[Fix] Remove all Scenarios, catch empty SMILES, prevent default Package delete (#134)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#134

epdb/views.py

@@ -233,6 +233,11 @@ def breadcrumbs(first_level_object=None, second_level_namespace=None, second_lev
 def set_scenarios(current_user, attach_object, scenario_urls: List[str]):
     scens = []
     for scenario_url in scenario_urls:
+
+        # As empty lists will be removed in POST request well send ['']
+        if scenario_url == '':
+            continue
+
         package = PackageManager.get_package_by_url(current_user, scenario_url)
         scen = Scenario.objects.get(package=package, uuid=scenario_url.split('/')[-1])
         scens.append(scen)
@@ -743,33 +748,43 @@ def package_model(request, package_uuid, model_uuid):
     current_model = EPModel.objects.get(package=current_package, uuid=model_uuid)
 
     if request.method == 'GET':
+        classify = request.GET.get('classify', False)
+        ad_assessment = request.GET.get('app-domain-assessment', False)
 
-        if request.GET.get('classify', False):
+        if classify or ad_assessment:
-            smiles = request.GET['smiles']
+            smiles = request.GET.get('smiles', '').strip()
-            stand_smiles = FormatConverter.standardize(smiles)
-            pred_res = current_model.predict(stand_smiles)
-            res = []
 
-            for pr in pred_res:
+            # Check if smiles is non empty and valid
-                if len(pr) > 0:
+            if smiles == '':
-                    products = []
+                return JsonResponse({'error': 'Received empty SMILES'}, status=400)
-                    for prod_set in pr.product_sets:
-                        logger.debug(f"Checking {prod_set}")
-                        products.append(tuple([x for x in prod_set]))
 
-                    res.append({
+            try:
-                        'products': list(set(products)),
+                stand_smiles = FormatConverter.standardize(smiles)
-                        'probability': pr.probability,
+            except ValueError as e:
-                        'btrule': {k: getattr(pr.rule, k) for k in ['url', 'name']} if pr.rule is not None else None
+                return JsonResponse({'error': f'"{smiles}" is not a valid SMILES'}, status=400)
-                    })
 
-            return JsonResponse(res, safe=False)
+            if classify:
+                pred_res = current_model.predict(stand_smiles)
+                res = []
 
-        elif request.GET.get('app-domain-assessment', False):
+                for pr in pred_res:
-            smiles = request.GET['smiles']
+                    if len(pr) > 0:
-            stand_smiles = FormatConverter.standardize(smiles)
+                        products = []
-            app_domain_assessment = current_model.app_domain.assess(stand_smiles)[0]
+                        for prod_set in pr.product_sets:
-            return JsonResponse(app_domain_assessment, safe=False)
+                            logger.debug(f"Checking {prod_set}")
+                            products.append(tuple([x for x in prod_set]))
+
+                        res.append({
+                            'products': list(set(products)),
+                            'probability': pr.probability,
+                            'btrule': {k: getattr(pr.rule, k) for k in ['url', 'name']} if pr.rule is not None else None
+                        })
+
+                return JsonResponse(res, safe=False)
+
+            else:
+                app_domain_assessment = current_model.app_domain.assess(stand_smiles)[0]
+                return JsonResponse(app_domain_assessment, safe=False)
 
         context = get_base_context(request)
         context['title'] = f'enviPath - {current_package.name} - {current_model.name}'
@@ -860,6 +875,11 @@ def package(request, package_uuid):
 
         if hidden := request.POST.get('hidden', None):
             if hidden == 'delete':
+
+                if current_user.default_package == current_package:
+                    return error(request, f'Package "{current_package.name}" is the default and cannot be deleted!',
+                                 'You cannot delete the default package. If you want to delete this package you have to set another default package first.')
+
                 logger.debug(current_package.delete())
                 return redirect(s.SERVER_URL + '/package')
             elif hidden == 'publish-package':
@@ -1017,9 +1037,9 @@ def package_compound(request, package_uuid, compound_uuid):
             else:
                 return HttpResponseBadRequest()
 
