Basic System (#31)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#31

envipath/settings.py

@@ -15,6 +15,7 @@ from pathlib import Path
 from dotenv import load_dotenv
 from envipy_plugins import Classifier, Property, Descriptor
 from sklearn.ensemble import RandomForestClassifier
+from sklearn.tree import DecisionTreeClassifier
 
 # Build paths inside the project like this: BASE_DIR / 'subdir'.
 BASE_DIR = Path(__file__).resolve().parent.parent
@@ -256,14 +257,29 @@ CELERY_RESULT_BACKEND = 'redis://localhost:6379/1'
 CELERY_ACCEPT_CONTENT = ['json']
 CELERY_TASK_SERIALIZER = 'json'
 
-DEFAULT_MODELS_PARAMS = {
+DEFAULT_RF_MODEL_PARAMS = {
-    'base_clf': RandomForestClassifier(n_estimators=100,
+    'base_clf': RandomForestClassifier(
-                                       max_features='log2',
+        n_estimators=100,
-                                       random_state=42,
+        max_features='log2',
-                                       criterion='entropy',
+        random_state=42,
-                                       ccp_alpha=0.0,
+        criterion='entropy',
-                                       max_depth=3,
+        ccp_alpha=0.0,
-                                       min_samples_leaf=1),
+        max_depth=3,
+        min_samples_leaf=1
+    ),
+    'num_chains': 10,
+}
+
+DEFAULT_DT_MODEL_PARAMS = {
+    'base_clf': DecisionTreeClassifier(
+        criterion='entropy',
+        max_depth=3,
+        min_samples_split=5,
+        min_samples_leaf=5,
+        max_features='sqrt',
+        class_weight='balanced',
+        random_state=42
+    ),
     'num_chains': 10,
 }
 

epdb/logic.py

@@ -7,13 +7,21 @@ from django.db import transaction
 from django.conf import settings as s
 
 from epdb.models import User, Package, UserPackagePermission, GroupPackagePermission, Permission, Group, Setting, \
-    EPModel, UserSettingPermission, Rule, Pathway, Node, Edge
+    EPModel, UserSettingPermission, Rule, Pathway, Node, Edge, Compound, Reaction, CompoundStructure
+from utilities.chem import FormatConverter
 
 logger = logging.getLogger(__name__)
 
+
 class UserManager(object):
+    user_pattern = re.compile(r".*/user/[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}")
+
     @staticmethod
-    def create_user(username, email, password, *args, **kwargs):
+    def is_user_url(url: str):
+        return bool(re.findall(UserManager.user_pattern, url))
+
+    @staticmethod
+    def create_user(username, email, password, set_setting=True, add_to_group=True, *args, **kwargs):
         # avoid circular import :S
         from .tasks import send_registration_mail
 
@@ -34,6 +42,17 @@ class UserManager(object):
             # send email for verification
             send_registration_mail.delay(u.pk)
 
+        if set_setting:
+            u.default_setting = Setting.objects.get(global_default=True)
+            u.save()
+
+        if add_to_group:
+            g = Group.objects.get(public=True, name='enviPath Users')
+            g.user_member.add(u)
+            g.save()
+            u.default_group = g
+            u.save()
+
         return u
 
     @staticmethod
@@ -54,7 +73,16 @@ class UserManager(object):
         uuid = user_url.strip().split('/')[-1]
         return get_user_model().objects.get(uuid=uuid)
 
+    @staticmethod
+    def writable(current_user, user):
+        return (current_user == user) or user.is_superuser
+
 class GroupManager(object):
+    group_pattern = re.compile(r".*/group/[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}")
+
+    @staticmethod
+    def is_group_url(url: str):
+        return bool(re.findall(GroupManager.group_pattern, url))
 
     @staticmethod
     def create_group(current_user, name, description):
@@ -110,9 +138,17 @@ class GroupManager(object):
 
         group.save()
 
+    @staticmethod
+    def writable(user, group):
+        return (user == group.owner) or user.is_superuser
+
 
 class PackageManager(object):
-    package_pattern = re.compile(r".*/package/[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}$")
+    package_pattern = re.compile(r".*/package/[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}")
+
+    @staticmethod
+    def is_package_url(url: str):
+        return bool(re.findall(PackageManager.package_pattern, url))
 
     @staticmethod
     def get_reviewed_packages():
@@ -120,7 +156,6 @@ class PackageManager(object):
 
     @staticmethod
     def readable(user, package):
-        # TODO Owner!
         if UserPackagePermission.objects.filter(package=package, user=user).exists() or \
                 GroupPackagePermission.objects.filter(package=package, group__in=GroupManager.get_groups(user)) or \
                 package.reviewed is True or \
@@ -131,14 +166,21 @@ class PackageManager(object):
 
     @staticmethod
     def writable(user, package):
-        # TODO Owner!
+        if UserPackagePermission.objects.filter(package=package, user=user, permission=Permission.WRITE[0]).exists() or \
-        if UserPackagePermission.objects.filter(package=package, user=user, permission=Permission.WRITE).exists() or \
+                GroupPackagePermission.objects.filter(package=package, group__in=GroupManager.get_groups(user), permission=Permission.WRITE[0]).exists() or \
-                GroupPackagePermission.objects.filter(package=package, group__in=GroupManager.get_groups(user),
+                UserPackagePermission.objects.filter(package=package, user=user, permission=Permission.ALL[0]).exists() or \
-                                                      permission=Permission.WRITE) or \
                 user.is_superuser:
             return True
         return False
 
+    @staticmethod
+    def get_package_lp(package_url):
+        match = re.findall(PackageManager.package_pattern, package_url)
+        if match:
+            package_id = match[0].split('/')[-1]
+            return Package.objects.get(uuid=package_id)
+        return None
+
     @staticmethod
     def get_package_by_url(user, package_url):
         match = re.findall(PackageManager.package_pattern, package_url)
@@ -229,8 +271,12 @@ class PackageManager(object):
     @staticmethod
     @transaction.atomic
     def update_permissions(caller: User, package: Package, grantee: Union[User, Group], new_perm: Optional[str]):
-        if not PackageManager.writable(caller, package):
+        caller_perm = None
-            raise ValueError(f"User {caller} is not allowed to modify permissions on {package}")
+        if not caller.is_superuser:
+            caller_perm = UserPackagePermission.objects.get(user=caller, package=package).permission
+
+        if caller_perm != Permission.ALL[0] and not caller.is_superuser:
+            raise ValueError(f"Only owner are allowed to modify permissions")
 
         data = {
             'package': package,
@@ -629,8 +675,6 @@ class PackageManager(object):
 
         return pack
 
-
-
 class SettingManager(object):
     setting_pattern = re.compile(r".*/setting/[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}$")
 
@@ -648,7 +692,8 @@ class SettingManager(object):
     def get_setting_by_id(user, setting_id):
         s = Setting.objects.get(uuid=setting_id)
 
-        if s.global_default or s.public or s.owner == user or user.is_superuser:
+        if s.global_default or s.public or  user.is_superuser or \
+                UserSettingPermission.objects.filter(user=user, setting=s).exists():
             return s
 
         raise ValueError(
@@ -697,6 +742,116 @@ class SettingManager(object):
     def set_default_setting(user: User, setting: Setting):
         pass
 
+class SearchManager(object):
+
+
+    @staticmethod
+    def search(packages: Union[Package, List[Package]], searchterm: str, mode: str):
+        match mode:
+            case 'text':
+                return SearchManager._search_text(packages, searchterm)
+            case 'default':
+                return SearchManager._search_default_smiles(packages, searchterm)
+            case 'exact':
+                return SearchManager._search_exact_smiles(packages, searchterm)
+            case 'canonical':
+                return SearchManager._search_canonical_smiles(packages, searchterm)
+            case 'inchikey':
+                return SearchManager._search_inchikey(packages, searchterm)
+            case _:
+                raise ValueError(f"Unknown search mode {mode}!")
+
+    @staticmethod
+    def _search_inchikey(packages: Union[Package, List[Package]], searchterm: str):
+        from django.db.models import Q
+
+        search_cond = Q(inchikey=searchterm)
+        compound_qs = Compound.objects.filter(Q(package__in=packages) & Q(compoundstructure__inchikey=searchterm)).distinct()
+        compound_structure_qs = CompoundStructure.objects.filter(Q(compound__package__in=packages) & search_cond)
+        reactions_qs = Reaction.objects.filter(Q(package__in=packages) & (Q(educts__inchikey=searchterm) | Q(products__inchikey=searchterm))).distinct()
+        pathway_qs = Pathway.objects.filter(Q(package__in=packages) & (Q(edge__edge_label__educts__inchikey=searchterm) | Q(edge__edge_label__products__inchikey=searchterm))).distinct()
+
+        return {
+            'Compounds': [{'name': c.name, 'description': c.description, 'url': c.url} for c in compound_qs],
+            'Compound Structures': [{'name': c.name, 'description': c.description, 'url': c.url} for c in compound_structure_qs],
+            'Reactions': [{'name': r.name, 'description': r.description, 'url': r.url} for r in reactions_qs],
+            'Pathways': [{'name': p.name, 'description': p.description, 'url': p.url} for p in pathway_qs],
+        }
+
+    @staticmethod
+    def _search_exact_smiles(packages: Union[Package, List[Package]], searchterm: str):
+        from django.db.models import Q
+
+        search_cond = Q(smiles=searchterm)
+        compound_qs = Compound.objects.filter(Q(package__in=packages) & Q(compoundstructure__smiles=searchterm)).distinct()
+        compound_structure_qs = CompoundStructure.objects.filter(Q(compound__package__in=packages) & search_cond)
+        reactions_qs = Reaction.objects.filter(Q(package__in=packages) & (Q(educts__smiles=searchterm) | Q(products__smiles=searchterm))).distinct()
+        pathway_qs = Pathway.objects.filter(Q(package__in=packages) & (Q(edge__edge_label__educts__smiles=searchterm) | Q(edge__edge_label__products__smiles=searchterm))).distinct()
+
+        return {
+            'Compounds': [{'name': c.name, 'description': c.description, 'url': c.url} for c in compound_qs],
+            'Compound Structures': [{'name': c.name, 'description': c.description, 'url': c.url} for c in compound_structure_qs],
+            'Reactions': [{'name': r.name, 'description': r.description, 'url': r.url} for r in reactions_qs],
+            'Pathways': [{'name': p.name, 'description': p.description, 'url': p.url} for p in pathway_qs],
+        }
+
+    @staticmethod
+    def _search_default_smiles(packages: Union[Package, List[Package]], searchterm: str):
+        from django.db.models import Q
+
+        inchi_front = FormatConverter.InChIKey(searchterm)[:14]
+
+        search_cond = Q(inchikey__startswith=inchi_front)
+        compound_qs = Compound.objects.filter(Q(package__in=packages) & Q(compoundstructure__inchikey__startswith=inchi_front)).distinct()
+        compound_structure_qs = CompoundStructure.objects.filter(Q(compound__package__in=packages) & search_cond)
+        reactions_qs = Reaction.objects.filter(Q(package__in=packages) & (Q(educts__inchikey__startswith=inchi_front) | Q(products__inchikey__startswith=inchi_front))).distinct()
+        pathway_qs = Pathway.objects.filter(Q(package__in=packages) & (Q(edge__edge_label__educts__inchikey__startswith=inchi_front) | Q(edge__edge_label__products__inchikey__startswith=inchi_front))).distinct()
+
+        return {
+            'Compounds': [{'name': c.name, 'description': c.description, 'url': c.url} for c in compound_qs],
+            'Compound Structures': [{'name': c.name, 'description': c.description, 'url': c.url} for c in compound_structure_qs],
+            'Reactions': [{'name': r.name, 'description': r.description, 'url': r.url} for r in reactions_qs],
+            'Pathways': [{'name': p.name, 'description': p.description, 'url': p.url} for p in pathway_qs],
+        }
+
+    @staticmethod
+    def _search_canonical_smiles(packages: Union[Package, List[Package]], searchterm: str):
+        from django.db.models import Q
+
+        search_cond = Q(canonical_smiles=searchterm)
+        compound_qs = Compound.objects.filter(Q(package__in=packages) & Q(compoundstructure__canonical_smiles=searchterm)).distinct()
+        compound_structure_qs = CompoundStructure.objects.filter(Q(compound__package__in=packages) & search_cond)
+        reactions_qs = Reaction.objects.filter(Q(package__in=packages) & (Q(educts__canonical_smiles=searchterm) | Q(products__canonical_smiles=searchterm))).distinct()
+        pathway_qs = Pathway.objects.filter(Q(package__in=packages) & (Q(edge__edge_label__educts__canonical_smiles=searchterm) | Q(edge__edge_label__products__canonical_smiles=searchterm))).distinct()
+
+        return {
+            'Compounds': [{'name': c.name, 'description': c.description, 'url': c.url} for c in compound_qs],
+            'Compound Structures': [{'name': c.name, 'description': c.description, 'url': c.url} for c in compound_structure_qs],
+            'Reactions': [{'name': r.name, 'description': r.description, 'url': r.url} for r in reactions_qs],
+            'Pathways': [{'name': p.name, 'description': p.description, 'url': p.url} for p in pathway_qs],
+        }
+
+    @staticmethod
+    def _search_text(packages: Union[Package, List[Package]], searchterm: str):
+        from django.db.models import Q
+
+        search_cond = (Q(name__icontains=searchterm) | Q(description__icontains=searchterm))
+        cond = Q(package__in=packages) & search_cond
+        compound_qs = Compound.objects.filter(cond)
+        compound_structure_qs = CompoundStructure.objects.filter(Q(compound__package__in=packages) & search_cond)
+        rule_qs = Rule.objects.filter(cond)
+        reactions_qs = Reaction.objects.filter(cond)
+        pathway_qs = Pathway.objects.filter(cond)
+
+        res = {
+            'Compounds': [{'name': c.name, 'description': c.description, 'url': c.url} for c in compound_qs],
+            'Compound Structures': [{'name': c.name, 'description': c.description, 'url': c.url} for c in compound_structure_qs],
+            'Rules': [{'name': r.name, 'description': r.description, 'url': r.url} for r in rule_qs],
+            'Reactions': [{'name': r.name, 'description': r.description, 'url': r.url} for r in reactions_qs],
+            'Pathways': [{'name': p.name, 'description': p.description, 'url': p.url} for p in pathway_qs],
+        }
+        return res
+
 
 class SNode(object):
 
@@ -719,7 +874,7 @@ class SNode(object):
 class SEdge(object):
 
     def __init__(self, educts: Union[SNode, List[SNode]], products: Union[SNode | List[SNode]],
-                 rule: Optional['Rule'] = None):
+                 rule: Optional['Rule'] = None, probability: Optional[float] = None):
 
         if not isinstance(educts, list):
             educts = [educts]
@@ -727,6 +882,7 @@ class SEdge(object):
         self.educts = educts
         self.products = products
         self.rule = rule
+        self.probability = probability
 
     def __hash__(self):
         full_hash = 0
@@ -799,11 +955,45 @@ class SPathway(object):
                 elif isinstance(n, SNode):
                     self.root_nodes.append(n)
 
-        self.queue = list()
         self.smiles_to_node: Dict[str, SNode] = dict(**{n.smiles: n for n in self.root_nodes})
         self.edges: Set['SEdge'] = set()
         self.done = False
 
+    @staticmethod
+    def from_pathway(pw: 'Pathway', persist: bool = True):
+        """ Initializes a SPathway with a state given by a Pathway """
+        spw = SPathway(root_nodes=pw.root_nodes, persist=pw if persist else None, prediction_setting=pw.setting)
+        # root_nodes are already added in __init__, add remaining nodes
+        for n in pw.nodes:
+            snode = SNode(n.default_node_label.smiles, n.depth)
+            if snode.smiles not in spw.smiles_to_node:
+                spw.smiles_to_node[snode.smiles] = snode
+                spw.snode_persist_lookup[snode] = n
+
+        for e in pw.edges:
+            sub = []
+            prod = []
+
+            for n in e.start_nodes.all():
+                sub.append(spw.smiles_to_node[n.default_node_label.smiles])
+
+            for n in e.end_nodes.all():
+                prod.append(spw.smiles_to_node[n.default_node_label.smiles])
+
+            rule = None
+            if e.edge_label.rules.all():
+                rule = e.edge_label.rules.all().first()
+
+            prob = None
+            if e.kv.get('probability'):
+                prob = float(e.kv['probability'])
+
+            sedge = SEdge(sub, prod, rule=rule, probability=prob)
+            spw.edges.add(sedge)
+            spw.sedge_persist_lookup[sedge] = e
+
+        return spw
+
     def num_nodes(self):
         return len(self.smiles_to_node.keys())
 
@@ -830,8 +1020,18 @@ class SPathway(object):
 
         return sorted(res, key=lambda x: hash(x))
 
-    def predict_step(self, from_depth: int = 0):
+    def predict_step(self, from_depth: int = None, from_node: 'Node' = None):
-        substrates = self._get_nodes_for_depth(from_depth)
+        substrates: List[SNode] = []
+
+        if from_depth is not None:
+            substrates = self._get_nodes_for_depth(from_depth)
+        elif from_node is not None:
+            for k,v in self.snode_persist_lookup.items():
+                if from_node == v:
+                    substrates = [k]
+                    break
+        else:
+            raise ValueError("Neither from_depth nor from_node_url specified")
 
         new_tp = False
         if substrates:
@@ -849,13 +1049,19 @@ class SPathway(object):
                                 node = self.smiles_to_node[c]
                                 cand_nodes.append(node)
 
-                            edge = SEdge(sub, cand_nodes, cand_set.rule)
+                            edge = SEdge(sub, cand_nodes, rule=cand_set.rule, probability=cand_set.probability)
                             self.edges.add(edge)
-        else:
+
+        # In case no substrates are found, we're done.
+        # For "predict from node" we're always done
+        if len(substrates) == 0 or from_node is not None:
             self.done = True
 
+        # Check if we need to write back data to database
         if new_tp and self.persist:
             self._sync_to_pathway()
+            # call save to update internal modified field
+            self.persist.save()
 
     def _sync_to_pathway(self):
         logger.info("Updating Pathway with SPathway")
@@ -876,6 +1082,11 @@ class SPathway(object):
                     product_nodes.append(self.snode_persist_lookup[snode])
 
                 e = Edge.create(self.persist, educt_nodes, product_nodes, sedge.rule)
+
+                if sedge.probability:
+                    e.kv.update({'probability': sedge.probability})
+                    e.save()
+
                 self.sedge_persist_lookup[sedge] = e
 
         logger.info("Update done!")

epdb/management/commands/bootstrap.py

@@ -13,12 +13,14 @@ class Command(BaseCommand):
     def create_users(self):
 
         if not User.objects.filter(email='anon@lorsba.ch').exists():
-            anon = UserManager.create_user("anonymous", "anon@lorsba.ch", "SuperSafe", is_active=True)
+            anon = UserManager.create_user("anonymous", "anon@lorsba.ch", "SuperSafe", is_active=True,
+                                           add_to_group=False, set_setting=False)
         else:
             anon = User.objects.get(email='anon@lorsba.ch')
 
         if not User.objects.filter(email='admin@lorsba.ch').exists():
-            admin = UserManager.create_user("admin", "admin@lorsba.ch", "SuperSafe", is_active=True)
+            admin = UserManager.create_user("admin", "admin@lorsba.ch", "SuperSafe", is_active=True, add_to_group=False,
+                                            set_setting=False)
             admin.is_staff = True
             admin.is_superuser = True
             admin.save()
@@ -26,6 +28,9 @@ class Command(BaseCommand):
             admin = User.objects.get(email='admin@lorsba.ch')
 
         g = GroupManager.create_group(admin, 'enviPath Users', 'All enviPath Users')
+        g.public = True
+        g.save()
+
         g.user_member.add(anon)
         g.save()
 
@@ -36,7 +41,8 @@ class Command(BaseCommand):
         admin.save()
 
         if not User.objects.filter(email='jebus@lorsba.ch').exists():
-            jebus = UserManager.create_user("jebus", "jebus@lorsba.ch", "SuperSafe", is_active=True)
+            jebus = UserManager.create_user("jebus", "jebus@lorsba.ch", "SuperSafe", is_active=True, add_to_group=False,
+                                            set_setting=False)
             jebus.is_staff = True
             jebus.is_superuser = True
             jebus.save()
@@ -94,6 +100,9 @@ class Command(BaseCommand):
         setting.make_global_default()
 
         for u in [anon, jebus]:
+            u.default_setting = setting
+            u.save()
+
             usp = UserSettingPermission()
             usp.user = u
             usp.setting = setting
@@ -119,7 +128,7 @@ class Command(BaseCommand):
 
         X, y = ml_model.build_dataset()
         ml_model.build_model(X, y)
-        ml_model.evaluate_model()
+        # ml_model.evaluate_model()
 
         # If available create EnviFormerModel
         if s.ENVIFORMER_PRESENT:

epdb/models.py

@@ -14,7 +14,7 @@ from django.contrib.auth.hashers import make_password, check_password
 from django.contrib.auth.models import AbstractUser
 from django.contrib.postgres.fields import ArrayField
 from django.db import models, transaction
-from django.db.models import JSONField
+from django.db.models import JSONField, Count, Q
 from django.utils import timezone
 from django.utils.functional import cached_property
 from model_utils.models import TimeStampedModel
@@ -43,8 +43,6 @@ class User(AbstractUser):
                                       on_delete=models.SET_NULL, related_name='default_group')
     default_setting = models.ForeignKey('epdb.Setting', on_delete=models.SET_NULL,
                                         verbose_name='The users default settings', null=True, blank=False)
-    # TODO remove
-    groups = models.ManyToManyField("Group", verbose_name='groups')
 
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ['username']
@@ -87,6 +85,7 @@ class Group(TimeStampedModel):
     uuid = models.UUIDField(null=False, blank=False, verbose_name='UUID of this object', unique=True, default=uuid4)
     name = models.TextField(blank=False, null=False, verbose_name='Group name')
     owner = models.ForeignKey("User", verbose_name='Group Owner', on_delete=models.CASCADE)
+    public = models.BooleanField(verbose_name='Public Group', default=False)
     description = models.TextField(blank=False, null=False, verbose_name='Descriptions', default='no description')
     user_member = models.ManyToManyField("User", verbose_name='User members', related_name='users_in_group')
     group_member = models.ManyToManyField("Group", verbose_name='Group member', related_name='groups_in_group')
@@ -314,7 +313,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin):
     @transaction.atomic
     def create(package: Package, smiles: str, name: str = None, description: str = None, *args, **kwargs) -> 'Compound':
 
-        if smiles is None or smiles == '':
+        if smiles is None or smiles.strip() == '':
             raise ValueError('SMILES is required')
 
         smiles = smiles.strip()
@@ -338,12 +337,14 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin):
         c = Compound()
         c.package = package
 
-        # For name and description we have defaults so only set them if they carry a real value
+        if name is None or name.strip() == '':
-        if name is not None and name != '':
+            name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
-            c.name = name
 
-        if description is not None and description != '':
+        c.name = name
-            c.description = description
+
+        # We have a default here only set the value if it carries some payload
+        if description is not None and description.strip() != '':
+            c.description = description.strip()
 
         c.save()
 
@@ -403,25 +404,27 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin):
 class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin):
     compound = models.ForeignKey('epdb.Compound', on_delete=models.CASCADE, db_index=True)
     smiles = models.TextField(blank=False, null=False, verbose_name='SMILES')
+    canonical_smiles = models.TextField(blank=False, null=False, verbose_name='Canonical SMILES')
+    inchikey = models.TextField(max_length=27, blank=False, null=False, verbose_name="InChIKey")
     normalized_structure = models.BooleanField(null=False, blank=False, default=False)
 
+    def save(self, *args, **kwargs):
+        # Compute these fields only on initial save call
+        if self.pk is None:
+            try:
+                # Generate canonical SMILES
+                self.canonical_smiles = FormatConverter.canonicalize(self.smiles)
+                # Generate InChIKey
+                self.inchikey = FormatConverter.InChIKey(self.smiles)
+            except Exception as e:
+                logger.error(f"Could compute canonical SMILES/InChIKey from {self.smiles}, error: {e}")
+
+        super().save(*args, **kwargs)
+
     @property
     def url(self):
         return '{}/structure/{}'.format(self.compound.url, self.uuid)
 
