")
-        at_matches = mol.GetSubstructMatches(pattern)
-        at_matches_list = [y[0] for y in at_matches]
-        if len(at_matches_list) > 0:
-            for at_idx in at_matches_list:
-                atom = mol.GetAtomWithIdx(at_idx)
-                chg = atom.GetFormalCharge()
-                hcount = atom.GetTotalNumHs()
-                atom.SetFormalCharge(0)
-                atom.SetNumExplicitHs(hcount - chg)
-                atom.UpdatePropertyCache()
-        return mol
-
     @staticmethod
     def sanitize_smiles(smiles_list: List):
         parsed_smiles = []
@@ -353,7 +333,8 @@ class FormatConverter(object):
                 #     smi = smi.replace("@", "")
 
                 mol = Chem.MolFromSmiles(smi)
-                mol = FormatConverter.neutralize_atoms(mol)
+                mol = FormatConverter.neutralize_molecule(mol)
+                Chem.RemoveStereochemistry(mol)
                 mol = Chem.RemoveAllHs(mol)
                 Chem.Kekulize(mol)
                 smi_p = Chem.MolToSmiles(mol, kekuleSmiles=True)

uv.lock

@@ -1,5 +1,5 @@
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