-        selected_scenarios = request.POST.getlist('selected-scenarios')
+        if 'selected-scenarios' in request.POST:
+            selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios is not None:
             set_scenarios(current_user, current_compound, selected_scenarios)
             return redirect(current_compound.url)
 
@@ -1126,9 +1146,9 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
             else:
                 return HttpResponseBadRequest()
 
-        selected_scenarios = request.POST.getlist('selected-scenarios')
+        if 'selected-scenarios' in request.POST:
+            selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios is not None:
             set_scenarios(current_user, current_structure, selected_scenarios)
             return redirect(current_structure.url)
 
@@ -1253,9 +1273,9 @@ def package_rule(request, package_uuid, rule_uuid):
             else:
                 return HttpResponseBadRequest()
 
-        selected_scenarios = request.POST.getlist('selected-scenarios')
+        if 'selected-scenarios' in request.POST:
+            selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios is not None:
             set_scenarios(current_user, current_rule, selected_scenarios)
             return redirect(current_rule.url)
 
@@ -1356,9 +1376,9 @@ def package_reaction(request, package_uuid, reaction_uuid):
             else:
                 return HttpResponseBadRequest()
 
-        selected_scenarios = request.POST.getlist('selected-scenarios')
+        if 'selected-scenarios' in request.POST:
+            selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios is not None:
             set_scenarios(current_user, current_reaction, selected_scenarios)
             return redirect(current_reaction.url)
 
@@ -1421,10 +1441,10 @@ def package_pathways(request, package_uuid):
 
         name = request.POST.get('name')
         description = request.POST.get('description')
-        pw_mode = request.POST.get('predict', 'predict')
+        pw_mode = request.POST.get('predict', 'predict').strip()
-        smiles = request.POST.get('smiles')
+        smiles = request.POST.get('smiles', '').strip()
 
-        if smiles is None or smiles.strip() == '':
+        if 'smiles' in request.POST and smiles == '':
             return error(request, "Pathway prediction failed!",
                          "Pathway prediction failed due to missing or empty SMILES")
 
@@ -1543,9 +1563,9 @@ def package_pathway(request, package_uuid, pathway_uuid):
             else:
                 return HttpResponseBadRequest()
 
-        selected_scenarios = request.POST.getlist('selected-scenarios')
+        if 'selected-scenarios' in request.POST:
+            selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios is not None:
             set_scenarios(current_user, current_pathway, selected_scenarios)
             return redirect(current_pathway.url)
 
@@ -1689,9 +1709,9 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
             else:
                 return HttpResponseBadRequest()
 
-        selected_scenarios = request.POST.getlist('selected-scenarios')
+        if 'selected-scenarios' in request.POST:
+            selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios is not None:
             set_scenarios(current_user, current_node, selected_scenarios)
             return redirect(current_node.url)
 
@@ -1798,9 +1818,9 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
                 current_edge.delete()
                 return redirect(current_pathway.url)
 
-        selected_scenarios = request.POST.getlist('selected-scenarios')
+        if 'selected-scenarios' in request.POST:
+            selected_scenarios = request.POST.getlist('selected-scenarios')
 
-        if selected_scenarios is not None:
             set_scenarios(current_user, current_edge, selected_scenarios)
             return redirect(current_edge.url)
 

templates/errors/error.html

@@ -6,8 +6,7 @@
         <h4 class="alert-heading">{{ error_message }}</h4>
         <hr>
         <p class="mb-0">
-            {{ error_detail }}<br>
+            {{ error_detail }}
-            The error was logged and will be investigated.
         </p>
     </div>
 

templates/framework.html

@@ -89,7 +89,7 @@
         <div class="collapse navbar-collapse collapse-framework navbar-collapse-framework" id="navbarCollapse">
             <ul class="nav navbar-nav navbar-nav-framework">
                 <li>
-                    <a class="button" data-toggle="modal" data-target="#predict_modal">
+                    <a href="#" data-toggle="modal" data-target="#predict_modal">
                         Predict Pathway
                     </a>
                 </li>