-    # @property
-    # def related_pathways(self):
-    #     pathways = Node.objects.filter(node_labels__in=[self]).values_list('pathway', flat=True)
-    #     return Pathway.objects.filter(package=self.compound.package, id__in=set(pathways)).order_by('name')
-
-    # @property
-    # def related_reactions(self):
-    #     return (
-    #             Reaction.objects.filter(package=self.compound.package, educts__in=[self])
-    #             |
-    #             Reaction.objects.filter(package=self.compound.package, products__in=[self])
-    #     ).order_by('name')
-
     @staticmethod
     @transaction.atomic
     def create(compound: Compound, smiles: str, name: str = None, description: str = None, *args, **kwargs):
@@ -448,19 +451,9 @@ class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin):
 
         return cs
 
-    # TODO add find method
-
     @property
-    def InChIKey(self):
+    def as_svg(self, width: int = 800, height: int = 400):
-        return FormatConverter.InChIKey(self.smiles)
+        return IndigoUtils.mol_to_svg(self.smiles, width=width, height=height)
-
-    @property
-    def canonical_smiles(self):
-        return FormatConverter.canonicalize(self.smiles)
-
-    @property
-    def as_svg(self):
-        return IndigoUtils.mol_to_svg(self.smiles)
 
 
 class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
@@ -492,19 +485,9 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
 
     @staticmethod
     @transaction.atomic
-    def create(package: Package, rule_type: str, name: str = None, description: str = None, *args, **kwargs):
+    def create(rule_type: str, *args, **kwargs):
-        r = Rule.cls_for_type(rule_type)()
+        cls = Rule.cls_for_type(rule_type)
-        r.package = package
+        return cls.create(*args, **kwargs)
-        r.name = name
-        r.description = description
-
-        # As we are setting params this way the "k" has to match the property name
-        for k, v in kwargs.items():
-            setattr(r, k, v)
-
-        r.save()
-        return r
-
 
 #
 #     @property
@@ -533,6 +516,54 @@ class SimpleAmbitRule(SimpleRule):
     reactant_filter_smarts = models.TextField(null=True, verbose_name='Reactant Filter SMARTS')
     product_filter_smarts = models.TextField(null=True, verbose_name='Product Filter SMARTS')
 
+    @staticmethod
+    @transaction.atomic
+    def create(package: Package, name: str = None, description: str = None, smirks: str = None,
+               reactant_filter_smarts: str = None, product_filter_smarts: str = None):
+
+        if smirks is None or smirks.strip() == '':
+            raise ValueError('SMIRKS is required!')
+
+        smirks = smirks.strip()
+
+        if not FormatConverter.is_valid_smirks(smirks):
+            raise ValueError(f'SMIRKS "{smirks}" is invalid!')
+
+        query = SimpleAmbitRule.objects.filter(package=package, smirks=smirks)
+
+        if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != '':
+            query = query.filter(reactant_filter_smarts=reactant_filter_smarts)
+
+        if product_filter_smarts is not None and product_filter_smarts.strip() != '':
+            query = query.filter(product_filter_smarts=product_filter_smarts)
+
+        if query.exists():
+            if query.count() > 1:
+                logger.error(f'More than one rule matched this one! {query}')
+            return query.first()
+
+        r = SimpleAmbitRule()
+        r.package = package
+
+        if name is None or name.strip() == '':
+            name = f'Rule {Rule.objects.filter(package=package).count() + 1}'
+
+        r.name = name
+
+        if description is not None and description.strip() != '':
+            r.description = description
+
+        r.smirks = smirks
+
+        if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != '':
+            r.reactant_filter_smarts = reactant_filter_smarts
+
+        if product_filter_smarts is not None and product_filter_smarts.strip() != '':
+            r.product_filter_smarts = product_filter_smarts
+
+        r.save()
+        return r
+
     @property
     def url(self):
         return '{}/simple-ambit-rule/{}'.format(self.package.url, self.uuid)
@@ -642,7 +673,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin):
     def create(package: Package, name: str = None, description: str = None,
                educts: Union[List[str], List[CompoundStructure]] = None,
                products: Union[List[str], List[CompoundStructure]] = None,
-               rule: Rule = None, multi_step: bool = True):
+               rules: Union[Rule|List[Rule]] = None, multi_step: bool = True):
 
         _educts = []
         _products = []
@@ -662,18 +693,61 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin):
             _products += products
 
         else:
-            raise ValueError("")
+            raise ValueError("Found mixed types for educts and/or products!")
+
+        if len(_educts) == 0 or len(_products) == 0:
+            raise ValueError("No educts or products specified!")
+
+        if rules is None:
+            rules = []
+
+        if isinstance(rules, Rule):
+            rules = [rules]
+
+
+        query = Reaction.objects.annotate(
+            educt_count=Count('educts', filter=Q(educts__in=_educts), distinct=True),
+            product_count=Count('products', filter=Q(products__in=_products), distinct=True),
+        )
+
+        # The annotate/filter wont work if rules is an empty list
+        if rules:
+            query = query.annotate(
+                rule_count=Count('rules', filter=Q(rules__in=rules), distinct=True)
+            ).filter(rule_count=len(rules))
+        else:
+            query = query.annotate(
+                rule_count=Count('rules', distinct=True)
+            ).filter(rule_count=0)
+
+        existing_reaction_qs = query.filter(
+            educt_count=len(_educts),
+            product_count=len(_products),
+            multi_step=multi_step,
+            package=package
+        )
+
+        if existing_reaction_qs.exists():
+            if existing_reaction_qs.count() > 1:
+                logger.error(f'Found more than one reaction for given input! {existing_reaction_qs}')
+            return existing_reaction_qs.first()
 
         r = Reaction()
         r.package = package
-        r.name = name
+
-        r.description = description
+        if name is not None and name.strip() != '':
+            r.name = name
+
+        if description is not None and name.strip() != '':
+            r.description = description
+
         r.multi_step = multi_step
 
         r.save()
 
-        if rule:
+        if rules:
-            r.rules.add(rule)
+            for rule in rules:
+                r.rules.add(rule)
 
         for educt in _educts:
             r.educts.add(educt)
@@ -700,6 +774,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin):
 
 class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey('epdb.Package', verbose_name='Package', on_delete=models.CASCADE, db_index=True)
+    setting = models.ForeignKey('epdb.Setting', verbose_name='Setting', on_delete=models.CASCADE, null=True, blank=True)
 
     @property
     def root_nodes(self):
@@ -709,6 +784,12 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     def nodes(self):
         return Node.objects.filter(pathway=self)
 
+    def get_node(self, node_url):
+        for n in self.nodes:
+            if n.url == node_url:
+                return n
+        return None
+
     @property
     def edges(self):
         return Edge.objects.filter(pathway=self)
@@ -717,6 +798,26 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     def url(self):
         return '{}/pathway/{}'.format(self.package.url, self.uuid)
 
+    # Mode
+    def is_built(self):
+        return self.kv.get('mode', 'build') == 'predicted'
+
+    def is_predicted(self):
+        return self.kv.get('mode', 'build') == 'predicted'
+
+    def is_predicted(self):
+        return self.kv.get('mode', 'build') == 'predicted'
+
+    # Status
+    def completed(self):
+        return self.kv.get('status', 'completed') == 'completed'
+
+    def running(self):
+        return self.kv.get('status', 'completed') == 'running'
+
+    def failed(self):
+        return self.kv.get('status', 'completed') == 'failed'
+
     def d3_json(self):
         # Ideally it would be something like this but
         # to reduce crossing in edges do a DFS
@@ -770,7 +871,11 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
                 new_link = {
                     'name': link['name'],
                     'id': link['id'],
+                    'url': link['url'],
+                    'image': link['image'],
                     'reaction': link['reaction'],
+                    'reaction_probability': link['reaction_probability'],
+                    'scenarios': link['scenarios'],
                     'source': node_url_to_idx[link['start_node_urls'][0]],
                     'target': pseudo_idx
                 }
@@ -781,7 +886,11 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
                     new_link = {
                         'name': link['name'],
                         'id': link['id'],
+                        'url': link['url'],
+                        'image': link['image'],
                         'reaction': link['reaction'],
+                        'reaction_probability': link['reaction_probability'],
+                        'scenarios': link['scenarios'],
                         'source': pseudo_idx,
                         'target': node_url_to_idx[target]
                     }
@@ -797,9 +906,9 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
             "completed": "true",
             "description": self.description,
             "id": self.url,
-            "isIncremental": False,
+            "isIncremental": self.kv.get('mode') == 'incremental',
-            "isPredicted": False,
+            "isPredicted": self.kv.get('mode') == 'predicted',
-            "lastModified": 1447842835894,
+            "lastModified": self.modified.strftime('%Y-%m-%d %H:%M:%S'),
             "pathwayName": self.name,
             "reviewStatus": "reviewed" if self.package.reviewed else 'unreviewed',
             "scenarios": [],
@@ -813,18 +922,38 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
 
     @staticmethod
     @transaction.atomic
-    def create(package, name, description, smiles):
+    def create(package: 'Package', smiles: str, name: Optional[str] = None, description: Optional[str] = None):
         pw = Pathway()
         pw.package = package
-        pw.name = name
-        pw.description = description
-        pw.save()
 
-        # create root node
+        if name is None:
-        Node.create(pw, smiles, 0)
+            name = f"Pathway {Pathway.objects.filter(package=package).count() + 1}"
+
+        pw.name = name
+
+        if description is not None:
+            pw.description = description
+
+        pw.save()
+        try:
+            # create root node
+            Node.create(pw, smiles, 0)
+        except ValueError as e:
+            # Node creation failed, most likely due to an invalid smiles
+            # delete this pathway...
+            pw.delete()
+            raise e
 
         return pw
 
+    @transaction.atomic
+    def add_node(self, smiles: str, name: Optional[str] = None, description: Optional[str] = None):
+        return Node.create(self, smiles, 0)
+
+    @transaction.atomic
+    def add_edge(self, start_nodes: List['Node'], end_nodes: List['Node'], rule: Optional['Rule'] = None,
+                 name: Optional[str] = None, description: Optional[str] = None):
+        return Edge.create(self, start_nodes, end_nodes, rule, name=name, description=description)
 
 class Node(EnviPathModel, AliasMixin, ScenarioMixin):
     pathway = models.ForeignKey('epdb.Pathway', verbose_name='belongs to', on_delete=models.CASCADE, db_index=True)
@@ -848,14 +977,14 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
             "imageSize": 490,  # TODO
             "name": self.default_node_label.name,
             "smiles": self.default_node_label.smiles,
+            "scenarios": [{'name': s.name, 'url': s.url} for s in self.scenarios.all()],
         }
 
     @staticmethod
-    def create(pathway, smiles, depth):
+    def create(pathway: 'Pathway', smiles: str, depth: int, name: Optional[str] = None, description: Optional[str] = None):
-        c = Compound.create(pathway.package, smiles)
+        c = Compound.create(pathway.package, smiles, name=name, description=description)
 
         if Node.objects.filter(pathway=pathway, default_node_label=c.default_structure).exists():
-            print("found node")
             return Node.objects.get(pathway=pathway, default_node_label=c.default_structure)
 
         n = Node()
@@ -886,34 +1015,21 @@ class Edge(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
         return '{}/edge/{}'.format(self.pathway.url, self.uuid)
 
     def d3_json(self):
-        # {
-        #     "ecNumbers": [
-        #         {
-        #             "ecName": "DDT 2,3-dioxygenase",
-        #             "ecNumber": "1.14.12.-"
-        #         }
-        #     ],
-        #     "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/3f58e4d4-1c63-4b30-bf31-7ae4b98899fe/edge/ff193e7b-f010-43d4-acb3-45f34d938824",
-        #     "idreaction": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/e11419cd-6b46-470b-8a06-a08d62281734",
-        #     "multistep": "false",
-        #     "name": "Eawag BBD reaction r0450",
-        #     "pseudo": False,
-        #     "scenarios": [],
-        #     "source": 0,
-        #     "target": 4
-        # }
-
         return {
             'name': self.name,
             'id': self.url,
-            'reaction': self.edge_label.url if self.edge_label else None,
+            'url': self.url,
+            'image': self.url + '?image=svg',
+            'reaction': {'name': self.edge_label.name, 'url': self.edge_label.url } if self.edge_label else None,
+            'reaction_probability': self.kv.get('probability'),
             # TODO
             'start_node_urls': [x.url for x in self.start_nodes.all()],
             'end_node_urls': [x.url for x in self.end_nodes.all()],
+            "scenarios": [{'name': s.name, 'url': s.url} for s in self.scenarios.all()],
         }
 
     @staticmethod
-    def create(pathway, start_nodes, end_nodes, rule: Optional[Rule] = None, name: Optional[str] = None,
+    def create(pathway, start_nodes: List[Node], end_nodes: List[Node], rule: Optional[Rule] = None, name: Optional[str] = None,
                description: Optional[str] = None):
         e = Edge()
         e.pathway = pathway
@@ -934,13 +1050,17 @@ class Edge(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
         r = Reaction.create(pathway.package, name=name, description=description,
                             educts=[n.default_node_label for n in e.start_nodes.all()],
                             products=[n.default_node_label for n in e.end_nodes.all()],
-                            rule=rule, multi_step=False
+                            rules=rule, multi_step=False
                             )
 
         e.edge_label = r
         e.save()
         return e
 
+    @property
+    def as_svg(self):
+        return self.edge_label.as_svg if self.edge_label else None
+
 
 class EPModel(PolymorphicModel, EnviPathModel):
     package = models.ForeignKey('epdb.Package', verbose_name='Package', on_delete=models.CASCADE, db_index=True)
@@ -976,6 +1096,9 @@ class MLRelativeReasoning(EPModel):
 
     eval_results = JSONField(null=True, blank=True, default=dict)
 
+    def status(self):
+        return self.PROGRESS_STATUS_CHOICES[self.model_status]
+
     @staticmethod
     @transaction.atomic
     def create(package, name, description, rule_packages, data_packages, eval_packages, threshold):
@@ -1201,7 +1324,7 @@ class MLRelativeReasoning(EPModel):
         self.save()
 
         mod = SparseLabelECC(
-            **s.DEFAULT_MODELS_PARAMS
+            **s.DEFAULT_DT_MODEL_PARAMS
         )
 
         mod.fit(X, y)
@@ -1247,7 +1370,7 @@ class MLRelativeReasoning(EPModel):
             y_train, y_test = y[train_index], y[test_index]
 
             model = SparseLabelECC(
-                **s.DEFAULT_MODELS_PARAMS
+                **s.DEFAULT_DT_MODEL_PARAMS
             )
             model.fit(X_train, y_train)
 
@@ -1500,11 +1623,15 @@ class Setting(EnviPathModel):
     max_nodes = models.IntegerField(null=False, blank=False, verbose_name='Setting Max Number of Nodes', default=30)
 
     rule_packages = models.ManyToManyField("Package", verbose_name="Setting Rule Packages",
-                                           related_name="setting_rule_packages")
+                                           related_name="setting_rule_packages", blank=True)
     model = models.ForeignKey('EPModel', verbose_name='Setting EPModel', on_delete=models.SET_NULL, null=True,
                               blank=True)
     model_threshold = models.FloatField(null=True, blank=True, verbose_name='Setting Model Threshold', default=0.25)
 
+    @property
+    def url(self):
+        return '{}/setting/{}'.format(s.SERVER_URL, self.uuid)
+
     @cached_property
     def applicable_rules(self):
         """

epdb/tasks.py

@@ -1,4 +1,6 @@
 import logging
+from typing import Optional
+
 from celery.signals import worker_process_init
 from celery import shared_task
 from epdb.models import Pathway, Node, Edge, EPModel, Setting
@@ -40,11 +42,40 @@ def evaluate_model(model_pk: int):
 
 
 @shared_task(queue='predict')
-def predict(pw_pk: int, pred_setting_pk: int):
+def predict(pw_pk: int, pred_setting_pk: int, limit: Optional[int] = None, node_pk: Optional[int] = None) -> Pathway:
     pw = Pathway.objects.get(id=pw_pk)
     setting = Setting.objects.get(id=pred_setting_pk)
-    spw = SPathway(prediction_setting=setting, persist=pw)
+
-    level = 0
+    pw.kv.update(**{'status': 'running'})
-    while not spw.done:
+    pw.save()
-        spw.predict_step(from_depth=level)
+
-        level += 1
+    try:
+        # regular prediction
+        if limit is not None:
+            spw = SPathway(prediction_setting=setting, persist=pw)
+            level = 0
+            while not spw.done:
+                spw.predict_step(from_depth=level)
+                level += 1
+
+                # break in case we are in incremental model
+                if limit != -1:
+                    if level >= limit:
+                        break
+
+        elif node_pk is not None:
+            n = Node.objects.get(id=node_pk, pathway=pw)
+            spw = SPathway.from_pathway(pw)
+            spw.predict_step(from_node=n)
+        else:
+            raise ValueError("Neither limit nor node_pk given!")
+
+
+
+    except Exception as e:
+        pw.kv.update({'status': 'failed'})
+        pw.save()
+        raise e
+
+    pw.kv.update(**{'status': 'completed'})
+    pw.save()

epdb/templatetags/envipytags.py

@@ -0,0 +1,7 @@
+from django import template
+
+register = template.Library()
+
+@register.filter
+def classname(obj):
+    return obj.__class__.__name__

epdb/urls.py

@@ -13,6 +13,8 @@ urlpatterns = [
     # Home
     re_path(r'^$', v.index, name='index'),
 
+    # re_path(r'^login', v.login, name='login'),
+
     # Top level urls
     re_path(r'^package$', v.packages, name='packages'),
     re_path(r'^compound$', v.compounds, name='compounds'),
@@ -53,11 +55,11 @@ urlpatterns = [
     re_path(rf'^package/(?P<package_uuid>{UUID})/pathway$', v.package_pathways, name='package pathway list'),
     re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})$', v.package_pathway, name='package pathway detail'),
     # Pathway Nodes
-    # re_path(rf'^package/(?P<package_uuid>{UUID})/pathway(?P<pathway_uuid>{UUID})/node$', v.package_pathway_nodes, name='package pathway node list'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$', v.package_pathway_nodes, name='package pathway node list'),
     re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node/(?P<node_uuid>{UUID})$', v.package_pathway_node, name='package pathway node detail'),
     # Pathway Edges
-    # re_path(rf'^package/(?P<package_uuid>{UUID})/pathway(?P<pathway_uuid>{UUID})/edge$', v.package_pathway_edges, name='package pathway edge list'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge$', v.package_pathway_edges, name='package pathway edge list'),
-    # re_path(rf'^package/(?P<package_uuid>{UUID})/pathway(?P<pathway_uuid>{UUID})/edge/(?P<edge_uuid>{UUID})$', v.package_pathway_edge, name='package pathway edge detail'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge/(?P<edge_uuid>{UUID})$', v.package_pathway_edge, name='package pathway edge detail'),
     # Scenario
     re_path(rf'^package/(?P<package_uuid>{UUID})/scenario$', v.package_scenarios, name='package scenario list'),
     re_path(rf'^package/(?P<package_uuid>{UUID})/scenario/(?P<scenario_uuid>{UUID})$', v.package_scenario, name='package scenario detail'),

epdb/views.py

@@ -1,5 +1,6 @@
 import json
 import logging
+from functools import wraps
 from typing import List, Dict, Any
 
 from django.conf import settings as s
@@ -7,29 +8,71 @@ from django.contrib.auth import get_user_model
 from django.http import JsonResponse, HttpResponse, HttpResponseNotAllowed, HttpResponseBadRequest
 from django.shortcuts import render, redirect
 from django.views.decorators.csrf import csrf_exempt
+from django.contrib.auth.decorators import login_required
 
 from utilities.chem import FormatConverter, IndigoUtils
-from .logic import GroupManager, PackageManager, UserManager, SettingManager
+from .logic import GroupManager, PackageManager, UserManager, SettingManager, SearchManager
 from .models import Package, GroupPackagePermission, Group, CompoundStructure, Compound, Reaction, Rule, Pathway, Node, \
     EPModel, EnviFormer, MLRelativeReasoning, RuleBaseRelativeReasoning, Scenario, SimpleAmbitRule, APIToken, \
-    UserPackagePermission, Permission, License, User
+    UserPackagePermission, Permission, License, User, Edge
 
 logger = logging.getLogger(__name__)
 
 def log_post_params(request):
-    for k, v in request.POST.items():
+    if s.DEBUG:
-        logger.debug(f"{k}\t{v}")
+        for k, v in request.POST.items():
+            logger.debug(f"{k}\t{v}")
+
+
+def catch_exceptions(view_func):
+    @wraps(view_func)
+    def _wrapped_view(request, *args, **kwargs):
+        try:
+            return view_func(request, *args, **kwargs)
+        except Exception as e:
+            # Optionally return JSON or plain HttpResponse
+            if request.headers.get('Accept') == 'application/json':
+                return JsonResponse(
+                    {'error': 'Internal server error. Please try again later.'},
+                    status=500
+                )
+            else:
+                return render(request, 'errors/error.html', get_base_context(request))
+    return _wrapped_view
+
+
+def editable(request, user):
+    url = request.build_absolute_uri(request.path)
+    if PackageManager.is_package_url(url):
+        _package = PackageManager.get_package_lp(request.build_absolute_uri())
+        return PackageManager.writable(user, _package)
+    elif GroupManager.is_group_url(url):
+        _group = GroupManager.get_group_lp(request.build_absolute_uri())
+        return GroupManager.writable(user, _group)
+    elif UserManager.is_user_url(url):
+        _user = UserManager.get_user_lp(request.build_absolute_uri())
+        return UserManager.writable(user, _user)
+    elif url in [s.SERVER_URL, f"{s.SERVER_URL}/", f"{s.SERVER_URL}/package", f"{s.SERVER_URL}/user",
+                 f"{s.SERVER_URL}/group", f"{s.SERVER_URL}/search"]:
+        return True
+    else:
+        print(f"Unknown url: {url}")
+        return False
+
 
 
 def get_base_context(request) -> Dict[str, Any]:
     current_user = _anonymous_or_real(request)
 
+    can_edit = editable(request, current_user)
+
     ctx = {
         'title': 'enviPath',
         'meta': {
             'version': '0.0.1',
             'server_url': s.SERVER_URL,
             'user': current_user,
+            'can_edit': can_edit,
             'readable_packages': PackageManager.get_all_readable_packages(current_user, include_reviewed=True),
             'writeable_packages': PackageManager.get_all_writeable_packages(current_user),
             'available_groups': GroupManager.get_groups(current_user),
@@ -65,8 +108,9 @@ def breadcrumbs(first_level_object=None, second_level_namespace=None, second_lev
     return bread
 
 
+# @catch_exceptions
+
 def index(request):
-    current_user = _anonymous_or_real(request)
     context = get_base_context(request)
     context['title'] = 'enviPath - Home'
     context['meta']['current_package'] = context['meta']['user'].default_package
@@ -77,6 +121,16 @@ def index(request):
     return render(request, 'index/index.html', context)
 
 
+# def login(request):
+#     current_user = _anonymous_or_real(request)
+#     if request.method == 'GET':
+#         context = get_base_context(request)
+#         context['title'] = 'enviPath'
+#         return render(request, 'login.html', context)
+#     else:
+#         return HttpResponseBadRequest()
+#
+# @login_required(login_url='/login')
 def packages(request):
     current_user = _anonymous_or_real(request)
 
@@ -86,9 +140,10 @@ def packages(request):
 
         context['object_type'] = 'package'
         context['meta']['current_package'] = context['meta']['user'].default_package
+        context['meta']['can_edit'] = True
 
-        reviewed_package_qs = Package.objects.filter(reviewed=True)
+        reviewed_package_qs = Package.objects.filter(reviewed=True).order_by('created')
-        unreviewed_package_qs = PackageManager.get_all_readable_packages(current_user)
+        unreviewed_package_qs = PackageManager.get_all_readable_packages(current_user).order_by('name')
 
         context['reviewed_objects'] = reviewed_package_qs
         context['unreviewed_objects'] = unreviewed_package_qs
@@ -103,7 +158,6 @@ def packages(request):
         else:
             package_name = request.POST.get('package-name')
             package_description = request.POST.get('package-description', s.DEFAULT_VALUES['description'])
-            # group = GroupManager.get_group_by_url(request.user, request.POST.get('package-group'))
 
             created_package = PackageManager.create_package(current_user, package_name, package_description)
 
@@ -342,7 +396,23 @@ def models(request):
 
 
 def search(request):
+    current_user = _anonymous_or_real(request)
+
     if request.method == 'GET':
+        package_urls = request.GET.getlist('packages')
+        searchterm = request.GET.get('search')
+        mode = request.GET.get('mode')
+
+        # add HTTP_ACCEPT check to differentiate between index and ajax call
+        if 'application/json' in request.META.get('HTTP_ACCEPT') and all([searchterm, mode]):
+            if package_urls:
+                packages = [PackageManager.get_package_by_url(current_user, p) for p in package_urls]
+            else:
+                packages = PackageManager.get_reviewed_packages()
+
+            search_result = SearchManager.search(packages, searchterm, mode)
+            return JsonResponse(search_result, safe=False)
+
         context = get_base_context(request)
         context['title'] = 'enviPath - Search'
 
@@ -352,13 +422,21 @@ def search(request):
             {'Home': s.SERVER_URL},
             {'Search': s.SERVER_URL + '/search'},
         ]
-        # TODO perm
+
-        reviewed_package_qs = Package.objects.filter(reviewed=True)
+        reviewed_package_qs = PackageManager.get_reviewed_packages()
-        unreviewed_package_qs = Package.objects.filter(reviewed=False)
+        unreviewed_package_qs = PackageManager.get_all_readable_packages(current_user)
 
         context['reviewed_objects'] = reviewed_package_qs
         context['unreviewed_objects'] = unreviewed_package_qs
 
+        if all([searchterm, mode]):
+            if package_urls:
+                packages = [PackageManager.get_package_by_url(current_user, p) for p in package_urls]
+            else:
+                packages = PackageManager.get_reviewed_packages()
+
+            context['search_result'] = SearchManager.search(packages, searchterm, mode)
+
         return render(request, 'search.html', context)
 
 
@@ -487,7 +565,7 @@ def package_model(request, package_uuid, model_uuid):
 
         return render(request, 'objects/model.html', context)
 
-    if request.method == 'POST':
+    elif request.method == 'POST':
         if hidden := request.POST.get('hidden', None):
             if hidden == 'delete-model':
                 current_model.delete()
@@ -496,21 +574,9 @@ def package_model(request, package_uuid, model_uuid):
                 return HttpResponseBadRequest()
         else:
             return HttpResponseBadRequest()
-        #
+
-        # new_compound_name = request.POST.get('compound-name')
+    else:
-        # new_compound_description = request.POST.get('compound-description')
+        return HttpResponseBadRequest()
-        #
-        # if new_compound_name:
-        #     current_compound.name = new_compound_name
-        #
-        # if new_compound_description:
-        #     current_compound.description = new_compound_description
-        #
-        # if any([new_compound_name, new_compound_description]):
-        #     current_compound.save()
-        #     return redirect(current_compound.url)
-        # else:
-        #     return HttpResponseBadRequest()
 
 
 def package(request, package_uuid):
@@ -803,8 +869,7 @@ def package_rules(request, package_uuid):
 
     elif request.method == 'POST':
 
-        for k, v in request.POST.items():
+        log_post_params(request)
-            print(k, v)
 
         # Generic params
         rule_name = request.POST.get('rule-name')
@@ -817,8 +882,8 @@ def package_rules(request, package_uuid):
         # Obtain parameters as required by rule type
         if rule_type == 'SimpleAmbitRule':
             params['smirks'] = request.POST.get('rule-smirks')
-            params['reactant_smarts'] = request.POST.get('rule-reactant-smarts')
+            params['reactant_filter_smarts'] = request.POST.get('rule-reactant-smarts')
-            params['product_smarts'] = request.POST.get('rule-product-smarts')
+            params['product_filter_smarts'] = request.POST.get('rule-product-smarts')
         elif rule_type == 'SimpleRDKitRule':
             params['reaction_smarts'] = request.POST.get('rule-reaction-smarts')
         elif rule_type == 'ParallelRule':
@@ -828,7 +893,7 @@ def package_rules(request, package_uuid):
         else:
             return HttpResponseBadRequest()
 
-        r = Rule.create(current_package, rule_type, name=rule_name, description=rule_description, **params)
+        r = Rule.create(rule_type=rule_type, package=current_package, name=rule_name, description=rule_description, **params)
         return redirect(r.url)
 
     else:
@@ -854,7 +919,7 @@ def package_rule(request, package_uuid, rule_uuid):
         else:  # isinstance(current_rule, ParallelRule) or isinstance(current_rule, SequentialRule):
             return render(request, 'objects/composite_rule.html', context)
 
-    if request.method == 'POST':
+    elif request.method == 'POST':
         if hidden := request.POST.get('hidden', None):
             if hidden == 'delete-rule':
                 current_rule.delete()
@@ -862,8 +927,23 @@ def package_rule(request, package_uuid, rule_uuid):
             else:
                 return HttpResponseBadRequest()
 
-        # TODO update!
+        rule_name = request.POST.get('rule-name', '').strip()
+        rule_description = request.POST.get('rule-description', '').strip()
 
+        if rule_name:
+            current_rule.name = rule_name
+
+        if rule_description:
+            current_rule.description = rule_description
+
+        if any([rule_name, rule_description]):
+            current_rule.save()
+            return redirect(current_rule.url)
+        else:
+            return HttpResponseBadRequest()
+
+    else:
+        return HttpResponseBadRequest()
 
 # https://envipath.org/package/<id>/reaction
 def package_reactions(request, package_uuid):
@@ -912,6 +992,8 @@ def package_reactions(request, package_uuid):
 
         return redirect(r.url)
 
+    else:
+        return HttpResponseBadRequest()
 
 # https://envipath.org/package/<id>/reaction/<id>
 def package_reaction(request, package_uuid, reaction_uuid):
@@ -931,7 +1013,7 @@ def package_reaction(request, package_uuid, reaction_uuid):
 
         return render(request, 'objects/reaction.html', context)
 
-    if request.method == 'POST':
+    elif request.method == 'POST':
         if hidden := request.POST.get('hidden', None):
             if hidden == 'delete-reaction':
                 current_reaction.delete()
@@ -954,6 +1036,8 @@ def package_reaction(request, package_uuid, reaction_uuid):
         else:
             return HttpResponseBadRequest()
 
+    else:
+        return HttpResponseBadRequest()
 
 # https://envipath.org/package/<id>/pathway
 def package_pathways(request, package_uuid):
@@ -989,7 +1073,7 @@ def package_pathways(request, package_uuid):
 
         return render(request, 'collections/objects_list.html', context)
 
-    if request.method == 'POST':
+    elif request.method == 'POST':
 
         log_post_params(request)
 
@@ -1002,15 +1086,34 @@ def package_pathways(request, package_uuid):
             return HttpResponseBadRequest()
 
         stand_smiles = FormatConverter.standardize(smiles)
-        pw = Pathway.create(current_package, name, description, stand_smiles)
 
-        if pw_mode != 'build':
+        if pw_mode not in ['predict', 'build', 'incremental']:
+            return HttpResponseBadRequest()
+
+        pw = Pathway.create(current_package, name, description, stand_smiles)
+        # set mode
+        pw.kv.update({'mode': pw_mode})
+        pw.save()
+
+        if pw_mode == 'predict' or pw_mode == 'incremental':
+            # unlimited pred (will be handled by setting)
+            limit = -1
+
+            # For incremental predict first level and return
+            if pw_mode == 'incremental':
+                limit = 1
+
             pred_setting = current_user.prediction_settings()
+            pw.setting = pred_setting
+            pw.save()
+
             from .tasks import predict
-            predict.delay(pw.pk, pred_setting.pk)
+            predict.delay(pw.pk, pred_setting.pk, limit=limit)
 
         return redirect(pw.url)
 
+    else:
+        return HttpResponseBadRequest()
 
 # https://envipath.org/package/<id>/pathway/<id>
 def package_pathway(request, package_uuid, pathway_uuid):
@@ -1043,7 +1146,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
         return render(request, 'objects/pathway.html', context)
         # return render(request, 'pathway_playground2.html', context)
 
-    if request.method == 'POST':
+    elif request.method == 'POST':
         if hidden := request.POST.get('hidden', None):
             if hidden == 'delete-pathway':
                 current_pathway.delete()
@@ -1051,30 +1154,92 @@ def package_pathway(request, package_uuid, pathway_uuid):
             else:
                 return HttpResponseBadRequest()
 
+        pathway_name = request.POST.get('pathway-name')
+        pathway_description = request.POST.get('pathway-description')
 
-#
+        if any([pathway_name, pathway_description]):
-#
+            if pathway_name is not None and pathway_name.strip() != '':
-#
+                pathway_name = pathway_name.strip()
-# def package_relative_reasonings(request, package_id):
+
-#     if request.method == 'GET':
+                current_pathway.name = pathway_name
-#         pass
+
-#
+            if pathway_description is not None and pathway_description.strip() != '':
-#
+                pathway_description = pathway_description.strip()
-# def package_relative_reasoning(request, package_id, relative_reasoning_id):
+
-#     current_user = _anonymous_or_real(request)
+                current_pathway.description = pathway_description
-#
+
-#     if request.method == 'GET':
+            current_pathway.save()
-#         pass
+            return redirect(current_pathway.url)
-#     elif request.method == 'POST':
+
-#         pass
+        node_url = request.POST.get('node')
-#
+
-# #
+        if node_url:
-# #
+            n = current_pathway.get_node(node_url)
-# # # https://envipath.org/package/<id>/pathway/<id>/node
+
-# # def package_pathway_nodes(request, package_id, pathway_id):
+            from .tasks import predict
-# #     pass
+            # Dont delay?
-# #
+            predict(current_pathway.pk, current_pathway.setting.pk, node_pk=n.pk)
-# #
+            return JsonResponse({'success': current_pathway.url})
+
+        return HttpResponseBadRequest()
+
+    else:
+        return HttpResponseBadRequest()
+
+# https://envipath.org/package/<id>/pathway/<id>/node
+def package_pathway_nodes(request, package_uuid, pathway_uuid):
+    current_user = _anonymous_or_real(request)
+    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
+    current_pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
+
+    if request.method == 'GET':
+        context = get_base_context(request)
+        context['title'] = f'enviPath - {current_package.name} - {current_pathway.name} - Nodes'
+
+        context['meta']['current_package'] = current_package
+        context['object_type'] = 'node'
+        context['breadcrumbs'] = [
+            {'Home': s.SERVER_URL},
+            {'Package': s.SERVER_URL + '/package'},
+            {current_package.name: current_package.url},
+            {'Pathway': current_package.url + '/pathway'},
+            {current_pathway.name: current_pathway.url},
+            {'Node': current_pathway.url + '/node'},
+        ]
+
+        reviewed_node_qs = Node.objects.none()
+        unreviewed_node_qs = Node.objects.none()
+
+        if current_package.reviewed:
+            reviewed_node_qs = Node.objects.filter(pathway=current_pathway).order_by('name')
+        else:
+            unreviewed_node_qs = Node.objects.filter(pathway=current_pathway).order_by('name')
+
+        if request.GET.get('all'):
+            return JsonResponse({
+                "objects": [
+                    {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                    for pw in (reviewed_node_qs if current_package.reviewed else unreviewed_node_qs)
+                ]
+            })
+
+        context['reviewed_objects'] = reviewed_node_qs
+        context['unreviewed_objects'] = unreviewed_node_qs
+
+        return render(request, 'collections/objects_list.html', context)
+
+    elif request.method == 'POST':
+
+        node_name = request.POST.get('node-name')
+        node_description = request.POST.get('node-description')
+        node_smiles = request.POST.get('node-smiles')
+
+        current_pathway.add_node(node_smiles, name=node_name, description=node_description)
+
+        return redirect(current_pathway.url)
+
+    else:
+        return HttpResponseBadRequest()
 
 
 # https://envipath.org/package/<id>/pathway/<id>/node/<id>
@@ -1091,19 +1256,129 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
                 svg_data = current_node.as_svg
                 return HttpResponse(svg_data, content_type="image/svg+xml")
 
+        context = get_base_context(request)
+        context['title'] = f'enviPath - {current_package.name} - {current_pathway.name}'
+
+        context['meta']['current_package'] = current_package
+        context['object_type'] = 'pathway'
+
+        context['breadcrumbs'] = [
+            {'Home': s.SERVER_URL},
+            {'Package': s.SERVER_URL + '/package'},
+            {current_package.name: current_package.url},
+            {'Pathway': current_package.url + '/pathway'},
+            {current_pathway.name: current_pathway.url},
+            {'Node': current_pathway.url + '/node'},
+            {current_node.name: current_node.url},
+        ]
+
+        context['node'] = current_node
+
+        return render(request, 'objects/node.html', context)
+
+    elif request.method == 'POST':
+        if s.DEBUG:
+            for k, v in request.POST.items():
+                print(k, v)
+
+        if hidden := request.POST.get('hidden', None):
+            if hidden == 'delete-node':
+                current_node.delete()
+                return redirect(current_pathway.url)
+
+    else:
+        return HttpResponseBadRequest()
+
+
+# https://envipath.org/package/<id>/pathway/<id>/edge
+def package_pathway_edges(request, package_uuid, pathway_uuid):
+    current_user = _anonymous_or_real(request)
+    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
+    current_pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
+
+    if request.method == 'GET':
+        context = get_base_context(request)
+        context['title'] = f'enviPath - {current_package.name} - {current_pathway.name} - Edges'
+
+        context['meta']['current_package'] = current_package
+        context['object_type'] = 'edge'
+        context['breadcrumbs'] = [
+            {'Home': s.SERVER_URL},
+            {'Package': s.SERVER_URL + '/package'},
+            {current_package.name: current_package.url},
+            {'Pathway': current_package.url + '/pathway'},
+            {current_pathway.name: current_pathway.url},
+            {'Edge': current_pathway.url + '/edge'},
+        ]
+
+        reviewed_edge_qs = Edge.objects.none()
+        unreviewed_edge_qs = Edge.objects.none()
+
+        if current_package.reviewed:
+            reviewed_edge_qs = Edge.objects.filter(pathway=current_pathway).order_by('name')
+        else:
+            unreviewed_edge_qs = Edge.objects.filter(pathway=current_pathway).order_by('name')
+
+        if request.GET.get('all'):
+            return JsonResponse({
+                "objects": [
+                    {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                    for pw in (reviewed_edge_qs if current_package.reviewed else unreviewed_edge_qs)
+                ]
+            })
+
+        context['reviewed_objects'] = reviewed_edge_qs
+        context['unreviewed_objects'] = unreviewed_edge_qs
+
+        return render(request, 'collections/objects_list.html', context)
+
+    elif request.method == 'POST':
+
+        edge_name = request.POST.get('edge-name')
+        edge_description = request.POST.get('edge-description')
+        edge_substrates = request.POST.getlist('edge-substrates')
+        edge_products = request.POST.getlist('edge-products')
+
+        substrate_nodes = [current_pathway.get_node(url) for url in edge_substrates]
+        product_nodes = [current_pathway.get_node(url) for url in edge_products]
+
+        # TODO in the future consider Rules here?
+        current_pathway.add_edge(substrate_nodes, product_nodes, name=edge_name, description=edge_description)
+
+        return redirect(current_pathway.url)
+
+    else:
+        return HttpResponseBadRequest()
+
+
+# https://envipath.org/package/<id>/pathway/<id>/edge/<id>
+def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
+    current_user = _anonymous_or_real(request)
+    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
+    current_pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
+    current_edge = Edge.objects.get(pathway=current_pathway, uuid=edge_uuid)
+
+    if request.method == 'GET':
+        is_image_request = request.GET.get('image')
+        if is_image_request:
+            if is_image_request == 'svg':
+                svg_data = current_edge.as_svg
+                return HttpResponse(svg_data, content_type="image/svg+xml")
+
+    elif request.method == 'POST':
+        if s.DEBUG:
+            for k, v in request.POST.items():
+                print(k, v)
+
+        if hidden := request.POST.get('hidden', None):
+            if hidden == 'delete-edge':
+                current_edge.delete()
+                return redirect(current_pathway.url)
+
+    else:
+        return HttpResponseBadRequest()
+
 
-# #
-# #
-# # # https://envipath.org/package/<id>/pathway/<id>/edge
-# # def package_pathway_edges(request, package_id, pathway_id):
-# #     pass
-# #
-# #
-# # # https://envipath.org/package/<id>/pathway/<id>/edge/<id>
-# # def package_pathway_edge(request, package_id, pathway_id, edge_id):
-# #     pass
-# #
-# #
 # https://envipath.org/package/<id>/scenario
 def package_scenarios(request, package_uuid):
     current_user = _anonymous_or_real(request)
@@ -1158,11 +1433,6 @@ def package_scenario(request, package_uuid, scenario_uuid):
         return render(request, 'objects/scenario.html', context)
 
 
-
-
-### END UNTESTED
-
-
 ##############
 # User/Group #
 ##############
@@ -1201,7 +1471,7 @@ def users(request):
                     return render(request, 'errors/user_account_inactive.html', status=403)
 
                 email = temp_user.email
-            except get_user_model().DoesNotExists:
+            except get_user_model().DoesNotExist:
                 return HttpResponseBadRequest()
 
             user = authenticate(username=email, password=password)
@@ -1289,6 +1559,18 @@ def user(request, user_uuid):
             logout(request)
             return redirect(s.SERVER_URL)
 
+        default_package = request.POST.get('default-package')
+        default_group = request.POST.get('default-group')
+        default_prediction_setting = request.POST.get('default-prediction-setting')
+
+        if any([default_package, default_group, default_prediction_setting]):
+            current_user.default_package = PackageManager.get_package_by_url(current_user, default_package)
+            current_user.default_group = GroupManager.get_group_by_url(current_user, default_group)
+            current_user.default_setting = SettingManager.get_setting_by_url(current_user, default_prediction_setting)
+            current_user.save()
+
+            return redirect(current_user.url)
+
         prediction_model_pk = request.POST.get('model')
         prediction_threshold = request.POST.get('threshold')
         prediction_max_nodes = request.POST.get('max_nodes')
@@ -1509,3 +1791,9 @@ def layout(request):
 def depict(request):
     if smiles := request.GET.get('smiles'):
         return HttpResponse(IndigoUtils.mol_to_svg(smiles), content_type='image/svg+xml')
+
+    elif smirks := request.GET.get('smirks'):
+        query_smirks = request.GET.get('is_query_smirks', False) == 'true'
+        return HttpResponse(IndigoUtils.smirks_to_svg(smirks, query_smirks), content_type='image/svg+xml')
+    else:
+        return HttpResponseBadRequest()

static/js/pps.js

@@ -507,28 +507,6 @@ function makeAccordionPanel(accordionId, panelName, panelContent, collapsed, id)
     + "</div>";
 }
 
-function makeSearchList(divToAppend, jsonob) {
-
-    if(jsonob.status){
-        $(divToAppend).append('<div class="alert alert-danger" role="alert"><p>'+"No results..."+'</p></div>');
-        return;
-    }
-
-    var content = makeAccordionHead("searchAccordion", "Results","");
-
-    for ( var type in jsonob){
-        var obj = jsonob[type];
-        var objs = "";
-        for ( var x in obj) {
-            objs += "<a class='list-group-item' href=\"" + obj[x].id + "\">"
-                + obj[x].name + "</a>";
-        }
-        content += makeAccordionPanel("searchAccordion", type, objs, true);
-    }
-    $(divToAppend).append(content);
-
-}
-
 function fillPRCurve(modelUri, onclick){
     if (modelUri == '') {
         return;

static/js/pw.js

@@ -1,5 +1,18 @@
 console.log("loaded")
 
+
+function predictFromNode(url) {
+    $.post("", {node: url})
+        .done(function (data) {
+            console.log("Success:", data);
+            window.location.href = data.success;
+        })
+        .fail(function (xhr, status, error) {
+            console.error("Error:", xhr.status, xhr.responseText);
+            // show user-friendly message or log error
+        });
+}
+
 // data = {{ pathway.d3_json | safe }};
 // elem = 'vizdiv'
 function draw(pathway, elem) {
@@ -48,7 +61,7 @@ function draw(pathway, elem) {
                     const avgY = d3.mean(childNodes, d => d.y);
                     n.fx = avgX;
                     // keep level as is
-                    n.fy =  n.y;
+                    n.fy = n.y;
                 }
             }
         });
@@ -77,8 +90,100 @@ function draw(pathway, elem) {
         d3.select(t).select("circle").classed("highlighted", !d3.select(t).select("circle").classed("highlighted"));
     }
 
+    // Wait one second before showing popup
+    var popupWaitBeforeShow = 1000;
+    // Keep Popup at least for one second
+    var popushowAtLeast = 1000;
 
-    const tooltip = d3.select("#tooltip");
+    function pop_show_e(element) {
+        var e = element;
+        setTimeout(function () {
+            if ($(e).is(':hover')) { // if element is still hovered
+                $(e).popover("show");
+
+                // workaround to set fixed positions
+                pop = $(e).attr("aria-describedby")
+                h = $('#' + pop).height();
+                $('#' + pop).attr("style", `position: fixed; top: ${clientY - (h / 2.0)}px; left: ${clientX + 10}px; margin: 0px; max-width: 1000px; display: block;`)
+            setTimeout(function () {
+                    var close = setInterval(function () {
+                        if (!$(".popover:hover").length // mouse outside popover
+                            && !$(e).is(':hover')) { // mouse outside element
+                            $(e).popover('hide');
+                            clearInterval(close);
+                        }
+                    }, 100);
+                }, popushowAtLeast);
+            }
+        }, popupWaitBeforeShow);
+    }
+
+    function pop_add(objects, title, contentFunction) {
+        objects.attr("id", "pop")
+            .attr("data-container", "body")
+            .attr("data-toggle", "popover")
+            .attr("data-placement", "right")
+            .attr("title", title);
+
+        objects.each(function (d, i) {
+            options = {trigger: "manual", html: true, animation: false};
+            this_ = this;
+            var p = $(this).popover(options).on("mouseenter", function () {
+                pop_show_e(this);
+            });
+            p.on("show.bs.popover", function (e) {
+                // this is to dynamically ajdust the content and bounds of the popup
+                p.attr('data-content', contentFunction(d));
+                p.data("bs.popover").setContent();
+                p.data("bs.popover").tip().css({"max-width": "1000px"});
+            });
+        });
+    }
+
+
+    function node_popup(n) {
+        popupContent = "<a href='" + n.url +"'>" + n.name + "</a><br>";
+        popupContent += "Depth " + n.depth + "<br>"
+        popupContent += "<img src='" + n.image + "' width='"+ 20 * nodeRadius +"'><br>"
+        if (n.scenarios.length > 0) {
+            popupContent += '<b>Half-lives and related scenarios:</b><br>'
+            for (var s of n.scenarios) {
+                popupContent += "<a href='" + s.url + "'>" + s.name + "</a><br>";
+            }
+        }
+
+        var isLeaf = pathway.links.filter(obj => obj.source.id === n.id).length === 0;
+        if(pathway.isIncremental && isLeaf) {
+            popupContent += '<br><a class="btn btn-primary" onclick="predictFromNode(\'' + n.url + '\')" href="#">Predict from here</a><br>';
+        }
+
+        return popupContent;
+    }
+
+    function edge_popup(e) {
+        popupContent = "<a href='" + e.url +"'>" + e.name + "</a><br>";
+        popupContent += "<img src='" + e.image + "' width='"+ 20 * nodeRadius +"'><br>"
+        if (e.reaction_probability) {
+            popupContent += '<b>Probability:</b><br>' + e.reaction_probability.toFixed(3) + '<br>';
+        }
+
+
+        if (e.scenarios.length > 0) {
+            popupContent += '<b>Half-lives and related scenarios:</b><br>'
+            for (var s of e.scenarios) {
+                popupContent += "<a href='" + s.url + "'>" + s.name + "</a><br>";
+            }
+        }
+
+        return popupContent;
+    }
+
+    var clientX;
+    var clientY;
+    document.addEventListener('mousemove', function(event) {
+        clientX = event.clientX;
+        clientY =event.clientY;
+    });
 
     const zoomable = d3.select("#zoomable");
 
@@ -102,10 +207,10 @@ function draw(pathway, elem) {
 
         orig_depth = n.depth
         // console.log(n.id, parents)
-        for(idx in parents) {
+        for (idx in parents) {
             p = nodes[parents[idx]]
             // console.log(p.depth)
-            if(p.depth >= n.depth) {
+            if (p.depth >= n.depth) {
                 // keep the .5 steps for pseudo nodes
                 n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
                 // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
@@ -128,13 +233,15 @@ function draw(pathway, elem) {
         .enter().append("line")
         // Check if target is pseudo and draw marker only if not pseudo
         .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
-        .on("mouseover", (event, d) => {
+        // .on("mouseover", (event, d) => {
-            tooltip.style("visibility", "visible")
+        //     tooltip.style("visibility", "visible")
-                   .text(`Link: ${d.source.id} → ${d.target.id}`)
+        //         .text(`Link: ${d.source.id} → ${d.target.id}`)
-                   .style("top", `${event.pageY + 5}px`)
+        //         .style("top", `${event.pageY + 5}px`)
-                   .style("left", `${event.pageX + 5}px`);
+        //         .style("left", `${event.pageX + 5}px`);
-        })
+        // })
-        .on("mouseout", () => tooltip.style("visibility", "hidden"));
+        // .on("mouseout", () => tooltip.style("visibility", "hidden"));
+
+    pop_add(link, "Reaction", edge_popup);
 