templates/index/index.html

@@ -103,6 +103,7 @@
             var textSmiles = $('#index-form-text-input').val().trim();
 
             if (textSmiles === '') {
+                $(this).prop("disabled", false);
                 return;
             }
 

templates/modals/objects/generic_set_scenario_modal.html

@@ -64,6 +64,9 @@
 
             $('#set_scenario_modal_form_submit').on('click', function (e) {
                 e.preventDefault();
+                if ($('##scenario-select').val().length == 0) {
+                    $('##scenario-select').val([''])
+                }
                 $('#set_scenario_modal_form').submit();
             });
         });

templates/objects/model.html

@@ -315,12 +315,18 @@
             $("#predict-button").on("click", function (e) {
                 e.preventDefault();
 
+                clear("predictResultTable");
+
                 data = {
                     "smiles": $("#smiles-to-predict").val(),
                     "classify": "ILikeCats!"
                 }
 
-                clear("predictResultTable");
+                if (data["smiles"].trim() === "") {
+                    $("#predictResultTable").addClass("alert alert-danger");
+                    $("#predictResultTable").append("Please enter a SMILES string to predict!");
+                    return;
+                }
 
                 makeLoadingGif("#predictLoading", "{% static '/images/wait.gif' %}");
                 $.ajax({
@@ -332,17 +338,17 @@
                             $("#predictLoading").empty();
                             handlePredictionResponse(data);
                         } catch (error) {
-                            console.log("Error");
+
                             $("#predictLoading").empty();
                             $("#predictResultTable").addClass("alert alert-danger");
-                            $("#predictResultTable").append("Error while processing request :/");
+                            $("#predictResultTable").append("Error while processing response :/");
                         }
                     },
-                    error: function (jqXHR, textStatus, errorThrown) {
+                    error: function (jqXHR, textStatus, errorThrown, x) {
                         $("#predictLoading").empty();
                         $("#predictResultTable").addClass("alert alert-danger");
-                        $("#predictResultTable").append("Error while processing request :/");
+                        $("#predictResultTable").append(jqXHR.responseJSON.error);
-                    }
+                    },
                 });
             });
         }
@@ -351,12 +357,20 @@
             $("#assess-button").on("click", function (e) {
                 e.preventDefault();
 
+                clear("appDomainAssessmentResultTable");
+
                 data = {
                     "smiles": $("#smiles-to-assess").val(),
                     "app-domain-assessment": "ILikeCats!"
                 }
 
-                clear("appDomainAssessmentResultTable");
+                if (data["smiles"].trim() === "") {
+                    $("#appDomainAssessmentResultTable").addClass("alert alert-danger");
+                    $("#appDomainAssessmentResultTable").append("Please enter a SMILES string to predict!");
+                    return;
+                }
+
+
 
                 makeLoadingGif("#appDomainLoading", "{% static '/images/wait.gif' %}");
                 $.ajax({
@@ -369,16 +383,15 @@
                             handleAssessmentResponse("{% url 'depict' %}", data);
                             console.log(data);
                         } catch (error) {
-                            console.log("Error");
                             $("#appDomainLoading").empty();
                             $("#appDomainAssessmentResultTable").addClass("alert alert-danger");
-                            $("#appDomainAssessmentResultTable").append("Error while processing request :/");
+                            $("#appDomainAssessmentResultTable").append("Error while processing response :/");
                         }
                     },
                     error: function (jqXHR, textStatus, errorThrown) {
                         $("#appDomainLoading").empty();
                         $("#appDomainAssessmentResultTable").addClass("alert alert-danger");
-                        $("#appDomainAssessmentResultTable").append("Error while processing request :/");
+                        $("#appDomainAssessmentResultTable").append(jqXHR.responseJSON.error);
                     }
                 });
             });