     // Knoten zeichnen
     const node = zoomable.append("g")
@@ -145,19 +252,19 @@ function draw(pathway, elem) {
             .on("start", dragstarted)
             .on("drag", dragged)
             .on("end", dragended))
-        .on("click", function(event, d) {
+        .on("click", function (event, d) {
             d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
         })
-        .on("mouseover", (event, d) => {
+        // .on("mouseover", (event, d) => {
-            if (d.pseudo) {
+        //     if (d.pseudo) {
-                return
+        //         return
-            }
+        //     }
-            tooltip.style("visibility", "visible")
+        //     tooltip.style("visibility", "visible")
-                   .text(`Node: ${d.id} Depth: ${d.depth}`)
+        //         .text(`Node: ${d.id} Depth: ${d.depth}`)
-                   .style("top", `${event.pageY + 5}px`)
+        //         .style("top", `${event.pageY + 5}px`)
-                   .style("left", `${event.pageX + 5}px`);
+        //         .style("left", `${event.pageX + 5}px`);
-        })
+        // })
-        .on("mouseout", () => tooltip.style("visibility", "hidden"));
+        // .on("mouseout", () => tooltip.style("visibility", "hidden"));
 
     // Kreise für die Knoten hinzufügen
     node.append("circle")
@@ -172,4 +279,6 @@ function draw(pathway, elem) {
         .attr("y", -nodeRadius)
         .attr("width", nodeRadius * 2)
         .attr("height", nodeRadius * 2);
+
+      pop_add(node, "Compound", node_popup);
 }

templates/actions/collections/compound.html

@@ -1,4 +1,6 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#new_compound_modal">
+    <li>
-        <span class="glyphicon glyphicon-plus"></span> New Compound</a>
+        <a role="button" data-toggle="modal" data-target="#new_compound_modal">
-</li>
+            <span class="glyphicon glyphicon-plus"></span> New Compound</a>
+    </li>
+{% endif %}

templates/actions/collections/compound_structure.html

@@ -1,4 +1,6 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#new_compound_structure_modal">
+    <li>
-        <span class="glyphicon glyphicon-plus"></span> New Compound Structure</a>
+        <a role="button" data-toggle="modal" data-target="#new_compound_structure_modal">
-</li>
+            <span class="glyphicon glyphicon-plus"></span> New Compound Structure</a>
+    </li>
+{% endif %}

templates/actions/collections/edge.html

@@ -0,0 +1,6 @@
+{% if meta.can_edit %}
+    <li>
+        <a role="button" data-toggle="modal" data-target="#new_edge_modal">
+            <span class="glyphicon glyphicon-plus"></span> New Edge</a>
+    </li>
+{% endif %}

templates/actions/collections/group.html

@@ -1,4 +1,4 @@
 <li>
     <a role="button" data-toggle="modal" data-target="#new_group_modal">
         <span class="glyphicon glyphicon-plus"></span> New Group</a>
-</li>
+</li>

templates/actions/collections/model.html

@@ -1,4 +1,6 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#new_model_modal">
+    <li>
-        <span class="glyphicon glyphicon-plus"></span> New Model</a>
+        <a role="button" data-toggle="modal" data-target="#new_model_modal">
-</li>
+            <span class="glyphicon glyphicon-plus"></span> New Model</a>
+    </li>
+{% endif %}

templates/actions/collections/node.html

@@ -0,0 +1,6 @@
+{% if meta.can_edit %}
+    <li>
+        <a role="button" data-toggle="modal" data-target="#new_node_modal">
+            <span class="glyphicon glyphicon-plus"></span> New Node</a>
+    </li>
+{% endif %}

templates/actions/collections/pathway.html

@@ -1,4 +1,6 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#predict_modal">
+    <li>
-        <span class="glyphicon glyphicon-plus"></span> New Pathway</a>
+        <a role="button" data-toggle="modal" data-target="#predict_modal">
-</li>
+            <span class="glyphicon glyphicon-plus"></span> New Pathway</a>
+    </li>
+{% endif %}

templates/actions/collections/reaction.html

@@ -1,4 +1,6 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#new_reaction_modal">
+    <li>
-        <span class="glyphicon glyphicon-plus"></span> New Reaction</a>
+        <a role="button" data-toggle="modal" data-target="#new_reaction_modal">
-</li>
+            <span class="glyphicon glyphicon-plus"></span> New Reaction</a>
+    </li>
+{% endif %}

templates/actions/collections/rule.html

@@ -1,4 +1,6 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#new_rule_modal">
+    <li>
-        <span class="glyphicon glyphicon-plus"></span> New Rule</a>
+        <a role="button" data-toggle="modal" data-target="#new_rule_modal">
-</li>
+            <span class="glyphicon glyphicon-plus"></span> New Rule</a>
+    </li>
+{% endif %}

templates/actions/collections/scenario.html

@@ -1,4 +1,6 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#new_pathway_modal">
+    <li>
-        <span class="glyphicon glyphicon-plus"></span> New Scenario</a>
+        <a role="button" data-toggle="modal" data-target="#new_pathway_modal">
-</li>
+            <span class="glyphicon glyphicon-plus"></span> New Scenario</a>
+    </li>
+{% endif %}

templates/actions/collections/setting.html

@@ -1,4 +1,6 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#new_setting_modal">
+    <li>
-        <span class="glyphicon glyphicon-plus"></span>New Setting</a>
+        <a role="button" data-toggle="modal" data-target="#new_setting_modal">
-</li>
+            <span class="glyphicon glyphicon-plus"></span>New Setting</a>
+    </li>
+{% endif %}

templates/actions/objects/compound.html

@@ -1,12 +1,14 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#edit_compound_modal">
+    <li>
-        <i class="glyphicon glyphicon-edit"></i> Edit Compound</a>
+        <a role="button" data-toggle="modal" data-target="#edit_compound_modal">
-</li>
+            <i class="glyphicon glyphicon-edit"></i> Edit Compound</a>
-<li>
+    </li>
-    <a role="button" data-toggle="modal" data-target="#add_structure_modal">
+    <li>
-        <i class="glyphicon glyphicon-plus"></i> Add Structure</a>
+        <a role="button" data-toggle="modal" data-target="#add_structure_modal">
-</li>
+            <i class="glyphicon glyphicon-plus"></i> Add Structure</a>
-<li>
+    </li>
-    <a class="button" data-toggle="modal" data-target="#delete_compound_modal">
+    <li>
-        <i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
+        <a class="button" data-toggle="modal" data-target="#delete_compound_modal">
-</li>
+            <i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
+    </li>
+{% endif %}

templates/actions/objects/compound_structure.html

@@ -1,8 +1,10 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#edit_compound_structure_modal">
+    <li>
-        <i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a>
+        <a role="button" data-toggle="modal" data-target="#edit_compound_structure_modal">
-</li>
+            <i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a>
-<li>
+    </li>
-    <a class="button" data-toggle="modal" data-target="#delete_compound_structure_modal">
+    <li>
-        <i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a>
+        <a class="button" data-toggle="modal" data-target="#delete_compound_structure_modal">
-</li>
+            <i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a>
+    </li>
+{% endif %}

templates/actions/objects/group.html

@@ -1,8 +1,10 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#delete_group_modal">
+    <li>
-        <i class="glyphicon glyphicon-trash"></i> Delete Group</a>
+        <a role="button" data-toggle="modal" data-target="#delete_group_modal">
-</li>
+            <i class="glyphicon glyphicon-trash"></i> Delete Group</a>
-<li>
+    </li>
-    <a role="button" data-toggle="modal" data-target="#edit_group_member_modal">
+    <li>
-        <i class="glyphicon glyphicon-trash"></i> Add/Remove Member</a>
+        <a role="button" data-toggle="modal" data-target="#edit_group_member_modal">
-</li>
+            <i class="glyphicon glyphicon-trash"></i> Add/Remove Member</a>
+    </li>
+{% endif %}

templates/actions/objects/model.html

@@ -0,0 +1,6 @@
+{% if meta.can_edit %}
+    <li>
+        <a class="button" data-toggle="modal" data-target="#delete_model_modal">
+            <i class="glyphicon glyphicon-trash"></i> Delete Model</a>
+    </li>
+{% endif %}

templates/actions/objects/node.html

@@ -0,0 +1,10 @@
+{% if meta.can_edit %}
+    <li>
+        <a role="button" data-toggle="modal" data-target="#edit_node_modal">
+            <i class="glyphicon glyphicon-edit"></i> Edit Node</a>
+    </li>
+    <li>
+        <a class="button" data-toggle="modal" data-target="#delete_node_modal">
+            <i class="glyphicon glyphicon-trash"></i> Delete Node</a>
+    </li>
+{% endif %}

templates/actions/objects/package.html

@@ -1,16 +1,18 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#edit_package_modal">
+    <li>
-        <i class="glyphicon glyphicon-edit"></i> Edit Package</a>
+        <a role="button" data-toggle="modal" data-target="#edit_package_modal">
-</li>
+            <i class="glyphicon glyphicon-edit"></i> Edit Package</a>
-<li>
+    </li>
-    <a role="button" data-toggle="modal" data-target="#edit_package_permissions_modal">
+    <li>
-        <i class="glyphicon glyphicon-user"></i> Edit Permissions</a>
+        <a role="button" data-toggle="modal" data-target="#edit_package_permissions_modal">
-</li>
+            <i class="glyphicon glyphicon-user"></i> Edit Permissions</a>
-<li>
+    </li>
-    <a role="button" data-toggle="modal" data-target="#set_license_modal">
+    <li>
-        <i class="glyphicon glyphicon-duplicate"></i> License</a>
+        <a role="button" data-toggle="modal" data-target="#set_license_modal">
-</li>
+            <i class="glyphicon glyphicon-duplicate"></i> License</a>
-<li>
+    </li>
-    <a class="button" data-toggle="modal" data-target="#delete_package_modal">
+    <li>
-        <i class="glyphicon glyphicon-trash"></i> Delete Package</a>
+        <a class="button" data-toggle="modal" data-target="#delete_package_modal">
-</li>
+            <i class="glyphicon glyphicon-trash"></i> Delete Package</a>
+    </li>
+{% endif %}

templates/actions/objects/pathway.html

@@ -1,8 +1,32 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#edit_pathway_modal">
+    <li>
-        <i class="glyphicon glyphicon-edit"></i> Edit Pathway</a>
+        <a class="button" data-toggle="modal" data-target="#add_pathway_node_modal">
-</li>
+            <i class="glyphicon glyphicon-plus"></i> Add Compound</a>
-<li>
+    </li>
-    <a class="button" data-toggle="modal" data-target="#delete_pathawy_modal">
+    <li>
-        <i class="glyphicon glyphicon-trash"></i> Delete Pathway</a>
+        <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">
-</li>
+            <i class="glyphicon glyphicon-plus"></i> Add Reaction</a>
+    </li>
+    <li role="separator" class="divider"></li>
+    <li>
+        <a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
+            <i class="glyphicon glyphicon-plus"></i> Edit Pathway</a>
+    </li>
+{#    <li>#}
+{#        <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">#}
+{#            <i class="glyphicon glyphicon-plus"></i> Calculate Compound Properties</a>#}
+{#    </li>#}
+    <li role="separator" class="divider"></li>
+    <li>
+        <a class="button" data-toggle="modal" data-target="#delete_pathway_node_modal">
+            <i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
+    </li>
+        <li>
+        <a class="button" data-toggle="modal" data-target="#delete_pathway_edge_modal">
+            <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
+    </li>
+    <li>
+        <a class="button" data-toggle="modal" data-target="#delete_pathway_modal">
+            <i class="glyphicon glyphicon-trash"></i> Delete Pathway</a>
+    </li>
+{% endif %}

templates/actions/objects/reaction.html

@@ -1,8 +1,10 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#edit_reaction_modal">
+    <li>
-        <i class="glyphicon glyphicon-edit"></i> Edit Reaction</a>
+        <a role="button" data-toggle="modal" data-target="#edit_reaction_modal">
-</li>
+            <i class="glyphicon glyphicon-edit"></i> Edit Reaction</a>
-<li>
+    </li>
-    <a class="button" data-toggle="modal" data-target="#delete_reaction_modal">
+    <li>
-        <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
+        <a class="button" data-toggle="modal" data-target="#delete_reaction_modal">
-</li>
+            <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
+    </li>
+{% endif %}

templates/actions/objects/rule.html

@@ -1,4 +1,6 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#edit_rule_modal">
+    <li>
-        <i class="glyphicon glyphicon-edit"></i> Edit Rule</a>
+        <a role="button" data-toggle="modal" data-target="#edit_rule_modal">
-</li>
+            <i class="glyphicon glyphicon-edit"></i> Edit Rule</a>
+    </li>
+{% endif %}

templates/actions/objects/scenario.html

@@ -0,0 +1,2 @@
+{% if meta.can_edit %}
+{% endif %}

templates/actions/objects/user.html

@@ -1,20 +1,22 @@
-<li>
+{% if meta.can_edit %}
-    <a role="button" data-toggle="modal" data-target="#edit_user_modal">
+    <li>
-        <i class="glyphicon glyphicon-edit"></i> Update</a>
+        <a role="button" data-toggle="modal" data-target="#edit_user_modal">
-</li>
+            <i class="glyphicon glyphicon-edit"></i> Update</a>
-<li>
+    </li>
-    <a role="button" data-toggle="modal" data-target="#edit_password_modal">
+    <li>
-        <i class="glyphicon glyphicon-lock"></i> Update Password</a>
+        <a role="button" data-toggle="modal" data-target="#edit_password_modal">
-</li>
+            <i class="glyphicon glyphicon-lock"></i> Update Password</a>
-<li>
+    </li>
-    <a role="button" data-toggle="modal" data-target="#new_prediction_setting_modal">
+    <li>
-        <i class="glyphicon glyphicon-plus"></i> New Prediction Setting</a>
+        <a role="button" data-toggle="modal" data-target="#new_prediction_setting_modal">
-</li>
+            <i class="glyphicon glyphicon-plus"></i> New Prediction Setting</a>
-<li>
+    </li>
-    <a role="button" data-toggle="modal" data-target="#manage_api_token_modal">
+{#    <li>#}
-        <i class="glyphicon glyphicon-console"></i> Manage API Token</a>
+{#        <a role="button" data-toggle="modal" data-target="#manage_api_token_modal">#}
-</li>
+{#            <i class="glyphicon glyphicon-console"></i> Manage API Token</a>#}
-<li>
+{#    </li>#}
-    <a role="button" data-toggle="modal" data-target="#delete_user_modal">
+    <li>
-        <i class="glyphicon glyphicon-trash"></i> Delete Account</a>
+        <a role="button" data-toggle="modal" data-target="#delete_user_modal">
-</li>
+            <i class="glyphicon glyphicon-trash"></i> Delete Account</a>
+    </li>
+{% endif %}

templates/collections/objects_list.html

@@ -35,12 +35,16 @@
 {% include "modals/collections/new_reaction_modal.html" %}
 {% elif object_type == 'pathway' %}
 {# {% include "modals/collections/new_pathway_modal.html" %} #}
+{% elif object_type == 'node' %}
+{% include "modals/collections/new_node_modal.html" %}
+{% elif object_type == 'edge' %}
+{% include "modals/collections/new_edge_modal.html" %}
 {% elif object_type == 'scenario' %}
 {% include "modals/collections/new_scenario_modal.html" %}
 {% elif object_type == 'model' %}
 {% include "modals/collections/new_model_modal.html" %}
 {% elif object_type == 'setting' %}
-{% include "modals/collections/new_setting_modal.html" %}
+{#{% include "modals/collections/new_setting_modal.html" %}#}
 {% elif object_type == 'user' %}
 <div></div>
 {% elif object_type == 'group' %}
@@ -63,6 +67,10 @@
             Reactions
             {% elif object_type == 'pathway' %}
             Pathways
+            {% elif object_type == 'node' %}
+            Nodes
+            {% elif object_type == 'edge' %}
+            Edges
             {% elif object_type == 'scenario' %}
             Scenarios
             {% elif object_type == 'model' %}
@@ -75,34 +83,38 @@
             Groups
             {% endif %}
             <div id="actionsButton"
-                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;"
+                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
                                      aria-haspopup="true" aria-expanded="false"><span
                     class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
                     style="padding-right:1em"></span></a>
                 <ul id="actionsList" class="dropdown-menu">
                     {% block actions %}
-                    {% if object_type == 'package' %}
+                        {% if object_type == 'package' %}
-                    {% include "actions/collections/package.html" %}
+                            {% include "actions/collections/package.html" %}
-                    {% elif object_type == 'compound' %}
+                        {% elif object_type == 'compound' %}
-                    {% include "actions/collections/compound.html" %}
+                            {% include "actions/collections/compound.html" %}
-                    {% elif object_type == 'structure' %}
+                        {% elif object_type == 'structure' %}
-                    {% include "actions/collections/compound_structure.html" %}
+                            {% include "actions/collections/compound_structure.html" %}
-                    {% elif object_type == 'rule' %}
+                        {% elif object_type == 'rule' %}
-                    {% include "actions/collections/rule.html" %}
+                            {% include "actions/collections/rule.html" %}
-                    {% elif object_type == 'reaction' %}
+                        {% elif object_type == 'reaction' %}
-                    {% include "actions/collections/reaction.html" %}
+                            {% include "actions/collections/reaction.html" %}
-                    {% elif object_type == 'setting' %}
+                        {% elif object_type == 'setting' %}
-                    {% include "actions/collections/setting.html" %}
+                            {% include "actions/collections/setting.html" %}
-                    {% elif object_type == 'scenario' %}
+                        {% elif object_type == 'scenario' %}
-                    {% include "actions/collections/scenario.html" %}
+                            {% include "actions/collections/scenario.html" %}
-                    {% elif object_type == 'model' %}
+                        {% elif object_type == 'model' %}
-                    {% include "actions/collections/model.html" %}
+                            {% include "actions/collections/model.html" %}
-                    {% elif object_type == 'pathway' %}
+                        {% elif object_type == 'pathway' %}
-                    {% include "actions/collections/pathway.html" %}
+                            {% include "actions/collections/pathway.html" %}
-                    {% elif object_type == 'group' %}
+                        {% elif object_type == 'node' %}
-                    {% include "actions/collections/group.html" %}
+                            {% include "actions/collections/node.html" %}
-                    {% endif %}
+                        {% elif object_type == 'edge' %}
+                            {% include "actions/collections/edge.html" %}
+                        {% elif object_type == 'group' %}
+                            {% include "actions/collections/group.html" %}
+                        {% endif %}
                     {% endblock %}
                 </ul>
             </div>
@@ -133,6 +145,14 @@
             <p>A pathway displays the (predicted) biodegradation of a compound as graph.
                 <a target="_blank" href="https://wiki.envipath.org/index.php/pathways" role="button">Learn more
                     &gt;&gt;</a></p>
+            {% elif object_type == 'node' %}
+            <p>Nodes represent the (predicted) compounds in a graph.
+                <a target="_blank" href="https://wiki.envipath.org/index.php/nodes" role="button">Learn more
+                    &gt;&gt;</a></p>
+            {% elif object_type == 'edge' %}
+            <p>Edges represent the links between Nodes in a graph
+                <a target="_blank" href="https://wiki.envipath.org/index.php/edges" role="button">Learn more
+                    &gt;&gt;</a></p>
             {% elif object_type == 'scenario' %}
             <p>A scenario contains meta-information that can be attached to other data (compounds, rules, ..).
                 <a target="_blank" href="https://wiki.envipath.org/index.php/scenarios" role="button">Learn more
@@ -185,7 +205,7 @@
                 {% endfor %}
                 {% else %}
                 {% for obj in reviewed_objects|slice:":50" %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}{# <i>({{ obj.package.name }})</i> #}
                     <span class="glyphicon glyphicon-star" aria-hidden="true"
                           style="float:right" data-toggle="tooltip"
                           data-placement="top" title="" data-original-title="Reviewed">
@@ -229,51 +249,52 @@
         {% endif %}
     </div>
 </div>
-<script>
+    <script>
-$(function() {
+        $(function () {
-	$('#modal-form-delete-submit').on('click', function (e) {
-		e.preventDefault();
-		$('#modal-form-delete').submit();
-	});
 
-    $('#object-search').show();
+            $('#modal-form-delete-submit').on('click', function (e) {
-
+                e.preventDefault();
-	if ($('#load-remaining').length) {
+                $('#modal-form-delete').submit();
-        $('#load-remaining').on('click', function() {
-
-            makeLoadingGif("#load-all-loading", "{% static '/images/wait.gif' %}");
-            $('#load-all-error').hide();
-
-            $.getJSON('?all=true', function(resp) {
-                $('#ReviewedContent').empty();
-                $('#UnreviewedContent').empty();
-
-                for(o in resp.objects) {
-                    obj = resp.objects[o];
-                    if (obj.reviewed) {
-                        $('#ReviewedContent').append('<a class="list-group-item" href="' + obj.url + '">' + obj.name + '</a>');
-                    } else {
-                        $('#UnreviewedContent').append('<a class="list-group-item" href="' + obj.url + '">' + obj.name + '</a>');
-                    }
-                }
-
-                $('#load-all-loading').empty();
-                $('#load-remaining').hide();
-            }).fail(function(resp) {
-                $('#load-all-loading').empty();
-                $('#load-all-error').show();
             });
-        });
-	}
 
-    $('#object-search').on('keyup', function() {
+            $('#object-search').show();
-        let query = $(this).val().toLowerCase();
-        $('a.list-group-item').each(function() {
-            let text = $(this).text().toLowerCase();
-            $(this).toggle(text.indexOf(query) !== -1);
-        });
-    });
 
-});
+            if ($('#load-remaining').length) {
-</script>
+                $('#load-remaining').on('click', function () {
+
+                    makeLoadingGif("#load-all-loading", "{% static '/images/wait.gif' %}");
+                    $('#load-all-error').hide();
+
+                    $.getJSON('?all=true', function (resp) {
+                        $('#ReviewedContent').empty();
+                        $('#UnreviewedContent').empty();
+
+                        for (o in resp.objects) {
+                            obj = resp.objects[o];
+                            if (obj.reviewed) {
+                                $('#ReviewedContent').append('<a class="list-group-item" href="' + obj.url + '">' + obj.name + '</a>');
+                            } else {
+                                $('#UnreviewedContent').append('<a class="list-group-item" href="' + obj.url + '">' + obj.name + '</a>');
+                            }
+                        }
+
+                        $('#load-all-loading').empty();
+                        $('#load-remaining').hide();
+                    }).fail(function (resp) {
+                        $('#load-all-loading').empty();
+                        $('#load-all-error').show();
+                    });
+                });
+            }
+
+            $('#object-search').on('keyup', function () {
+                let query = $(this).val().toLowerCase();
+                $('a.list-group-item').each(function () {
+                    let text = $(this).text().toLowerCase();
+                    $(this).toggle(text.indexOf(query) !== -1);
+                });
+            });
+
+        });
+    </script>
 {% endblock content %}

templates/errors/error.html

@@ -0,0 +1,14 @@
+{% extends "framework.html" %}
+{% load static %}
+{% block content %}
+
+    <div class="alert alert-danger" role="alert">
+        <h4 class="alert-heading">Something went wrong!</h4>
+        <p>An unexpected Error occurred...</p>
+        <hr>
+        <p class="mb-0">
+            The error was logged and will be investigated.
+        </p>
+    </div>
+
+{% endblock content %}

templates/errors/user_account_inactive.html

@@ -2,9 +2,9 @@
 {% load static %}
 {% block content %}
 
-    <div class="alert alert-error" role="alert">
+    <div class="alert alert-danger" role="alert">
         <h4 class="alert-heading">Your account has not been activated yet!</h4>
-        <p>Your account has not been activated yet. If you have question <a href="mailto:admin@envipath.org">contact
+        <p>Your account has not been activated yet. If you have questions <a href="mailto:admin@envipath.org">contact
             us.</a>
         </p>
     </div>

templates/framework.html

@@ -14,13 +14,25 @@
           href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/css/bootstrap-select.min.css">
     <script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/js/bootstrap-select.min.js"></script>
     <!-- CDN END -->
+    <meta name="csrf-token" content="{{ csrf_token }}">
+    <script>
+        const csrftoken = document.querySelector('[name=csrf-token]').content;
 
+        // Setup CSRF header for all jQuery AJAX requests
+        $.ajaxSetup({
+            beforeSend: function(xhr, settings) {
+                if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
+                    xhr.setRequestHeader("X-CSRFToken", csrftoken);
+                }
+            }
+        });
+    </script>
     {# Favicon #}
     <link rel="shortcut icon" type="image/png" href="{% static 'images/favicon.ico' %}"/>
-<!--    {# C3 CSS #}-->
+    <!--    {# C3 CSS #}-->
-<!--    <link id="css-c3" href="{% static 'css/c3.css' %}" rel="stylesheet" type="text/css"/>-->
+    <!--    <link id="css-c3" href="{% static 'css/c3.css' %}" rel="stylesheet" type="text/css"/>-->
-<!--    {# EP CSS #}-->
+    <!--    {# EP CSS #}-->
-<!--    <link id="css-pps_white_general" href="{% static 'css/epp.css' %}" rel="stylesheet" type="text/css"/>-->
+    <!--    <link id="css-pps_white_general" href="{% static 'css/epp.css' %}" rel="stylesheet" type="text/css"/>-->
 
 
     {# General EP JS #}
@@ -29,21 +41,23 @@
     <script src="{% static 'js/jquery-bootstrap-modal-steps.js' %}"></script>
 
     {% if not debug %}
-    <!-- Matomo -->
+        <!-- Matomo -->
-    <script>
+        <script>
-      var _paq = window._paq = window._paq || [];
+            var _paq = window._paq = window._paq || [];
-      /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
+            /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
-      _paq.push(['trackPageView']);
+            _paq.push(['trackPageView']);
-      _paq.push(['enableLinkTracking']);
+            _paq.push(['enableLinkTracking']);
-      (function() {
+            (function () {
-        var u="//matomo.envipath.com/";
+                var u = "//matomo.envipath.com/";
-        _paq.push(['setTrackerUrl', u+'matomo.php']);
+                _paq.push(['setTrackerUrl', u + 'matomo.php']);
-        _paq.push(['setSiteId', '7']);
+                _paq.push(['setSiteId', '7']);
-        var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
+                var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
-        g.async=true; g.src=u+'matomo.js'; s.parentNode.insertBefore(g,s);
+                g.async = true;
-      })();
+                g.src = u + 'matomo.js';
-    </script>
+                s.parentNode.insertBefore(g, s);
-    <!-- End Matomo Code -->
+            })();
+        </script>
+        <!-- End Matomo Code -->
     {% endif %}
 
 </head>
@@ -52,13 +66,13 @@
     <div class="container-fluid">
         <!-- Brand and toggle get grouped for better mobile display -->
         <div class="navbar-header navbar-header-framework">
-<!--            <button type="button" class="navbar-toggle navbar-toggle-framework" data-toggle="collapse"-->
+            <!--            <button type="button" class="navbar-toggle navbar-toggle-framework" data-toggle="collapse"-->
-<!--                    data-target="#navbarCollapse">-->
+            <!--                    data-target="#navbarCollapse">-->
-<!--                <span class="sr-only">Toggle navigation</span>-->
+            <!--                <span class="sr-only">Toggle navigation</span>-->
-<!--                <span class="icon-bar"></span>-->
+            <!--                <span class="icon-bar"></span>-->
-<!--                <span class="icon-bar"></span>-->
+            <!--                <span class="icon-bar"></span>-->
-<!--                <span class="icon-bar"></span>-->
+            <!--                <span class="icon-bar"></span>-->
-<!--            </button>-->
+            <!--            </button>-->
             <a id="pictureLink" href="{{ meta.server_url }}" class="navbar-brand">
                 <img id="image-logo-short-white.svg" src='{% static "/images/logo-short-white.svg" %}' width="100"
                      alt="enviPath">
@@ -95,16 +109,16 @@
                         <li><a href="{{ meta.server_url }}/reaction" id="reactionLink">Reaction</a></li>
                         <li><a href="{{ meta.server_url }}/model" id="relative-reasoningLink">Model</a></li>
                         <li><a href="{{ meta.server_url }}/scenario" id="scenarioLink">Scenario</a></li>
-                        <li><a href="{{ meta.server_url }}/setting" id="settingLink">Setting</a></li>
+                        {#                        <li><a href="{{ meta.server_url }}/setting" id="settingLink">Setting</a></li>#}
-<!--                        <li><a href="{{ meta.server_url }}/user" id="userLink">User</a></li>-->
+                        {#                        <li><a href="{{ meta.server_url }}/user" id="userLink">User</a></li>#}
-<!--                        <li><a href="{{ meta.server_url }}/group" id="groupLink">Group</a></li>-->
+                        {#                        <li><a href="{{ meta.server_url }}/group" id="groupLink">Group</a></li>#}
                     </ul>
                 </li>
 
             </ul>
 
             <ul class="nav navbar-nav navbar-right navbar-nav-framework navbar-right-framework">
-<!--                <li><a href="{{ meta.server_url }}/search" id="searchLink">Search</a></li>-->
+                {#                <li><a href="{{ meta.server_url }}/search" id="searchLink">Search</a></li>#}
                 <li class="dropdown">
                     <a data-toggle="dropdown" class="dropdown-toggle" href="#">Info <b class="caret"></b></a>
                     <ul role="menu" class="dropdown-menu">
@@ -120,31 +134,33 @@
                     </ul>
                 </li>
                 {% if meta.user.username == 'anonymous' %}
-                <li>
+                    <li>
-                    <a href="#signup" id="loginButton" data-toggle="modal" data-target="#signupmodal"
+                        <a href="#signup" id="loginButton" data-toggle="modal" data-target="#signupmodal"
-                       style="margin-right:10px">Login</a>
+                           style="margin-right:10px">Login</a>
-                </li>
+                    </li>
                 {% else %}
-                <li class="dropdown">
+                    <li class="dropdown">
-                    <a data-toggle="dropdown" id="loggedInButton" class="dropdown-toggle" id="logedInButton" href="#">
+                        <a data-toggle="dropdown" id="loggedInButton" class="dropdown-toggle" id="logedInButton"
-                        <div id="username">
+                           href="#">
-                            {{ user.username }}<b class="caret"></b>
+                            <div id="username">
-                        </div>
+                                {{ user.username }}<b class="caret"></b>
-                    </a>
-                    <ul role="menu" class="dropdown-menu">
-                        <li>
-                            <a href="{{ meta.user.url }}" id="accountbutton">My Account</a>
-                        </li>
-                        <li class="divider"></li>
-                        <form class="navbar-form navbar-left navbar-left-framework" role="logout" action="{{ meta.user.url }}" method="post">
-                            {% csrf_token %}
-                            <div class="form-group">
-                                <input type="hidden" name="logout" value="true">
                             </div>
-                            <button type="submit" class="btn btn-default">Logout</button>
+                        </a>
-                        </form>
+                        <ul role="menu" class="dropdown-menu">
-                    </ul>
+                            <li>
-                </li>
+                                <a href="{{ meta.user.url }}" id="accountbutton">My Account</a>
+                            </li>
+                            <li class="divider"></li>
+                            <form class="navbar-form navbar-left navbar-left-framework" role="logout"
+                                  action="{{ meta.user.url }}" method="post">
+                                {% csrf_token %}
+                                <div class="form-group">
+                                    <input type="hidden" name="logout" value="true">
+                                </div>
+                                <button type="submit" class="btn btn-default">Logout</button>
+                            </form>
+                        </ul>
+                    </li>
                 {% endif %}
             </ul>
         </div>
@@ -152,26 +168,26 @@
 </nav>
 <div id="docContent" class="content container">
     {% if breadcrumbs %}
-    <div id="bread">
+        <div id="bread">
-        <ol class="breadcrumb">
+            <ol class="breadcrumb">
-            {% for elem in breadcrumbs %}
+                {% for elem in breadcrumbs %}
-                {% for name, url in elem.items %}
+                    {% for name, url in elem.items %}
-                {% if forloop.parentloop.last %}
+                        {% if forloop.parentloop.last %}
-                <li class="active">{{ name }}</li>
+                            <li class="active">{{ name }}</li>
-                {% else %}
+                        {% else %}
-                <li>
+                            <li>
-                    <a href="{{ url }}">{{ name }}</a>
+                                <a href="{{ url }}">{{ name }}</a>
-                </li>
+                            </li>
-                {% endif %}
+                        {% endif %}
+                    {% endfor %}
                 {% endfor %}
-            {% endfor %}
+            </ol>
-        </ol>
+        </div>
-    </div>
     {% endif %}
     {% if message %}
-    <div id="message">
+        <div id="message">
-        {{ message }}
+            {{ message }}
-    </div>
+        </div>
     {% endif %}
     {% block content %}
     {% endblock content %}
@@ -206,19 +222,26 @@
 <div class="row">
     <div class="col-lg-12">
         <ul class="nav nav-pills nav-justified">
-<!--            <li><a href="https://envipath.com/imprint/" target="_blank">Impressum/Imprint</a></li>-->
+            <!--            <li><a href="https://envipath.com/imprint/" target="_blank">Impressum/Imprint</a></li>-->
             <li><a href="mailto:admin@envipath.org" target="_blank">Contact</a></li>
-<!--            <li><a href="http://envipath.com" target="_blank"> enviPath UG (haftungsbeschr&auml;nkt) &amp; Co. KG &copy;-->
+            <!--            <li><a href="http://envipath.com" target="_blank"> enviPath UG (haftungsbeschr&auml;nkt) &amp; Co. KG &copy;-->
-<!--                {{ YEAR }}</a></li>-->
+            <!--                {{ YEAR }}</a></li>-->
         </ul>
     </div>
 </div>
-
+<script>
+    $(function () {
+        // Hide actionsbutton if theres no action defined
+        if ($('#actionsButton ul').children().length > 0) {
+            $('#actionsButton').show();
+        }
+    });
+</script>
 {% block modals %}
-{% include "modals/cite_modal.html" %}
+    {% include "modals/cite_modal.html" %}
-{% include "modals/signup_modal.html" %}
+    {% include "modals/signup_modal.html" %}
-{% include "modals/predict_modal.html" %}
+    {% include "modals/predict_modal.html" %}
-{% include "modals/batch_predict_modal.html" %}
+    {% include "modals/batch_predict_modal.html" %}
 {% endblock %}
 </body>
 </html>

templates/index/index.html

@@ -2,139 +2,166 @@
 {% load static %}
 {% block content %}
 
-<!-- TODO rename ids as well as remove pathways if modal is closed!-->
+    <!-- TODO rename ids as well as remove pathways if modal is closed!-->
-<div class="modal fade" tabindex="-1" id="foundMatching" role="dialog" aria-labelledby="foundModal" aria-hidden="true">
+    <div class="modal fade" tabindex="-1" id="foundMatching" role="dialog" aria-labelledby="foundModal"
-    <div class="modal-dialog">
+         aria-hidden="true">
-        <div class="modal-content">
+        <div class="modal-dialog">
-            <div class="modal-header">
+            <div class="modal-content">
-                <button type="button" class="close" data-dismiss="modal">
+                <div class="modal-header">
-                    <span aria-hidden="true">&times;</span>
+                    <button type="button" class="close" data-dismiss="modal">
-                    <span class="sr-only">Close</span>
+                        <span aria-hidden="true">&times;</span>
-                </button>
+                        <span class="sr-only">Close</span>
-                <h4 class="modal-title" id="newPackMod">Found Pathway in Database</h4>
+                    </button>
-            </div>
+                    <h4 class="modal-title" id="newPackMod">Found Pathway in Database</h4>
-            <div class="modal-body">
+                </div>
-                <p>We found at least one pathway in the database with the given root
+                <div class="modal-body">
-                    compound. Do you want to open any of the existing pathways or
+                    <p>We found at least one pathway in the database with the given root
-                    predict a new one? To open an existing pathway, simply click
+                        compound. Do you want to open any of the existing pathways or
-                    on the pathway, to predict a new one, click Predict. The predicted
+                        predict a new one? To open an existing pathway, simply click
-                    pathway might differ from the ones in the database due to the
+                        on the pathway, to predict a new one, click Predict. The predicted
-                    settings used in the prediction.</p>
+                        pathway might differ from the ones in the database due to the
-                <div id="foundPathways"></div>
+                        settings used in the prediction.</p>
-            </div>
+                    <div id="foundPathways"></div>
-            <div class="modal-footer">
+                </div>
-                <a id="modal-predict" class="btn btn-primary" href="#">Predict</a>
+                <div class="modal-footer">
-                <button type="button" id="cancel-predict" class="btn btn-default" data-dismiss="modal">Cancel</button>
+                    <a id="modal-predict" class="btn btn-primary" href="#">Predict</a>
+                    <button type="button" id="cancel-predict" class="btn btn-default" data-dismiss="modal">Cancel
+                    </button>
+                </div>
             </div>
         </div>
     </div>
-</div>
+    <div class="jumbotron">
-<div class="jumbotron">
+        <h1>
-    <h1>
+            <img id="image-logo-long" class="img-responsive" alt="enviPath" width="1000ex"
-        <img id="image-logo-long" class="img-responsive" alt="enviPath" width="1000ex"
+                 src='{% static "/images/logo-long.svg" %}'/>
-             src='{% static "/images/logo-long.svg" %}'/>
+        </h1>
-    </h1>
+        <p>enviPath is a database and prediction system for the microbial
-    <p>enviPath is a database and prediction system for the microbial
+            biotransformation of organic environmental contaminants. The
-        biotransformation of organic environmental contaminants. The
+            database provides the possibility to store and view experimentally
-        database provides the possibility to store and view experimentally
+            observed biotransformation pathways. The pathway prediction system
-        observed biotransformation pathways. The pathway prediction system
+            provides different relative reasoning models to predict likely biotransformation
-        provides different relative reasoning models to predict likely biotransformation
+            pathways and products. You can try it out below.
-        pathways and products. You can try it out below.
+        </p>
-    </p>
+        <p>
-    <p>
+            <a class="btn" style="background-color:#222222;color:#9d9d9d" role="button" target="_blank"
-        <a class="btn" style="background-color:#222222;color:#9d9d9d" role="button" target="_blank"
+               href="https://wiki.envipath.org/index.php/Main_Page">Learn more &gt;&gt;</a>
-           href="https://wiki.envipath.org/index.php/Main_Page">Learn more &gt;&gt;</a>
+        </p>
-    </p>
-</div>
-<p></p>
-
-<div class="input-group" id="index-form-bar">
-    <div class="input-group-btn">
-        <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown" aria-expanded="false">
-            <span class="caret"></span>
-        </button>
-        <ul class="dropdown-menu" role="menu">
-            <li>
-                <iframe id="index-form-ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-                        height="510"></iframe>
-            </li>
-        </ul>
     </div>
-    <input type="text" class="form-control" id='index-form-text-input' placeholder="Enter a SMILES to predict a Pathway or type something to search">
+    <p></p>
-    <div class="input-group-btn">
+    <form id="index-form" action="{{ meta.current_package.url }}/pathway" method="POST">
-        <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown" aria-haspopup="true"
+        {% csrf_token %}
-                aria-expanded="false" id="action-button">Predict <span class="caret"></span></button>
+        <div class="input-group" id="index-form-bar">
-        <ul class="dropdown-menu">
+            <div class="input-group-btn">
-            <li><a id="dropdown-predict">Predict</a></li>
+                <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown"
-            <li><a id="dropdown-search">Search</a></li>
+                        aria-expanded="false">
-        </ul>
+                    <span class="caret"></span>
-        <button class="btn" style="background-color:#222222;color:#9d9d9d" type="button" id="run-button">Go!</button>
+                </button>
-    </div>
+                <ul class="dropdown-menu" role="menu">
-</div>
+                    <li>
+                        <iframe id="index-form-ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
+                                height="510"></iframe>
+                    </li>
+                </ul>
+            </div>
+            <input type="text" class="form-control" id='index-form-text-input'
+                   placeholder="Enter a SMILES to predict a Pathway or type something to search">
+            <div class="input-group-btn">
+                <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown"
+                        aria-haspopup="true"
+                        aria-expanded="false" id="action-button">Predict <span class="caret"></span></button>
+                <ul class="dropdown-menu">
+                    <li><a id="dropdown-predict">Predict</a></li>
+                    <li><a id="dropdown-search">Search</a></li>
+                </ul>
+                <button class="btn" style="background-color:#222222;color:#9d9d9d" type="button" id="run-button">Go!
+                </button>
+            </div>
+        </div>
+        <input type="hidden" id="index-form-smiles" name="smiles" value="smiles">
+        <input type="hidden" id="index-form-predict" name="predict" value="predict">
+    </form>
+    <div id="loading"></div>
+    <script language="javascript">
+        var currentPackage = "{{ meta.current_package.url }}";
 
-<div id="loading"></div>
+        function goButtonClicked() {
-<script language="javascript">
+            $(this).prop("disabled", true);
 
-    function goButtonClicked() {
+            var action = $('#action-button').text().trim();
-        $(this).prop("disabled", true);
 
-        var action = $('#action-button').text().trim();
+            var textSmiles = $('#index-form-text-input').val().trim();
 
-        var textSmiles = $('#index-form-text-input').val().trim();
+            if (textSmiles === '') {
-        var ketcherSmiles = getKetcher('index-form-ketcher').getSmiles().trim();
+                return;
+            }
 
-        if (action != 'Search' && ketcherSmiles != '' && textSmiles != ketcherSmiles) {
+            var ketcherSmiles = getKetcher('index-form-ketcher').getSmiles().trim();
-            console.log("Ketcher and TextInput differ!");
+
+            if (action !== 'Search' && ketcherSmiles !== '' && textSmiles !== ketcherSmiles) {
+                console.log("Ketcher and TextInput differ!");
+            }
+
+            if (action === 'Search') {
+                var par = {};
+                par['search'] = textSmiles;
+                par['mode'] = 'text';
+                var queryString = $.param(par, true);
+                window.location.href = "/search?" + queryString;
+            } else {
+                $('#index-form-smiles').val(textSmiles);
+                $('#index-form').submit();
+            }
         }
 
-        if (action == 'Search') {
+        function actionDropdownClicked() {
-            console.log("Searching...");
+            var suffix = ' <span class="caret"></span>';
-        } else {
+            var dropdownVal = $(this).text();
-            console.log("Predicting");
+
+            if (dropdownVal === 'Search') {
+                $("#index-form").attr("action", '/search');
+                $("#index-form").attr("method", 'GET');
+            } else {
+                $("#index-form").attr("action", currentPackage + "/pathway");
+            }
+
+            $('#action-button').html(dropdownVal + suffix);
         }
 
-    }
+        function ketcherToTextInput() {
+            $('#index-form-text-input').val(this.ketcher.getSmiles());
+        }
 
-    function actionDropdownClicked() {
+        $(function () {
-        var suffix = ' <span class="caret"></span>';
+            // Code that should be executed once DOM is ready goes here
-        var dropdownVal = $(this).text();
+            $('#dropdown-predict').on('click', actionDropdownClicked);
-        $('#action-button').html(dropdownVal + suffix);
+            $('#dropdown-search').on('click', actionDropdownClicked);
-    }
 
-    function ketcherToTextInput() {
+            $('#run-button').on('click', goButtonClicked);
-        $('#index-form-text-input').val(this.ketcher.getSmiles());
-    }
 
-    $(function() {
+            // Update Ketcher Width
-        // Code that should be executed once DOM is ready goes here
+            var fullWidth = $('#index-form-bar').width();
-        $('#dropdown-predict').on('click', actionDropdownClicked);
+            $('#index-form-ketcher').width(fullWidth);
-        $('#dropdown-search').on('click', actionDropdownClicked);
 
-        $('#run-button').on('click', goButtonClicked);
+            // add a listener that gets triggered whenever the structure in ketcher has changed
+            $('#index-form-ketcher').on('load', function () {
+                const checkKetcherReady = () => {
+                    win = this.contentWindow
+                    if (win.ketcher && 'editor' in win.ketcher) {
+                        win.ketcher.editor.event.change.handlers.push({
+                            once: false,
+                            priority: 0,
+                            f: ketcherToTextInput,
+                            ketcher: win.ketcher
+                        });
+                    } else {
+                        setTimeout(checkKetcherReady, 100);
+                    }
+                };
 
-        // Update Ketcher Width
+                checkKetcherReady();
-        var fullWidth = $('#index-form-bar').width();
+            });
-        $('#index-form-ketcher').width(fullWidth);
 
-        // add a listener that gets triggered whenever the structure in ketcher has changed
-        $('#index-form-ketcher').on('load', function() {
-            const checkKetcherReady = () => {
-                win = this.contentWindow
-                if (win.ketcher && 'editor' in win.ketcher) {
-                    win.ketcher.editor.event.change.handlers.push({
-                        once: false,
-                        priority: 0,
-                        f: ketcherToTextInput,
-                        ketcher: win.ketcher
-                    });
-                } else {
-                    setTimeout(checkKetcherReady, 100);
-                }
-            };
-
-            checkKetcherReady();
         });
-
+    </script>
-    });
-</script>
 {% endblock content %}

templates/login.html

@@ -0,0 +1,189 @@
+{% load static %}
+
+
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>Login Modal with Blur</title>
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+
+    <!-- Bootstrap 3.3.7 CSS -->
+    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
+
+    <style>
+        body, html {
+            margin: 0;
+            height: 100%;
+            overflow: hidden;
+        }
+
+        .bg-blur {
+            position: fixed;
+            top: 0;
+            left: 0;
+            width: 100%;
+            height: 100%;
+            background: url('{% static "/images/enviPy-screenshot.png" %}') no-repeat center center/cover;
+            filter: blur(8px);
+            z-index: -1;
+        }
+
+        /* Optional: dim layer */
+        .bg-dim {
+            position: fixed;
+            top: 0;
+            left: 0;
+            width: 100%;
+            height: 100%;
+            background-color: rgba(0, 0, 0, 0.4);
+            z-index: 0;
+        }
+
+        .center-button {
+            position: absolute;
+            top: 50%;
+            left: 50%;
+            transform: translate(-50%, -50%);
+            z-index: 1;
+        }
+    </style>
+</head>
+<body>
+
+<!-- Blurred Background -->
+<div class="bg-blur"></div>
+<div class="bg-dim"></div>
+
+<!-- Trigger Button -->
+<div class="center-button">
+    <button class="btn btn-primary btn-lg" data-toggle="modal" data-target="#signupmodal">Login / Sign Up</button>
+</div>
+
+<!-- Bootstrap Modal -->
+<div class="modal fade bs-modal-sm" id="signupmodal" tabindex="-1" role="dialog"
+     aria-labelledby="mySmallModalLabel"
+     aria-hidden="true">
+    <div class="modal-dialog modal-sm">
+        <div class="modal-content">
+            <br>
+            <div class="bs-example bs-example-tabs">
+                <ul id="myTab" class="nav nav-tabs">
+                    <li class="active">
+                        <a href="#signin" data-toggle="tab">Sign In</a>
+                    </li>
+                    <li class="">
+                        <a href="#signup" data-toggle="tab">Register</a>
+                    </li>
+                    <li class="">
+                        <a href="#why" data-toggle="tab">Why?</a>
+                    </li>
+                </ul>
+            </div>
+            <div class="modal-body">
+                <div id="myTabContent" class="tab-content">
+                    <div class="tab-pane fade active in" id="signin">
+                        <form class="form-horizontal" method="post" action="{{ meta.server_url }}/user">
+                            {% csrf_token %}
+                            <fieldset>
+                                <input type="hidden" name="login" id="login" value="true"/>
+                                <div class="control-group">
+                                    <label class="control-label" for="username">Username:</label>
+                                    <div class="controls">
+                                        <input required id="username" name="username" type="text"
+                                               class="form-control"
+                                               placeholder="username" autocomplete="username">
+                                    </div>
+                                    <label class="control-label" for="passwordinput">Password:</label>
+                                    <div class="controls">
+                                        <input required id="passwordinput" name="password" class="form-control"
+                                               type="password" placeholder="********"
+                                               autocomplete="current-password">
+                                    </div>
+                                </div>
+
+                                <!-- Button -->
+                                <div class="control-group">
+                                    <label class="control-label" for="signin"></label>
+                                    <div class="controls">
+                                        <button id="signin" name="signin" class="btn btn-success">Sign In
+                                        </button>
+                                    </div>
+                                </div>
+                            </fieldset>
+                        </form>
+                    </div>
+
+                    <!-- Why tab -->
+                    <div class="tab-pane fade in" id="why">
+                        <p>After you register, you have more permissions on
+                            this site, e.g., can create your own
+                            packages, submit data for review, and set access
+                            permissions to your data.</p>
+                        <p></p>
+                        <p>
+                            <br> Please
+                            contact <a href="mailto:admin@envipath.org">admin@envipath.org</a>
+                            if you have any questions.</p>
+                    </div>
+
+
+                    <!-- Register -->
+                    <div class="tab-pane fade"
+                         id="signup">
+                        <div id="passwordGuideline" class="alert alert-info">
+                            The password must contain 8 to 30 characters<br>
+                            The following characters are allowed:
+                            - Upper and lower case characters<br>
+                            - Digits<br>
+                            - Special characters _, -, +<br>
+
+                        </div>
+
+                        <form id="signup-action" class="form-horizontal" action="{{ meta.server_url }}/user"
+                              method="post">
+                            {% csrf_token %}
+                            <input type="hidden" name="register" id="register" value="true"/>
+
+                            <label class="control-label" for="userid">Username:</label>
+                            <input id="userid" name="username" class="form-control" type="text"
+                                   placeholder="user" required autocomplete="username">
+
+                            <label class="control-label" for="email">Email:</label>
+                            <input id="email" name="email" class="form-control" type="email"
+                                   placeholder="user@envipath.org" required>
+
+                            <label class="control-label" for="password">Password:</label>
+                            <input id="password" name="password" class="form-control" type="password"
+                                   placeholder="********" required autocomplete="new-password">
+
+                            <label class="control-label" for="rpassword">Repeat Password:</label>
+                            <input id="rpassword" name="rpassword" class="form-control" type="password"
+                                   placeholder="********" required autocomplete="new-password">
+
+                            <div class="control-group">
+                                <label class="control-label" for="confirmsignup"></label>
+                                <div class="controls">
+                                    <button id="confirmsignup" name="confirmsignup" class="btn btn-success">Sign
+                                        Up
+                                    </button>
+                                </div>
+                            </div>
+                        </form>
+                    </div>
+                </div>
+            </div>
+            <div class="modal-footer">
+                <center>
+                    <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+                </center>
+            </div>
+        </div>
+    </div>
+</div>
+
+<!-- Bootstrap 3.3.7 JS + jQuery -->
+<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
+</body>
+</html>