tests/views/test_model_views.py

@@ -0,0 +1,113 @@
+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, Package, User
+
+
+@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.model_package = Package.objects.get(name='Fixtures')
+
+    def setUp(self):
+        self.client.force_login(self.user1)
+
+    def test_predict(self):
+        self.client.force_login(User.objects.get(username="admin"))
+        response = self.client.get(
+            reverse("package model detail", kwargs={
+                'package_uuid': str(self.model_package.uuid),
+                'model_uuid': str(self.model_package.models.first().uuid)
+            }), {
+                'classify': 'ILikeCats!',
+                'smiles': 'CCN(CC)C(=O)C1=CC(=CC=C1)CO',
+            }
+        )
+
+        expected = [
+            {
+                'products': [
+                    [
+                        'O=C(O)C1=CC(CO)=CC=C1',
+                        'CCNCC'
+                    ]
+                ],
+                'probability': 0.25,
+                'btrule': {
+                    'url': 'http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/0e6e9290-b658-4450-b291-3ec19fa19206',
+                    'name': 'bt0430-4011'
+                }
+            }, {
+                'products': [
+                    [
+                        'CCNC(=O)C1=CC(CO)=CC=C1',
+                        'CC=O'
+                    ]
+                ], 'probability': 0.0,
+                'btrule': {
+                    'url': 'http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/27a3a353-0b66-4228-bd16-e407949e90df',
+                    'name': 'bt0243-4301'
+                }
+            }, {
+                'products': [
+                    [
+                        'CCN(CC)C(=O)C1=CC(C=O)=CC=C1'
+                    ]
+                ], 'probability': 0.75,
+                'btrule': {
+                    'url': 'http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022',
+                    'name': 'bt0001-3568'
+                }
+            }
+        ]
+
+        actual = response.json()
+        self.assertEqual(actual, expected)
+
+        response = self.client.get(
+            reverse("package model detail", kwargs={
+                'package_uuid': str(self.model_package.uuid),
+                'model_uuid': str(self.model_package.models.first().uuid)
+            }), {
+                'classify': 'ILikeCats!',
+                'smiles': '',
+            }
+        )
+
+        self.assertEqual(response.status_code, 400)
+        self.assertEqual(response.json()['error'], 'Received empty SMILES')
+
+        response = self.client.get(
+            reverse("package model detail", kwargs={
+                'package_uuid': str(self.model_package.uuid),
+                'model_uuid': str(self.model_package.models.first().uuid)
+            }), {
+                'classify': 'ILikeCats!',
+                'smiles': '  ',  # Input should be stripped
+            }
+        )
+
+        self.assertEqual(response.status_code, 400)
+        self.assertEqual(response.json()['error'], 'Received empty SMILES')
+
+        response = self.client.get(
+            reverse("package model detail", kwargs={
+                'package_uuid': str(self.model_package.uuid),
+                'model_uuid': str(self.model_package.models.first().uuid)
+            }), {
+                'classify': 'ILikeCats!',
+                'smiles': 'RandomInput',
+            }
+        )
+
+        self.assertEqual(response.status_code, 400)
+        self.assertEqual(response.json()['error'], '"RandomInput" is not a valid SMILES')

tests/views/test_package_views.py

@@ -178,3 +178,15 @@ class PackageViewTest(TestCase):
 
         response = self.client.get(package_url)
         self.assertEqual(response.status_code, 404)
+
+    def test_delete_default_package(self):
+        self.client.force_login(self.user1)
+        # Try to delete the default package
+        response = self.client.post(self.user1.default_package.url, {
+            "hidden": "delete"
+        })
+
+        self.assertEqual(response.status_code, 400)
+        self.assertTrue(f'You cannot delete the default package. '
+                        f'If you want to delete this package you have to '
+                        f'set another default package first' in response.content.decode())

tests/views/test_rule_views.py

@@ -161,7 +161,8 @@ class RuleViewTest(TestCase):
                 'package_uuid': str(r.package.uuid),
                 'rule_uuid': str(r.uuid)
             }), {
-                "selected-scenarios": []
+                # We have to set an empty string to avoid that the parameter is removed
+                "selected-scenarios": ""
             }
         )