templates/modals/collections/new_rule_modal.html

@@ -16,23 +16,11 @@
                     <input id="rule-name" class="form-control" name="rule-name" placeholder="Name"/>
                     <label for="rule-description">Description</label>
                     <input id="rule-description" class="form-control" name="rule-description" placeholder="Description"/>
+                    <label for="rule-smirks">SMIRKS</label>
+                    <input id="rule-smirks" class="form-control" name="rule-smirks" placeholder="SMIRKS"/>
                     <p></p>
-<!--                    TODO Ruletypes -->
+                    <div id="rule-smirks-viz"></div>
-<!--                    TODO Decide on rules to use?-->
                     <input type="hidden" name="rule-type" id="rule-type" value="SimpleAmbitRule">
-
-<!--                    <select id="rule-type" name="rule-type" class="form-control" data-width='100%'>-->
-<!--                        <option disabled selected>Select Rule Type</option>-->
-<!--                        {% for k, v in rule_types.items %}-->
-<!--                        <option value="{{ v }}">{{ k }}</option>-->
-<!--                        {% endfor %}-->
-<!--                    </select>-->
-<!--                    -->
-                    <div>
-                        <iframe id="new_rule_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-                                height="510"></iframe>
-                    </div>
-                    <input type="hidden" name="rule-smirks" id="rule-smirks">
                     <p></p>
                 </form>
             </div>
@@ -47,13 +35,36 @@
 </div>
 <script>
 $(function() {
+
+    $('#rule-smirks').on('input', function(e) {
+        $('#rule-smirks-viz').empty()
+
+        smirks = $('#rule-smirks').val()
+
+        const img = new Image();
+        img.src = "{% url 'depict' %}?is_query_smirks=true&smirks=" + encodeURIComponent(smirks);
+        img.style.width = '100%';
+        img.style.height = '100%';
+        img.style.objectFit = 'cover';
+
+        img.onload = function () {
+            $('#rule-smirks-viz').append(img);
+        };
+
+        img.onerror = function () {
+            error_tpl = `
+                <div class="alert alert-error" role="alert">
+                    <h4 class="alert-heading">Could not render SMIRKS!</h4>
+                    <p>Could not render SMIRKS - Have you entered a valid SMIRKS?</a>
+                    </p>
+                </div>`
+            $('#rule-smirks-viz').append(error_tpl);
+        };
+    });
+
     $('#new_rule_modal_form_submit').on('click', function(e) {
         e.preventDefault();
         $(this).prop("disabled",true);
-
-        k = getKetcher('new_rule_ketcher');
-        $('#rule-smirks').val(k.getSmiles());
-
         // submit form
         $('#new_rule_modal_form').submit();
     });

templates/modals/objects/add_pathway_edge_modal.html

@@ -0,0 +1,126 @@
+{% load static %}
+<div class="modal fade bs-modal-lg" id="add_pathway_edge_modal" tabindex="-1" aria-labelledby="add_pathway_edge_modal"
+     aria-modal="true"
+     role="dialog">
+    <div class="modal-dialog modal-lg">
+        <div class="modal-content">
+            <div class="modal-header">
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+                <h4 class="modal-title">Add a Reaction</h4>
+            </div>
+            <div class="modal-body">
+                <form id="add_pathway_edge_modal_form" accept-charset="UTF-8"
+                      action="{% url 'package pathway edge list' meta.current_package.uuid pathway.uuid %}"
+                      data-remote="true" method="post">
+                    {% csrf_token %}
+                    <label for="edge-name">Name</label>
+                    <input id="edge-name" class="form-control" name="edge-name" placeholder="Name"/>
+                    <label for="edge-description">Description</label>
+                    <input id="edge-description" class="form-control" name="edge-description" placeholder="Description"/>
+                    <p></p>
+                    <div class="row">
+                        <div class="col-xs-5">
+                            <legend>Substrate(s)</legend>
+                        </div>
+                        <div class="col-xs-2">
+
+                        </div>
+                        <div class="col-xs-5">
+                            <legend>Product(s)</legend>
+                        </div>
+                    </div>
+                    <div class="row">
+                        <div class="col-xs-5">
+                            <select id="add_pathway_edge_substrates" name="edge-substrates"
+                                    data-actions-box='true' class="form-control" multiple data-width='100%'>
+                                {% for n in pathway.nodes %}
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
+                                {% endfor %}
+                            </select>
+                        </div>
+                        <div class="col-xs-2" style="display: flex; justify-content: center; align-items: center;">
+                            <i class="glyphicon glyphicon-arrow-right"></i>
+                        </div>
+                        <div class="col-xs-5">
+                            <select id="add_pathway_edge_products" name="edge-products"
+                                    data-actions-box='true' class="form-control" multiple data-width='100%'>
+                                {% for n in pathway.nodes %}
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
+                                {% endfor %}
+                            </select>
+                        </div>
+                    </div>
+                    <div class="row">
+                        <p></p>
+                        <div class="col-xs-12" id="reaction_image">
+
+                        </div>
+                    </div>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+                </button>
+                <button type="button" class="btn btn-primary" id="add_pathway_edge_modal_form_submit">Submit</button>
+            </div>
+        </div>
+    </div>
+
+</div>
+<script>
+
+    function reactionImage() {
+        var substrates = [];
+        $('#add_pathway_edge_substrates option:selected').each(function () {
+          var smiles = $(this).data('smiles'); // read data-smiles attribute
+          substrates.push(smiles);
+        });
+
+        var products = []
+        $('#add_pathway_edge_products option:selected').each(function () {
+          var smiles = $(this).data('smiles'); // read data-smiles attribute
+          products.push(smiles);
+        });
+
+        if (substrates.length > 0 && products.length > 0) {
+            reaction = substrates.join('.') + ">>" + products.join('.');
+            $('#reaction_image').empty();
+            $('#reaction_image').append(
+                "<img width='100%' src='{% url 'depict' %}?smirks=" + encodeURIComponent(reaction) +"'>"
+            );
+        }
+    }
+
+    $(function () {
+        $("#add_pathway_edge_substrates").selectpicker();
+        $("#add_pathway_edge_products").selectpicker();
+
+        $("#add_pathway_edge_substrates").on('change', function (e) {
+            reactionImage();
+        })
+
+        $("#add_pathway_edge_products").on('change', function (e) {
+            reactionImage();
+        })
+
+        $(function () {
+            $('#add_pathway_edge_modal_form_submit').on('click', function (e) {
+                e.preventDefault();
+                $(this).prop("disabled", true);
+
+
+                // submit form
+                $('#add_pathway_edge_modal_form').submit();
+            });
+        });
+
+    });
+
+</script>
+
+
+
+
+

templates/modals/objects/add_pathway_node_modal.html

@@ -0,0 +1,78 @@
+{% load static %}
+<div class="modal fade bs-modal-lg" id="add_pathway_node_modal" tabindex="-1" aria-labelledby="add_pathway_node_modal" aria-modal="true"
+     role="dialog">
+    <div class="modal-dialog modal-lg">
+        <div class="modal-content">
+            <div class="modal-header">
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+                <h4 class="modal-title">Add a Node</h4>
+            </div>
+            <div class="modal-body">
+                <form id="add_pathway_node_modal_form" accept-charset="UTF-8" action="{% url 'package pathway node list' meta.current_package.uuid pathway.uuid %}" data-remote="true" method="post">
+                    {% csrf_token %}
+                    <label for="node-name">Name</label>
+                    <input id="node-name" class="form-control" name="node-name" placeholder="Name"/>
+                    <label for="node-description">Description</label>
+                    <input id="node-description" class="form-control" name="node-description" placeholder="Description"/>
+                    <label for="node-smiles">SMILES</label>
+                    <input type="text" class="form-control" name="node-smiles" placeholder="SMILES" id="node-smiles">
+                    <p></p>
+                    <div>
+                        <iframe id="add_node_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
+                                height="510"></iframe>
+                    </div>
+                    <p></p>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+                </button>
+                <button type="button" class="btn btn-primary" id="add_pathway_node_modal_form_submit">Submit</button>
+            </div>
+        </div>
+    </div>
+
+</div>
+<script>
+
+function newStructureModalketcherToNewStructureModalTextInput() {
+    $('#node-smiles').val(this.ketcher.getSmiles());
+}
+
+$(function() {
+
+    $('#add_node_ketcher').on('load', function() {
+        const checkKetcherReady = () => {
+            win = this.contentWindow
+            if (win.ketcher && 'editor' in win.ketcher) {
+                win.ketcher.editor.event.change.handlers.push({
+                    once: false,
+                    priority: 0,
+                    f: newStructureModalketcherToNewStructureModalTextInput,
+                    ketcher: win.ketcher
+                });
+            } else {
+                setTimeout(checkKetcherReady, 100);
+            }
+        };
+
+        checkKetcherReady();
+    })
+
+    $(function() {
+        $('#add_pathway_node_modal_form_submit').on('click', function(e) {
+            e.preventDefault();
+            $(this).prop("disabled",true);
+
+
+
+            // submit form
+            $('#add_pathway_node_modal_form').submit();
+        });
+    });
+
+});
+
+</script>

templates/modals/objects/delete_model_modal.html

@@ -0,0 +1,35 @@
+{% load static %}
+<!-- Delete Model -->
+<div id="delete_model_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <h3 class="modal-title">Delete Model</h3>
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+            </div>
+            <div class="modal-body">
+                Deletes the Model.
+                <form id="delete-model-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+                    {% csrf_token %}
+                    <input type="hidden" id="hidden" name="hidden" value="delete-model"/>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="delete-model-modal-submit">Delete</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+    $(function () {
+
+        $('#delete-model-modal-submit').click(function (e) {
+            e.preventDefault();
+            $('#delete-model-modal-form').submit();
+        });
+
+    })
+</script>

templates/modals/objects/delete_node_modal.html

@@ -0,0 +1,35 @@
+{% load static %}
+<!-- Delete Node -->
+<div id="delete_node_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <h3 class="modal-title">Delete Node</h3>
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+            </div>
+            <div class="modal-body">
+                Deletes the Node as well as ingoing and outgoing edges.
+                <form id="delete-node-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+                    {% csrf_token %}
+                    <input type="hidden" id="hidden" name="hidden" value="delete-node"/>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="delete-node-modal-submit">Delete</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+    $(function () {
+
+        $('#delete-node-modal-submit').click(function (e) {
+            e.preventDefault();
+            $('#delete-node-modal-form').submit();
+        });
+
+    })
+</script>

templates/modals/objects/delete_pathway_edge_modal.html

@@ -0,0 +1,65 @@
+{% load static %}
+<!-- Delete Edge -->
+<div id="delete_pathway_edge_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <h3 class="modal-title">Delete Edge</h3>
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+            </div>
+            <div class="modal-body">
+                Deletes the Edge. Nodes referenced by this edge will remain.
+                <p></p>
+                <form id="delete-pathway-edge-modal-form" accept-charset="UTF-8" action="" data-remote="true"
+                      method="post">
+                    {% csrf_token %}
+                    <select id="delete_pathway_edge_edges" name="edge-url"
+                            data-actions-box='true' class="form-control" data-width='100%'>
+                        <option value="" disabled selected>Select Reaction to delete</option>
+                        {% for e in pathway.edges %}
+                            <option value="{{ e.url }}">{{ e.edge_label.name }}</option>
+                        {% endfor %}
+                    </select>
+                    <input type="hidden" id="hidden" name="hidden" value="delete-edge"/>
+                </form>
+                <p></p>
+                <div id="delete_pathway_edge_image"></div>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="delete-pathway-edge-modal-submit">Delete</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+    $(function () {
+        $("#delete_pathway_edge_edges").selectpicker();
+
+        $("#delete_pathway_edge_edges").on('change', function (e) {
+            edge_url = $('#delete_pathway_edge_edges option:selected').val()
+
+            if (edge_url !== "") {
+                $('#delete_pathway_edge_image').empty();
+                $('#delete_pathway_edge_image').append(
+                    "<img width='100%' src='" + edge_url + "?image=svg'>"
+                );
+            }
+        })
+
+        $('#delete-pathway-edge-modal-submit').click(function (e) {
+            e.preventDefault();
+            edge_url = $('#delete_pathway_edge_edges option:selected').val()
+
+            if (edge_url === "") {
+                return;
+            }
+
+            $('#delete-pathway-edge-modal-form').attr('action', edge_url)
+            $('#delete-pathway-edge-modal-form').submit();
+        });
+
+    })
+</script>

templates/modals/objects/delete_pathway_modal.html

@@ -0,0 +1,35 @@
+{% load static %}
+<!-- Delete Pathway -->
+<div id="delete_pathway_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <h3 class="modal-title">Delete Pathway</h3>
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+            </div>
+            <div class="modal-body">
+                Deletes the Pathway together with all Nodes and Edges.
+                <form id="delete-pathway-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+                    {% csrf_token %}
+                    <input type="hidden" id="hidden" name="hidden" value="delete-pathway"/>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="delete-pathway-modal-submit">Delete</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+    $(function () {
+
+        $('#delete-pathway-modal-submit').click(function (e) {
+            e.preventDefault();
+            $('#delete-pathway-modal-form').submit();
+        });
+
+    })
+</script>

templates/modals/objects/delete_pathway_node_modal.html

@@ -0,0 +1,65 @@
+{% load static %}
+<!-- Delete Node -->
+<div id="delete_pathway_node_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <h3 class="modal-title">Delete Node</h3>
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+            </div>
+            <div class="modal-body">
+                Deletes the Node. Edges having this Node as Substrate or Product will be removed as well.
+                <p></p>
+                <form id="delete-pathway-node-modal-form" accept-charset="UTF-8" action="" data-remote="true"
+                      method="post">
+                    {% csrf_token %}
+                    <select id="delete_pathway_node_nodes" name="node-url"
+                            data-actions-box='true' class="form-control" data-width='100%'>
+                        <option value="" disabled selected>Select Compound to delete</option>
+                        {% for n in pathway.nodes %}
+                            <option value="{{ n.url }}">{{ n.default_node_label.name }}</option>
+                        {% endfor %}
+                    </select>
+                    <input type="hidden" id="hidden" name="hidden" value="delete-node"/>
+                </form>
+                <p></p>
+                <div id="delete_pathway_node_image"></div>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="delete-pathway-node-modal-submit">Delete</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+    $(function () {
+        $("#delete_pathway_node_nodes").selectpicker();
+
+        $("#delete_pathway_node_nodes").on('change', function (e) {
+            node_url = $('#delete_pathway_node_nodes option:selected').val()
+
+            if (node_url !== "") {
+                $('#delete_pathway_node_image').empty();
+                $('#delete_pathway_node_image').append(
+                    "<img width='100%' src='" + node_url + "?image=svg'>"
+                );
+            }
+        })
+
+        $('#delete-pathway-node-modal-submit').click(function (e) {
+            e.preventDefault();
+            node_url = $('#delete_pathway_node_nodes option:selected').val()
+
+            if (node_url === "") {
+                return;
+            }
+
+            $('#delete-pathway-node-modal-form').attr('action', node_url)
+            $('#delete-pathway-node-modal-form').submit();
+        });
+
+    })
+</script>

templates/modals/objects/delete_reaction_modal.html

@@ -0,0 +1,35 @@
+{% load static %}
+<!-- Delete Reaction -->
+<div id="delete_reaction_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <h3 class="modal-title">Delete Reaction</h3>
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+            </div>
+            <div class="modal-body">
+                Deletes the Reaction.
+                <form id="delete-reaction-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+                    {% csrf_token %}
+                    <input type="hidden" id="hidden" name="hidden" value="delete-reaction"/>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="delete-reaction-modal-submit">Delete</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+    $(function () {
+
+        $('#delete-reaction-modal-submit').click(function (e) {
+            e.preventDefault();
+            $('#delete-reaction-modal-form').submit();
+        });
+
+    })
+</script>

templates/modals/objects/edit_compound_modal.html

@@ -4,13 +4,13 @@
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
-                <h5 class="modal-title">Create a Compound</h5>
+                <h5 class="modal-title">Edit Compound</h5>
                 <button type="button" class="close" data-dismiss="modal" aria-label="Close">
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
-                <p>Edit a Compound.</p>
+                <p>Edit Compound.</p>
                 <form id="edit-compound-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
                     {% csrf_token %}
                     <p>

templates/modals/objects/edit_node_modal.html

@@ -0,0 +1,46 @@
+{% load static %}
+<!-- Edit Node -->
+<div id="edit_node_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <h5 class="modal-title">Edit Node</h5>
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+            </div>
+            <div class="modal-body">
+                <p>Edit Node.</p>
+                <form id="edit-node-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+                    {% csrf_token %}
+                    <p>
+                        <label for="node-name">Name</label>
+                        <input id="node-name" class="form-control" name="node-name" value="{{ node.name}}">
+                    </p>
+                    <p>
+                        <label for="node-description">Description</label>
+                        <input id="node-description" type="text" class="form-control"
+                               value="{{ node.description }}"
+                               name="node-description">
+                    </p>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="edit-node-modal-submit">Create</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+$(function() {
+
+    $('#edit-node-modal-submit').click(function(e){
+        e.preventDefault();
+        $('#edit-node-modal-form').submit();
+    });
+
+});
+
+
+</script>

templates/modals/objects/edit_pathway_modal.html

@@ -0,0 +1,43 @@
+{% load static %}
+<!-- Edit Pathway -->
+<div id="edit_pathway_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <h5 class="modal-title">Edit Pathway</h5>
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+            </div>
+            <div class="modal-body">
+                <p>Edit Pathway.</p>
+                <form id="edit-pathway-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+                    {% csrf_token %}
+                    <p>
+                        <label for="pathway-name">Name</label>
+                        <input id="pathway-name" class="form-control" name="pathway-name" value="{{ pathway.name }}">
+                    </p>
+                    <p>
+                        <label for="pathway-description">Description</label>
+                        <textarea id="pathway-description" type="text" class="form-control" name="pathway-description"
+                                  rows="10">{{ pathway.description }}</textarea>
+                    </p>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="edit-pathway-modal-submit">Update</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+$(function() {
+
+    $('#edit-pathway-modal-submit').click(function(e){
+        e.preventDefault();
+        $('#edit-pathway-modal-form').submit();
+    });
+
+})
+</script>

templates/modals/objects/edit_reaction_modal.html

@@ -10,7 +10,6 @@
                 <h3 class="modal-title">Update Reaction</h3>
             </div>
             <div class="modal-body">
-<!--                <p>Edit a Reaction.</p>-->
                 <form id="edit-reaction-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
                     {% csrf_token %}
                     <p>

templates/modals/objects/edit_rule_modal.html

@@ -0,0 +1,44 @@
+{% load static %}
+<!-- Edit Rule -->
+<div id="edit_rule_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+                <h3 class="modal-title">Update Rule</h3>
+            </div>
+            <div class="modal-body">
+                <form id="edit-rule-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+                    {% csrf_token %}
+                    <p>
+                        <label for="rule-name">Name</label>
+                        <input id="rule-name" class="form-control" name="rule-name" value="{{ rule.name }}">
+                    </p>
+                    <p>
+                        <label for="rule-description">Description</label>
+                        <input id="rule-description" type="text" class="form-control"
+                               value="{{ rule.description }}" name="rule-description">
+                    </p>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="edit-rule-modal-submit">Update</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+$(function() {
+
+    $('#edit-rule-modal-submit').click(function(e){
+        e.preventDefault();
+        $('#edit-rule-modal-form').submit();
+    });
+
+});
+
+
+</script>

templates/modals/objects/manage_api_token_modal.html

@@ -70,7 +70,6 @@ $(function() {
         e.preventDefault();
 
         const formData = $('#request_api_token_form').serialize();
-        console.log(formData)
         $.post('', formData, function(response) {
             $('#new-token-pre').text(response.raw_token);
             $('#new-token').show();

templates/objects/composite_rule.html

@@ -11,7 +11,7 @@
         <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
             {{ rule.name }}
             <div id="actionsButton"
-                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;"
+                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
                                      aria-haspopup="true" aria-expanded="false"><span
                     class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span

templates/objects/compound.html

@@ -2,135 +2,141 @@
 
 {% block content %}
 
-{% block action_modals %}
+    {% block action_modals %}
-{% include "modals/objects/edit_compound_modal.html" %}
+        {% include "modals/objects/edit_compound_modal.html" %}
-{% include "modals/objects/add_structure_modal.html" %}
+        {% include "modals/objects/add_structure_modal.html" %}
-{% include "modals/objects/delete_compound_modal.html" %}
+        {% include "modals/objects/delete_compound_modal.html" %}
-{% endblock action_modals %}
+    {% endblock action_modals %}
 
-<div class="panel-group" id="compound-detail">
+    <div class="panel-group" id="compound-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">
-            {{ compound.name }}
+                {{ compound.name }}
-            <div id="actionsButton"
+                <div id="actionsButton"
-                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;"
+                     style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
-                 class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
+                     class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
-                                     aria-haspopup="true" aria-expanded="false"><span
+                                         aria-haspopup="true" aria-expanded="false"><span
-                    class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
+                        class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
-                    style="padding-right:1em"></span></a>
+                        style="padding-right:1em"></span></a>
-                <ul id="actionsList" class="dropdown-menu">
+                    <ul id="actionsList" class="dropdown-menu">
-                    {% block actions %}
+                        {% block actions %}
-                    {% include "actions/objects/compound.html" %}
+                            {% include "actions/objects/compound.html" %}
-                    {% endblock %}
+                        {% endblock %}
-                </ul>
+                    </ul>
-            </div>
-        </div>
-        <div class="panel-body">
-            <p>
-                The structures stored in this compound can be found at  <a target="_blank" href="{{compound.url}}/structure" role="button">Compound structures &gt;&gt;</a>
-            </p>
-        </div>
-
-        <!-- Description -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
-                <a id="compound-desc-link" data-toggle="collapse" data-parent="#compound-detail"
-                   href="#compound-desc">Description</a>
-            </h4>
-        </div>
-        <div id="compound-desc" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                {{ compound.description }}
-            </div>
-        </div>
-
-        <!-- Image -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
-                <a id="compound-image-link" data-toggle="collapse" data-parent="#compound-detail"
-                   href="#compound-image">Image Representation</a>
-            </h4>
-        </div>
-        <div id="compound-image" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                <div id="image-div" align="center">
-                    {{ compound.default_structure.as_svg|safe }}
                 </div>
             </div>
-        </div>
+            <div class="panel-body">
-
+                <p>
-        <!-- SMILES -->
+                    The structures stored in this compound can be found at <a target="_blank"
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                                                                              href="{{ compound.url }}/structure"
-            <h4 class="panel-title">
+                                                                              role="button">Compound structures
-                <a id="compound-smiles-link" data-toggle="collapse" data-parent="#compound-detail"
+                    &gt;&gt;</a>
-                   href="#compound-smiles">SMILES Representation</a>
+                </p>
-            </h4>
-        </div>
-        <div id="compound-smiles" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                {{ compound.default_structure.smiles }}
             </div>
-        </div>
 
-        <!-- Canonical SMILES -->
+            <!-- Description -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
+                <h4 class="panel-title">
-                <a id="compound-canonical-smiles-link" data-toggle="collapse" data-parent="#compound-detail"
+                    <a id="compound-desc-link" data-toggle="collapse" data-parent="#compound-detail"
-                   href="#compound-canonical-smiles">Canonical SMILES Representation</a>
+                       href="#compound-desc">Description</a>
-            </h4>
+                </h4>
-        </div>
-        <div id="compound-canonical-smiles" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                {{ compound.default_structure.canonical_smiles }}
             </div>
-        </div>
+            <div id="compound-desc" class="panel-collapse collapse in">
-
+                <div class="panel-body list-group-item">
-        <!-- InChiKey -->
+                    {{ compound.description }}
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                </div>
-            <h4 class="panel-title">
-                <a id="compound-inchi-link" data-toggle="collapse" data-parent="#compound-detail"
-                   href="#compound-inchi">InChIKey</a>
-            </h4>
-        </div>
-        <div id="compound-inchi" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                {{ compound.default_structure.InChIKey }}
             </div>
-        </div>
 
-        <!-- Reactions -->
+            <!-- Image -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
+                <h4 class="panel-title">
-                <a id="compound-reaction-link" data-toggle="collapse" data-parent="#compound-detail"
+                    <a id="compound-image-link" data-toggle="collapse" data-parent="#compound-detail"
-                   href="#compound-reaction">Reactions</a>
+                       href="#compound-image">Image Representation</a>
-            </h4>
+                </h4>
-        </div>
-        <div id="compound-reaction" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                {% for r in compound.related_reactions %}
-                <a class="list-group-item" href="{{ r.url }}">{{ r.name }} <i>({{ r.package.name }})</i></a>
-                {% endfor %}
             </div>
-        </div>
+            <div id="compound-image" class="panel-collapse collapse in">
-
+                <div class="panel-body list-group-item">
-        <!-- Pathways -->
+                    <div id="image-div" align="center">
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                        {{ compound.default_structure.as_svg|safe }}
-            <h4 class="panel-title">
+                    </div>
-                <a id="compound-pathway-link" data-toggle="collapse" data-parent="#compound-detail"
+                </div>
-                   href="#compound-pathway">Pathways</a>
-            </h4>
-        </div>
-        <div id="compound-pathway" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                {% for r in compound.related_pathways %}
-                <a class="list-group-item" href="{{ r.url }}">{{ r.name }} <i>({{ r.package.name }})</i></a>
-                {% endfor %}
             </div>
-        </div>
 
-        <!-- External Identifiers -->
+            <!-- SMILES -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="compound-smiles-link" data-toggle="collapse" data-parent="#compound-detail"
+                       href="#compound-smiles">SMILES Representation</a>
+                </h4>
+            </div>
+            <div id="compound-smiles" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {{ compound.default_structure.smiles }}
+                </div>
+            </div>
+
+            <!-- Canonical SMILES -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="compound-canonical-smiles-link" data-toggle="collapse" data-parent="#compound-detail"
+                       href="#compound-canonical-smiles">Canonical SMILES Representation</a>
+                </h4>
+            </div>
+            <div id="compound-canonical-smiles" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {{ compound.default_structure.canonical_smiles }}
+                </div>
+            </div>
+
+            <!-- InChiKey -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="compound-inchi-link" data-toggle="collapse" data-parent="#compound-detail"
+                       href="#compound-inchi">InChIKey</a>
+                </h4>
+            </div>
+            <div id="compound-inchi" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {{ compound.default_structure.inchikey }}
+                </div>
+            </div>
+
+            <!-- Reactions -->
+            {% if compound.related_reactions %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="compound-reaction-link" data-toggle="collapse" data-parent="#compound-detail"
+                           href="#compound-reaction">Reactions</a>
+                    </h4>
+                </div>
+                <div id="compound-reaction" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for r in compound.related_reactions %}
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }} <i>({{ r.package.name }})</i></a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
+            <!-- Pathways -->
+            {% if compound.related_pathways %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="compound-pathway-link" data-toggle="collapse" data-parent="#compound-detail"
+                           href="#compound-pathway">Pathways</a>
+                    </h4>
+                </div>
+                <div id="compound-pathway" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for r in compound.related_pathways %}
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }} <i>({{ r.package.name }})</i></a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+            <!-- External Identifiers -->
+
+        </div>
 
     </div>
-
-</div>
 {% endblock content %}

templates/objects/compound_structure.html

@@ -11,7 +11,7 @@
         <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
             {{ compound_structure.name }}
             <div id="actionsButton"
-                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;"
+                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
                                      aria-haspopup="true" aria-expanded="false"><span
                     class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span

templates/objects/group.html

@@ -13,7 +13,7 @@
         <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
             {{ group.name }}
             <div id="actionsButton"
-                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;"
+                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
                                      aria-haspopup="true" aria-expanded="false"><span
                     class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span

templates/objects/model.html

@@ -1,263 +1,322 @@
 {% extends "framework.html" %}
 {% load static %}
-
+{% load envipytags %}
 {% block content %}
 
-{% block action_modals %}
+    {% block action_modals %}
-{% endblock action_modals %}
+        {% include "modals/objects/delete_model_modal.html" %}
+    {% endblock action_modals %}
 
-<!-- Include required libs -->
+    <!-- Include required libs -->
-<script src="https://d3js.org/d3.v5.min.js"></script>
+    <script src="https://d3js.org/d3.v5.min.js"></script>
-<script src="https://cdn.jsdelivr.net/npm/c3@0.7.20/c3.min.js"></script>
+    <script src="https://cdn.jsdelivr.net/npm/c3@0.7.20/c3.min.js"></script>
-<link href="https://cdn.jsdelivr.net/npm/c3@0.7.20/c3.min.css" rel="stylesheet">
+    <link href="https://cdn.jsdelivr.net/npm/c3@0.7.20/c3.min.css" rel="stylesheet">
 
-<div class="panel-group" id="model-detail">
+    <div class="panel-group" id="model-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">
-            {{ model.name }}
+                {{ model.name }}
-            <div id="actionsButton"
+                <div id="actionsButton"
-                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;"
+                     style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
-                 class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
+                     class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
-                                     aria-haspopup="true" aria-expanded="false"><span
+                                         aria-haspopup="true" aria-expanded="false"><span
-                    class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
+                        class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
-                    style="padding-right:1em"></span></a>
+                        style="padding-right:1em"></span></a>
-                <ul id="actionsList" class="dropdown-menu">
+                    <ul id="actionsList" class="dropdown-menu">
-                    {% block actions %}
+                        {% block actions %}
-                    {% endblock %}
+                            {% include "actions/objects/model.html" %}
-                </ul>
+                        {% endblock %}
-            </div>
+                    </ul>
-        </div>
-        <div class="panel-body">
-            <p> {{ model.description }} </p>
-        </div>
-        <!-- Predict Panel -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
-                <a id="predict-smiles-link" data-toggle="collapse" data-parent="#model-detail"
-                   href="#predict-smiles">Predict</a>
-            </h4>
-        </div>
-        <div id="predict-smiles" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                <div class="input-group">
-                <input id="smiles-to-predict" type="text" class="form-control" placeholder="CCN(CC)C(=O)C1=CC(=CC=C1)C">
-                    <span class="input-group-btn">
-                        <button class="btn btn-default" type="submit" id="predict-button">Predict!</button>
-                    </span>
                 </div>
-                <div id="loading"></div>
-                <div id="predictResultTable"></div>
             </div>
-        </div>
+            <div class="panel-body">
-        <!-- End Predict Panel       -->
+                <p> {{ model.description }} </p>
-        {% if model.model_status == 'FINISHED' %}
+            </div>
-        <!-- Single Gen Curve Panel -->
+            {% if model|classname == 'MLRelativeReasoning' %}
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <!-- Rule Packages -->
-            <h4 class="panel-title">
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-                <a id="sg-curve-link" data-toggle="collapse" data-parent="#model-detail"
+                    <h4 class="panel-title">
-                   href="#sg-curve">Predict</a>
+                        <a id="rule-package-link" data-toggle="collapse" data-parent="#model-detail"
-            </h4>
+                           href="#rule-package">Rule Packages</a>
-        </div>
+                    </h4>
-        <div id="sg-curve" class="panel-collapse collapse in">
+                </div>
-            <div class="panel-body list-group-item">
+                <div id="rule-package" class="panel-collapse collapse in">
-                <!-- Center container contents -->
+                    <div class="panel-body list-group-item">
-                <div class="container" style="display: flex;justify-content: center;">
+                        {% for p in model.rule_packages.all %}
-                    <div id="sg-curve-plotdiv" class="chart">
+                            <a class="list-group-item" href="{{ p.url }}">{{ p.name }}</a>
-                        <div id="sg-chart"></div>
+                        {% endfor %}
                     </div>
                 </div>
-
+                <!-- Reaction Packages -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="reaction-package-link" data-toggle="collapse" data-parent="#model-detail"
+                           href="#reaction-package">Rule Packages</a>
+                    </h4>
+                </div>
+                <div id="reaction-package" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for p in model.data_packages.all %}
+                            <a class="list-group-item" href="{{ p.url }}">{{ p.name }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+                {% if model.eval_packages.all|length > 0 %}
+                    <!-- Eval Packages -->
+                    <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                        <h4 class="panel-title">
+                            <a id="eval-package-link" data-toggle="collapse" data-parent="#model-detail"
+                               href="#eval-package">Rule Packages</a>
+                        </h4>
+                    </div>
+                    <div id="eval-package" class="panel-collapse collapse in">
+                        <div class="panel-body list-group-item">
+                            {% for p in model.eval_packages.all %}
+                                <a class="list-group-item" href="{{ p.url }}">{{ p.name }}</a>
+                            {% endfor %}
+                        </div>
+                    </div>
+                {% endif %}
+                <!-- Model Status -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="model-status-link" data-toggle="collapse" data-parent="#model-detail"
+                           href="#model-status">Model Status</a>
+                    </h4>
+                </div>
+                <div id="model-status" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {{ model.status }}
+                    </div>
+                </div>
+            {% endif %}
+            <!-- Predict Panel -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="predict-smiles-link" data-toggle="collapse" data-parent="#model-detail"
+                       href="#predict-smiles">Predict</a>
+                </h4>
             </div>
-        </div>
+            <div id="predict-smiles" class="panel-collapse collapse in">
-        <script>
+                <div class="panel-body list-group-item">
-                $(function() {
+                    <div class="input-group">
-                    if(!($('#sg-chart').length > 0)) {
+                        <input id="smiles-to-predict" type="text" class="form-control"
-                        return;
+                               placeholder="CCN(CC)C(=O)C1=CC(=CC=C1)C">
-                    }
+                        <span class="input-group-btn">
-                    console.log($('#sg-chart').length)
+                        <button class="btn btn-default" type="submit" id="predict-button">Predict!</button>
-                    //$('#sg-curve-plotdiv').empty();
+                    </span>
+                    </div>
+                    <div id="loading"></div>
+                    <div id="predictResultTable"></div>
+                </div>
+            </div>
+            <!-- End Predict Panel       -->
+            {% if model.model_status == 'FINISHED' %}
+                <!-- Single Gen Curve Panel -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="sg-curve-link" data-toggle="collapse" data-parent="#model-detail"
+                           href="#sg-curve">Precision Recall Curve</a>
+                    </h4>
+                </div>
+                <div id="sg-curve" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        <!-- Center container contents -->
+                        <div class="container" style="display: flex;justify-content: center;">
+                            <div id="sg-curve-plotdiv" class="chart">
+                                <div id="sg-chart"></div>
+                            </div>
+                        </div>
 
-                    var x = ['Recall'];
+                    </div>
-                    var y = ['Precision'];
+                </div>
-                    var thres = ['threshold'];
+                <script>
+                    $(function () {
+                        if (!($('#sg-chart').length > 0)) {
+                            return;
+                        }
 
-                    // Compare function for the given array
+                        var x = ['Recall'];
-                    function compare(a, b) {
+                        var y = ['Precision'];
-                        if (a.threshold < b.threshold)
+                        var thres = ['threshold'];
+
+                        // Compare function for the given array
+                        function compare(a, b) {
+                            if (a.threshold < b.threshold)
+                                return -1;
+                            else if (a.threshold > b.threshold)
+                                return 1;
+                            else
+                                return 0;
+                        }
+
+                        function getIndexForValue(data, val, val_name) {
+                            for (var idx in data) {
+                                if (data[idx][val_name] == val) {
+                                    return idx;
+                                }
+                            }
                             return -1;
-                        else if (a.threshold > b.threshold)
-                            return 1;
-                        else
-                            return 0;
-                    }
-
-                    function getIndexForValue(data, val, val_name) {
-                        for(var idx in data) {
-                            if(data[idx][val_name] == val) {
-                                return idx;
-                            }
                         }
-                        return -1;
-                    }
 
-                    var data = {{ model.pr_curve|safe }}
+                        var data = {{ model.pr_curve|safe }}
-                    var dataLength = Object.keys(data).length;
+                        var dataLength = Object.keys(data).length;
-                    data.sort(compare);
+                        data.sort(compare);
 
-                    for (var idx in data) {
+                        for (var idx in data) {
-                        var d = data[idx];
+                            var d = data[idx];
-                        x.push(d.recall);
+                            x.push(d.recall);
-                        y.push(d.precision);
+                            y.push(d.precision);
-                        thres.push(d.threshold);
+                            thres.push(d.threshold);
-                    }
+                        }
-                    var chart = c3.generate({
+                        var chart = c3.generate({
-                        bindto: '#sg-chart',
+                            bindto: '#sg-chart',
-                        data: {
+                            data: {
-                            onclick: function (d, e) {
+                                onclick: function (d, e) {
-                                var idx = d.index;
+                                    var idx = d.index;
-                                var thresh = data[dataLength-idx-1].threshold;
+                                    var thresh = data[dataLength - idx - 1].threshold;
 
-                                //onclick(thresh)
+                                    //onclick(thresh)
 
-                            },
-                            x: 'Recall',
-                            y: 'Precision',
-                            columns: [
-                                x,
-                                y,
-                                //thres
-                            ]
-                        },
-                        size: {
-                            height: 400, // TODO: Make variable to current modal width
-                            width: 480
-                        },
-                        axis: {
-                            x: {
-                                max: 1,
-                                min: 0,
-                                label: 'Recall',
-                                padding: 0,
-                                tick: {
-                                    fit: true,
-                                    values: [0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
-                                }
-                            },
-                            y: {
-                                max: 1,
-                                min: 0,
-                                label: 'Precision',
-                                padding: 0,
-                                tick: {
-                                    fit: true,
-                                    values: [0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
-                                }
-                            }
-                        },
-                        point: {
-                            r: 4
-                        },
-                        tooltip: {
-                            format: {
-                                title: function (recall) {
-                                    idx = getIndexForValue(data, recall, "recall");
-                                    if(idx != -1) {
-                                        return "Threshold: " + data[idx].threshold;
-                                    }
-                                    return "";
                                 },
-                                value: function (precision, ratio, id) {
+                                x: 'Recall',
-                                    return undefined;
+                                y: 'Precision',
+                                columns: [
+                                    x,
+                                    y,
+                                    //thres
+                                ]
+                            },
+                            size: {
+                                height: 400, // TODO: Make variable to current modal width
+                                width: 480
+                            },
+                            axis: {
+                                x: {
+                                    max: 1,
+                                    min: 0,
+                                    label: 'Recall',
+                                    padding: 0,
+                                    tick: {
+                                        fit: true,
+                                        values: [0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
+                                    }
+                                },
+                                y: {
+                                    max: 1,
+                                    min: 0,
+                                    label: 'Precision',
+                                    padding: 0,
+                                    tick: {
+                                        fit: true,
+                                        values: [0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
+                                    }
                                 }
+                            },
+                            point: {
+                                r: 4
+                            },
+                            tooltip: {
+                                format: {
+                                    title: function (recall) {
+                                        idx = getIndexForValue(data, recall, "recall");
+                                        if (idx != -1) {
+                                            return "Threshold: " + data[idx].threshold;
+                                        }
+                                        return "";
+                                    },
+                                    value: function (precision, ratio, id) {
+                                        return undefined;
+                                    }
+                                }
+                            },
+                            zoom: {
+                                enabled: true
                             }
-                        },
+                        });
-                        zoom: {
-                            enabled: true
-                        }
                     });
-                });
+                </script>
-        </script>
+                <!-- End Single Gen Curve Panel       -->
-        <!-- End Single Gen Curve Panel       -->
+            {% endif %}
-        {% endif %}
+        </div>
     </div>
-</div>
 
-<script>
+    <script>
 
-    function handleResponse(data) {
+        function handleResponse(data) {
-        res = "<table class='table table-striped'>"
+            res = "<table class='table table-striped'>"
-        res += "<thead>"
+            res += "<thead>"
-        res += "<th scope='col'>#</th>"
+            res += "<th scope='col'>#</th>"
 
-        columns = ['products', 'image', 'probability', 'btrule']
+            columns = ['products', 'image', 'probability', 'btrule']
 
-        for(col in columns) {
+            for (col in columns) {
-            res += "<th scope='col'>" + columns[col] + "</th>"
+                res += "<th scope='col'>" + columns[col] + "</th>"
-        }
-
-        res += "</thead>"
-        res += "<tbody>"
-        var cnt = 1;
-        for(transformation in data) {
-            res += "<tr>"
-            res += "<th scope='row'>" + cnt + "</th>"
-            res += "<th scope='row'>" + data[transformation]['products'][0].join(', ') + "</th>"
-            res += "<th scope='row'>" + "<img width='400' src='{% url 'depict' %}?smiles=" + encodeURIComponent(data[transformation]['products'][0].join('.')) + "'></th>"
-            res += "<th scope='row'>" + data[transformation]['probability'].toFixed(3) + "</th>"
-            if (data[transformation]['btrule'] != null) {
-                res += "<th scope='row'>" + "<a href='" + data[transformation]['btrule']['url'] + "'>" + data[transformation]['btrule']['name'] + "</a>" + "</th>"
-            } else {
-               res += "<th scope='row'>N/A</th>"
-            }
-            res += "</tr>"
-            cnt += 1;
-        }
-
-        res += "</tbody>"
-        res += "</table>"
-        $("#predictResultTable").append(res);
-    }
-
-    function clear() {
-        $("#predictResultTable").removeClass("alert alert-danger");
-        $("#predictResultTable").empty();
-    }
-
-    if($('#predict-button').length > 0) {
-        $("#predict-button").on("click", function(e) {
-            e.preventDefault();
-
-            data = {
-                "smiles": $("#smiles-to-predict").val(),
-                "classify": "ILikeCats!"
             }
 
-            clear();
+            res += "</thead>"
+            res += "<tbody>"
+            var cnt = 1;
+            for (transformation in data) {
+                res += "<tr>"
+                res += "<th scope='row'>" + cnt + "</th>"
+                res += "<th scope='row'>" + data[transformation]['products'][0].join(', ') + "</th>"
+                res += "<th scope='row'>" + "<img width='400' src='{% url 'depict' %}?smiles=" + encodeURIComponent(data[transformation]['products'][0].join('.')) + "'></th>"
+                res += "<th scope='row'>" + data[transformation]['probability'].toFixed(3) + "</th>"
+                if (data[transformation]['btrule'] != null) {
+                    res += "<th scope='row'>" + "<a href='" + data[transformation]['btrule']['url'] + "'>" + data[transformation]['btrule']['name'] + "</a>" + "</th>"
+                } else {
+                    res += "<th scope='row'>N/A</th>"
+                }
+                res += "</tr>"
+                cnt += 1;
+            }
 
-            makeLoadingGif("#loading", "{% static '/images/wait.gif' %}");
+            res += "</tbody>"
-            $.ajax({
+            res += "</table>"
-                type : 'get',
+            $("#predictResultTable").append(res);
-                data : data,
+        }
-                url : '',
+
-                success: function(data, textStatus) {
+        function clear() {
-                    try {
+            $("#predictResultTable").removeClass("alert alert-danger");
-                        $("#loading").empty();
+            $("#predictResultTable").empty();
-                        handleResponse(data);
+        }
-                    } catch (error) {
+
-                        console.log("Error");
+        if ($('#predict-button').length > 0) {
+            $("#predict-button").on("click", function (e) {
+                e.preventDefault();
+
+                data = {
+                    "smiles": $("#smiles-to-predict").val(),
+                    "classify": "ILikeCats!"
+                }
+
+                clear();
+
+                makeLoadingGif("#loading", "{% static '/images/wait.gif' %}");
+                $.ajax({
+                    type: 'get',
+                    data: data,
+                    url: '',
+                    success: function (data, textStatus) {
+                        try {
+                            $("#loading").empty();
+                            handleResponse(data);
+                        } catch (error) {
+                            console.log("Error");
+                            $("#loading").empty();
+                            $("#predictResultTable").addClass("alert alert-danger");
+                            $("#predictResultTable").append("Error while processing request :/");
+                        }
+                    },
+                    error: function (jqXHR, textStatus, errorThrown) {
                         $("#loading").empty();
                         $("#predictResultTable").addClass("alert alert-danger");
                         $("#predictResultTable").append("Error while processing request :/");
                     }
-                },
+                });
-                error : function(jqXHR, textStatus, errorThrown) {
-                    $("#loading").empty();
-                    $("#predictResultTable").addClass("alert alert-danger");
-                    $("#predictResultTable").append("Error while processing request :/");
-                }
             });
-        });
+        }
-    }
+    </script>
-</script>
 
 {% endblock content %}

templates/objects/node.html

@@ -0,0 +1,75 @@
+{% extends "framework.html" %}
+
+{% block content %}
+
+    {% block action_modals %}
+        {% include "modals/objects/edit_node_modal.html" %}
+        {% include "modals/objects/delete_node_modal.html" %}
+    {% endblock action_modals %}
+
+    <div class="panel-group" id="node-detail">
+        <div class="panel panel-default">
+            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+                {{ node.name }}
+                <div id="actionsButton"
+                     style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
+                     class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
+                                         aria-haspopup="true" aria-expanded="false"><span
+                        class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
+                        style="padding-right:1em"></span></a>
+                    <ul id="actionsList" class="dropdown-menu">
+                        {% block actions %}
+                            {% include "actions/objects/node.html" %}
+                        {% endblock %}
+                    </ul>
+                </div>
+            </div>
+            <div class="panel-body">
+                The underlying structure can be found <a href="{{ node.default_node_label.url }}">here</a>.
+            </div>
+
+            <!-- Description -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="node-desc-link" data-toggle="collapse" data-parent="#node-detail"
+                       href="#node-desc">Description</a>
+                </h4>
+            </div>
+            <div id="node-desc" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {{ node.description }}
+                </div>
+            </div>
+
+            <!-- Image -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="node-image-link" data-toggle="collapse" data-parent="#node-detail"
+                       href="#node-image">Image Representation</a>
+                </h4>
+            </div>
+            <div id="node-image" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    <div id="image-div" align="center">
+                        {{ node.default_node_label.as_svg|safe }}
+                    </div>
+                </div>
+            </div>
+
+            <!-- SMILES -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="node-smiles-link" data-toggle="collapse" data-parent="#node-detail"
+                       href="#node-smiles">SMILES Representation</a>
+                </h4>
+            </div>
+            <div id="node-smiles" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {{ node.default_node_label.smiles }}
+                </div>
+            </div>
+
+        </div>
+
+    </div>
+{% endblock content %}

templates/objects/package.html

@@ -14,7 +14,7 @@
         <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
             {{ package.name }}
             <div id="actionsButton"
-                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;"
+                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
                                      aria-haspopup="true" aria-expanded="false"><span
                     class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span

templates/objects/pathway.html

@@ -1,113 +1,182 @@
 {% extends "framework.html" %}
 
 {% block content %}
-{% load static %}
+    {% load static %}
-<script src="https://d3js.org/d3.v7.min.js"></script>
+    <script src="https://d3js.org/d3.v7.min.js"></script>
-<style>
+    <style>
-    svg { width: 100%; height: 600px; color: red;}
+        svg {
-    .link { stroke: #999; stroke-opacity: 0.6; marker-end: url(#arrow); }
+            width: 100%;
-    .link_no_arrow { stroke: #999; stroke-opacity: 0.6; }
+            height: 600px;
-    .node image { cursor: pointer; }
+            color: red;
-    .node circle { fill: lightblue; stroke: steelblue; stroke-width: 1.5px; }
+        }
-    .highlighted { stroke: red; stroke-width: 3px; }
-    .tooltip { position: absolute; background: lightgrey; padding: 5px; border-radius: 5px; visibility: hidden; opacity: 1}
-</style>
-<script src="{% static 'js/pw.js' %}"></script>
 
-<p></p>
+        .link {
+            stroke: #999;
+            stroke-opacity: 0.6;
+            marker-end: url(#arrow);
+        }
 
-<div class="panel-group" id="pwAccordion">
+        .link_no_arrow {
-    <div class="panel panel-default">
+            stroke: #999;
-        <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+            stroke-opacity: 0.6;
-            {{ pathway.name }}
+        }
-        </div>
+
-    </div>
+        .node image {
-    <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            cursor: pointer;
-        <h4 class="panel-title">
+        }
-            <a id="vizLink" data-toggle="collapse" data-parent="#pwAccordion" href="#viz">
+
-                Graphical Representation
+        .node circle {
-            </a>
+            fill: lightblue;
-        </h4>
+            stroke: steelblue;
-    </div>
+            stroke-width: 1.5px;
-    <div id="viz" class="panel-collapse collapse in">
+        }
-        <nav role="navigation" class="navbar navbar-default" style="margin: 0;">
+
-            <div class="navbar-header">
+        .highlighted {
+            stroke: red;
+            stroke-width: 3px;
+        }
+
+        .tooltip {
+            position: absolute;
+            background: lightgrey;
+            padding: 5px;
+            border-radius: 5px;
+            visibility: hidden;
+            opacity: 1
+        }
+    </style>
+    <script src="{% static 'js/pw.js' %}"></script>
+
+    {% block action_modals %}
+        {% include "modals/objects/add_pathway_node_modal.html" %}
+        {% include "modals/objects/add_pathway_edge_modal.html" %}
+        {% include "modals/objects/edit_pathway_modal.html" %}
+        {% include "modals/objects/delete_pathway_node_modal.html" %}
+        {% include "modals/objects/delete_pathway_edge_modal.html" %}
+        {% include "modals/objects/delete_pathway_modal.html" %}
+    {% endblock action_modals %}
+
+    <p></p>
+    <div id="pwcontent">
+        <div class="panel-group" id="pwAccordion">
+            <div class="panel panel-default">
+                <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+                    {{ pathway.name }}
+                </div>
             </div>
-            <div id="editbarCollapse" class="collapse navbar-collapse ">
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-                <ul class="nav navbar-nav">
+                <h4 class="panel-title">
-                    <li class="dropdown requiresWritePerm">
+                    <a id="vizLink" data-toggle="collapse" data-parent="#pwAccordion" href="#viz">
-                        <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true"
+                        Graphical Representation
-                           aria-expanded="false">
+                    </a>
-                            <span class="glyphicon glyphicon-edit"></span>
+                </h4>
-                            Edit
+            </div>
-                            <span class="caret"></span></a>
+            <div id="viz" class="panel-collapse collapse in">
-                            <ul id="editingList" class="dropdown-menu">
+                <nav role="navigation" class="navbar navbar-default" style="margin: 0;">
-                                <li>
+                    <div class="navbar-header">
-                                    <a role="button" data-toggle="modal" id="showCompoundNames">
+                    </div>
-                                        <span class="glyphicon glyphicon-eye-open"></span> Show Compound Names</a>
+                    <div id="editbarCollapse" class="collapse navbar-collapse ">
-                                </li>
+                        <ul class="nav navbar-nav">
-                            </ul>
+                            <li class="dropdown requiresWritePerm">
-                    </li>
+                                <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
-                </ul>
+                                   aria-haspopup="true"
-
+                                   aria-expanded="false">
-                <ul class="nav navbar-nav navbar-right">
+                                    <span class="glyphicon glyphicon-edit"></span>
-                    <li>
+                                    Edit
-                        <a role="button" data-toggle="modal" onclick="goFullscreen('pwcontent')">
+                                    <span class="caret"></span></a>
-                            <span class="glyphicon glyphicon-fullscreen"></span>Fullscreen
+                                <ul id="editingList" class="dropdown-menu">
-                        </a>
+                                    {% block actions %}
-                    </li>
+                                        {% include "actions/objects/pathway.html" %}
-                    <li>
+                                    {% endblock %}
-                        <button type="button" class="btn btn-default navbar-btn" data-toggle="tooltip" id="status"
+                                </ul>
-                                data-original-title="" title="" data-content="Pathway prediction complete."><span
+                            </li>
-                                class="glyphicon glyphicon-ok"></span></button>
+                        </ul>
-                        &nbsp;
+
-                    </li>
+                        <ul class="nav navbar-nav navbar-right">
-                </ul>
+                            <li>
-
+                                <a role="button" data-toggle="modal" onclick="goFullscreen('pwcontent')">
+                                    <span class="glyphicon glyphicon-fullscreen"></span>
+                                    Fullscreen
+                                </a>
+                            </li>
+                            <li>
+                                {% if pathway.completed %}
+                                    <button type="button" class="btn btn-default navbar-btn" data-toggle="tooltip"
+                                            id="status" data-original-title="" title=""
+                                            data-content="Pathway prediction complete.">
+                                        <span class="glyphicon glyphicon-ok"></span>
+                                    </button>
+                                {% elif pathway.failed %}
+                                    <button type="button" class="btn btn-default navbar-btn" data-toggle="tooltip"
+                                            id="status" data-original-title="" title=""
+                                            data-content="Pathway prediction failed.">
+                                        <span class="glyphicon glyphicon-remove"></span>
+                                    </button>
+                                {% else %}
+                                    <button type="button" class="btn btn-default navbar-btn" data-toggle="tooltip"
+                                            id="status" data-original-title="" title=""
+                                            data-content="Pathway prediction running.">
+                                        <img height="20" src="{% static '/images/wait.gif' %}">
+                                    </button>
+                                {% endif %}
+                                &nbsp;
+                            </li>
+                        </ul>
+
+                    </div>
+                </nav>
+                <div id="vizdiv">
+                    <svg width="2000" height="2000">
+                        {% if debug %}
+                            <rect width="100%" height="100%" fill="aliceblue"/>
+                        {% endif %}
+                        <defs>
+                            <marker id="arrow" viewBox="0 0 10 10" refX="43" refY="5" markerWidth="6" markerHeight="6"
+                                    orient="auto-start-reverse">
+                                <path d="M 0 0 L 10 5 L 0 10 z" fill="#999"/>
+                            </marker>
+                        </defs>
+                        <g id="zoomable"></g>
+                    </svg>
+                    <div id="tooltip" class="tooltip"></div>
+                </div>
+            </div>
+
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="DescriptionLink" data-toggle="collapse" data-parent="#pathwayAccordion"
+                       href="#Description">Description</a></h4>
+            </div>
+            <div id="Description" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item" id="DescriptionContent">
+                    {{ pathway.description | safe }}
+                </div>
             </div>
-        </nav>
-        <div id="vizdiv">
-            <svg width="2000" height="2000">
-                {% if debug %}
-                <rect width="100%" height="100%" fill="aliceblue"/>
-                {% endif %}
-                <defs>
-                    <marker id="arrow" viewBox="0 0 10 10" refX="43" refY="5" markerWidth="6" markerHeight="6"
-                            orient="auto-start-reverse">
-                        <path d="M 0 0 L 10 5 L 0 10 z" fill="#999"/>
-                    </marker>
-                </defs>
-                <g id="zoomable"></g>
-            </svg>
-            <div id="tooltip" class="tooltip"></div>
         </div>
     </div>
+    <script>
 
-    <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+        function goFullscreen(id) {
-        <h4 class="panel-title">
+            var element = document.getElementById(id);
-            <a id="DescriptionLink" data-toggle="collapse" data-parent="#pathwayAccordion"
+            if (element.mozRequestFullScreen) {
-               href="#Description">Description</a></h4>
+                element.mozRequestFullScreen();
-    </div>
+            } else if (element.webkitRequestFullScreen) {
-    <div id="Description" class="panel-collapse collapse in">
+                element.webkitRequestFullScreen();
-        <div class="panel-body list-group-item" id="DescriptionContent">
+            }
-            {{ pathway.description | safe }}
+        }
-        </div>
-    </div>
-</div>
-<script>
 
-function transformReferences(text) {
+        function transformReferences(text) {
-    return text.replace(/\[\s*(http[^\]|]+)\s*\|\s*([^\]]+)\s*\]/g, '<a target="parent" href="$1">$2</a>');
+            return text.replace(/\[\s*(http[^\]|]+)\s*\|\s*([^\]]+)\s*\]/g, '<a target="parent" href="$1">$2</a>');
-}
+        }
 
-pathway = {{ pathway.d3_json | safe }};
+        pathway = {{ pathway.d3_json | safe }};
 
-$(function() {
+        $(function () {
-    draw(pathway, 'vizdiv');
+            draw(pathway, 'vizdiv');
-    // TODO fix somewhere else...
+            // TODO fix somewhere else...
-    var newDesc = transformReferences($('#DescriptionContent')[0].innerText);
+            var newDesc = transformReferences($('#DescriptionContent')[0].innerText);
-    $('#DescriptionContent').html(newDesc);
+            $('#DescriptionContent').html(newDesc);
-});
+        });
 
-</script>
+    </script>
 {% endblock content %}

templates/objects/reaction.html

@@ -2,104 +2,125 @@
 
 {% block content %}
 
-{% block action_modals %}
+    {% block action_modals %}
-{% include "modals/objects/edit_reaction_modal.html" %}
+        {% include "modals/objects/edit_reaction_modal.html" %}
-{% endblock action_modals %}
+        {% include "modals/objects/delete_reaction_modal.html" %}
+    {% endblock action_modals %}
 
-<div class="panel-group" id="reaction-detail">
+    <div class="panel-group" id="reaction-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">
-            {{ reaction.name }}
+                {{ reaction.name }}
-            <div id="actionsButton"
+                <div id="actionsButton"
-                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;"
+                     style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
-                 class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
+                     class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
-                                     aria-haspopup="true" aria-expanded="false"><span
+                                         aria-haspopup="true" aria-expanded="false"><span
-                    class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
+                        class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
-                    style="padding-right:1em"></span></a>
+                        style="padding-right:1em"></span></a>
-                <ul id="actionsList" class="dropdown-menu">
+                    <ul id="actionsList" class="dropdown-menu">
-                    {% block actions %}
+                        {% block actions %}
-                    {% include "actions/objects/reaction.html" %}
+                            {% include "actions/objects/reaction.html" %}
-                    {% endblock %}
+                        {% endblock %}
-                </ul>
+                    </ul>
-            </div>
-        </div>
-
-        <!-- Description -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
-                <a id="reaction-desc-link" data-toggle="collapse" data-parent="#reaction-detail"
-                   href="#reaction-desc">Description</a>
-            </h4>
-        </div>
-        <div id="reaction-desc" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                {{ reaction.description }}
-            </div>
-        </div>
-
-        <!-- Image -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
-                <a id="reaction-image-link" data-toggle="collapse" data-parent="#reaction-detail"
-                   href="#reaction-image">Image Representation</a>
-            </h4>
-        </div>
-        <div id="reaction-image" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                <div id="image-div" align="center">
-                    {{ reaction.as_svg|safe }}
                 </div>
             </div>
-        </div>
 
-        <!-- Reaction Description -->
+            <!-- Description -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
+                <h4 class="panel-title">
-                <a id="reaction-description-link" data-toggle="collapse" data-parent="#reaction-description-detail"
+                    <a id="reaction-desc-link" data-toggle="collapse" data-parent="#reaction-detail"
-                   href="#reaction-description-smiles">Reaction Description</a>
+                       href="#reaction-desc">Description</a>
-            </h4>
+                </h4>
-        </div>
+            </div>
-        <div id="reaction-description-smiles" class="panel-collapse collapse in">
+            <div id="reaction-desc" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
+                <div class="panel-body list-group-item">
-                {% for educt in reaction.educts.all %}
+                    {{ reaction.description }}
-                <a class="btn btn-default" href="{{ educt.url }}">{{ educt.name }}</a>
+                </div>
-                {% endfor %}
-                <span class="glyphicon glyphicon-arrow-right" style="margin-left:5em;margin-right:5em;" aria-hidden="true"></span>
-                {% for product in reaction.products.all %}
-                <a class="btn btn-default" href="{{ product.url }}">{{ product.name }}</a>
-                {% endfor %}
             </div>
-        </div>
 
-        <!-- SMIRKS -->
+            <!-- Image -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
+                <h4 class="panel-title">
-                <a id="reaction-smirks-link" data-toggle="collapse" data-parent="#reaction-detail"
+                    <a id="reaction-image-link" data-toggle="collapse" data-parent="#reaction-detail"
-                   href="#reaction-smirks">SMIRKS Representation</a>
+                       href="#reaction-image">Image Representation</a>
-            </h4>
+                </h4>
-        </div>
+            </div>
-        <div id="reaction-smirks" class="panel-collapse collapse in">
+            <div id="reaction-image" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
+                <div class="panel-body list-group-item">
-                {{ reaction.smirks }}
+                    <div id="image-div" align="center">
+                        {{ reaction.as_svg|safe }}
+                    </div>
+                </div>
             </div>
-        </div>
 
-       <!-- Pathways -->
+            <!-- Reaction Description -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
+                <h4 class="panel-title">
-                <a id="reaction-pathway-link" data-toggle="collapse" data-parent="#reaction-detail"
+                    <a id="reaction-description-link" data-toggle="collapse" data-parent="#reaction-description-detail"
-                   href="#reaction-pathway">Pathways</a>
+                       href="#reaction-description-smiles">Reaction Description</a>
-            </h4>
+                </h4>
-        </div>
-        <div id="reaction-pathway" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                {% for r in reaction.related_pathways %}
-                <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
-                {% endfor %}
             </div>
-        </div>
+            <div id="reaction-description-smiles" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {% for educt in reaction.educts.all %}
+                        <a class="btn btn-default" href="{{ educt.url }}">{{ educt.name }}</a>
+                    {% endfor %}
+                    <span class="glyphicon glyphicon-arrow-right" style="margin-left:5em;margin-right:5em;"
+                          aria-hidden="true"></span>
+                    {% for product in reaction.products.all %}
+                        <a class="btn btn-default" href="{{ product.url }}">{{ product.name }}</a>
+                    {% endfor %}
+                </div>
+            </div>
+
+            <!-- SMIRKS -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="reaction-smirks-link" data-toggle="collapse" data-parent="#reaction-detail"
+                       href="#reaction-smirks">SMIRKS Representation</a>
+                </h4>
+            </div>
+            <div id="reaction-smirks" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {{ reaction.smirks }}
+                </div>
+            </div>
+
+            {% if reaction.rules.all %}
+                <!-- Rules -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="reaction-rules-link" data-toggle="collapse" data-parent="#reaction-detail"
+                           href="#reaction-rules">Rules</a>
+                    </h4>
+                </div>
+                <div id="reaction-rules" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for r in reaction.rules.all %}
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
+            {% if reaction.related_pathways %}
+                <!-- Pathways -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="reaction-pathway-link" data-toggle="collapse" data-parent="#reaction-detail"
+                           href="#reaction-pathway">Pathways</a>
+                    </h4>
+                </div>
+                <div id="reaction-pathway" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for r in reaction.related_pathways %}
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+
+                </div>
+            {% endif %}
 
     </div>
-
-</div>
 {% endblock content %}

templates/objects/scenario.html

@@ -10,7 +10,7 @@
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
                 {{ scenario.name }}
                 <div id="actionsButton"
-                     style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;"
+                     style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
                                          aria-haspopup="true" aria-expanded="false"><span
                         class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span

templates/objects/simple_rule.html

@@ -2,173 +2,184 @@
 
 {% block content %}
 
-{% block action_modals %}
+    {% block action_modals %}
-{% include "modals/objects/edit_rule_modal.html" %}
+        {% include "modals/objects/edit_rule_modal.html" %}
-{% endblock action_modals %}
+    {% endblock action_modals %}
 
-<div class="panel-group" id="rule-detail">
+    <div class="panel-group" id="rule-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">
-            {{ rule.name }}
+                {{ rule.name }}
-            <div id="actionsButton"
+                <div id="actionsButton"
-                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;"
+                     style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
-                 class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
+                     class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
-                                     aria-haspopup="true" aria-expanded="false"><span
+                                         aria-haspopup="true" aria-expanded="false"><span
-                    class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
+                        class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
-                    style="padding-right:1em"></span></a>
+                        style="padding-right:1em"></span></a>
-                <ul id="actionsList" class="dropdown-menu">
+                    <ul id="actionsList" class="dropdown-menu">
-                    {% block actions %}
+                        {% block actions %}
-                    {% include "actions/objects/rule.html" %}
+                            {% include "actions/objects/rule.html" %}
-                    {% endblock %}
+                        {% endblock %}
-                </ul>
+                    </ul>
-            </div>
-        </div>
-        <div class="panel-body">
-            <p>
-                {{ rule.description }}
-            </p>
-        </div>
-
-        <!-- Representation -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
-                <a id="rule-image-link" data-toggle="collapse" data-parent="#rule-detail"
-                   href="#rule-image">Image Representation</a>
-            </h4>
-        </div>
-        <div id="rule-image" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                <div id="image-div" align="center">
-                    {{ rule.as_svg|safe }}
                 </div>
             </div>
-        </div>
+            <div class="panel-body">
+                <p>
+                    {{ rule.description }}
+                </p>
+            </div>
 
-        <!-- SMIRKS -->
+            <!-- Representation -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
+                <h4 class="panel-title">
-                <a id="rule-smirks-link" data-toggle="collapse" data-parent="#rule-detail"
+                    <a id="rule-image-link" data-toggle="collapse" data-parent="#rule-detail"
-                   href="#rule-smirks">SMIRKS Representation</a>
+                       href="#rule-image">Image Representation</a>
-            </h4>
+                </h4>
-        </div>
+            </div>
-        <div id="rule-smirks" class="panel-collapse collapse in">
+            <div id="rule-image" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
+                <div class="panel-body list-group-item">
-                <p> {{ rule.smirks }} </p>
+                    <div id="image-div" align="center">
+                        {{ rule.as_svg|safe }}
+                    </div>
+                </div>
             </div>
-        </div>
 
-        <!-- Reactants SMARTS -->
+            <!-- SMIRKS -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
+                <h4 class="panel-title">
-                <a id="rule-reactants-smarts-link" data-toggle="collapse" data-parent="#rule-detail"
+                    <a id="rule-smirks-link" data-toggle="collapse" data-parent="#rule-detail"
-                   href="#rule-reactants-smarts">Reactant SMARTS</a>
+                       href="#rule-smirks">SMIRKS Representation</a>
-            </h4>
+                </h4>
-        </div>
+            </div>
-        <div id="rule-reactants-smarts" class="panel-collapse collapse in">
+            <div id="rule-smirks" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
+                <div class="panel-body list-group-item">
-                <p> {{ rule.reactants_smarts }} </p>
+                    <p> {{ rule.smirks }} </p>
+                </div>
             </div>
-        </div>
 
-        <!-- Reactant Filter SMARTS -->
+            <!-- Reactants SMARTS -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
+                <h4 class="panel-title">
-                <a id="rule-reactant-filter-smarts-link" data-toggle="collapse" data-parent="#rule-detail"
+                    <a id="rule-reactants-smarts-link" data-toggle="collapse" data-parent="#rule-detail"
-                   href="#rule-reactant-filter-smarts">Reactant Filter SMARTS</a>
+                       href="#rule-reactants-smarts">Reactant SMARTS</a>
-            </h4>
+                </h4>
-        </div>
+            </div>
-        <div id="rule-reactant-filter-smarts" class="panel-collapse collapse in">
+            <div id="rule-reactants-smarts" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
+                <div class="panel-body list-group-item">
-                <p> {{ rule.reactant_filter_smarts }} </p>
+                    <p> {{ rule.reactants_smarts }} </p>
+                </div>
             </div>
-        </div>
 
-        <!-- Products SMARTS -->
+            <!-- Reactant Filter SMARTS -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            {% if rule.reactant_filter_smarts %}
-            <h4 class="panel-title">
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-                <a id="rule-products-smarts-link" data-toggle="collapse" data-parent="#rule-detail"
+                    <h4 class="panel-title">
-                   href="#rule-products-smarts">Reactant SMARTS</a>
+                        <a id="rule-reactant-filter-smarts-link" data-toggle="collapse" data-parent="#rule-detail"
-            </h4>
+                           href="#rule-reactant-filter-smarts">Reactant Filter SMARTS</a>
-        </div>
+                    </h4>
-        <div id="rule-products-smarts" class="panel-collapse collapse in">
+                </div>
-            <div class="panel-body list-group-item">
+                <div id="rule-reactant-filter-smarts" class="panel-collapse collapse in">
-                <p> {{ rule.products_smarts }} </p>
+                    <div class="panel-body list-group-item">
-            </div>
+                        <p> {{ rule.reactant_filter_smarts }} </p>
-        </div>
+                    </div>
+                </div>
+            {% endif %}
 
-        <!-- Product Filter SMARTS -->
+            <!-- Products SMARTS -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
+                <h4 class="panel-title">
-                <a id="rule-product-filter-smarts-link" data-toggle="collapse" data-parent="#rule-detail"
+                    <a id="rule-products-smarts-link" data-toggle="collapse" data-parent="#rule-detail"
-                   href="#rule-product-filter-smarts">Product Filter SMARTS</a>
+                       href="#rule-products-smarts">Reactant SMARTS</a>
-            </h4>
+                </h4>
-        </div>
+            </div>
-        <div id="rule-product-filter-smarts" class="panel-collapse collapse in">
+            <div id="rule-products-smarts" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
+                <div class="panel-body list-group-item">
-                <p> {{ rule.product_filter_smarts }} </p>
+                    <p> {{ rule.products_smarts }} </p>
+                </div>
             </div>
-        </div>
 
-        <!-- Included in Composite Rules -->
+            <!-- Product Filter SMARTS -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            {% if rule.product_filter_smarts %}
-            <h4 class="panel-title">
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-                <a id="rule-composite-rule-link" data-toggle="collapse" data-parent="#rule-detail"
+                    <h4 class="panel-title">
-                   href="#rule-composite-rule">Included in Composite Rules</a>
+                        <a id="rule-product-filter-smarts-link" data-toggle="collapse" data-parent="#rule-detail"
-            </h4>
+                           href="#rule-product-filter-smarts">Product Filter SMARTS</a>
-        </div>
+                    </h4>
-        <div id="rule-composite-rule" class="panel-collapse collapse in">
+                </div>
-            <div class="panel-body list-group-item">
+                <div id="rule-product-filter-smarts" class="panel-collapse collapse in">
-                {% for cr in rule.parallelrule_set.all %}
+                    <div class="panel-body list-group-item">
-                <a class="list-group-item" href="{{ cr.url }}">{{ cr.name }}</a>
+                        <p> {{ rule.product_filter_smarts }} </p>
-                {% endfor %}
+                    </div>
-            </div>
+                </div>
-        </div>
+            {% endif %}
-        
-        <!-- Scenarios -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
-                <a id="rule-scenario-link" data-toggle="collapse" data-parent="#rule-detail"
-                   href="#rule-scenario">Scenarios</a>
-            </h4>
-        </div>
-        <div id="rule-scenario" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                {% for s in rule.scenarios.all %}
-                <a class="list-group-item" href="{{ s.url }}">{{ s.name }}</a>
-                {% endfor %}
-            </div>
-        </div>
 
-        <!-- Reactions -->
+            <!-- Included in Composite Rules -->
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            {% if rule.parallelrule_set.all %}
-            <h4 class="panel-title">
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-                <a id="rule-reaction-link" data-toggle="collapse" data-parent="#rule-detail"
+                    <h4 class="panel-title">
-                   href="#rule-reaction">Reactions</a>
+                        <a id="rule-composite-rule-link" data-toggle="collapse" data-parent="#rule-detail"
-            </h4>
+                           href="#rule-composite-rule">Included in Composite Rules</a>
-        </div>
+                    </h4>
-        <div id="rule-reaction" class="panel-collapse collapse">
+                </div>
-            <div class="panel-body list-group-item">
+                <div id="rule-composite-rule" class="panel-collapse collapse in">
-                {% for r in rule.related_reactions %}
+                    <div class="panel-body list-group-item">
-                <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
+                        {% for cr in rule.parallelrule_set.all %}
-                {% endfor %}
+                            <a class="list-group-item" href="{{ cr.url }}">{{ cr.name }}</a>
-            </div>
+                        {% endfor %}
-        </div>
+                    </div>
-        
+                </div>
-        <!-- Pathways -->
+            {% endif %}
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
-                <a id="rule-pathway-link" data-toggle="collapse" data-parent="#rule-detail"
-                   href="#rule-pathway">Pathways</a>
-            </h4>
-        </div>
-        <div id="rule-pathway" class="panel-collapse collapse">
-            <div class="panel-body list-group-item">
-                {% for r in rule.related_pathways %}
-                <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
-                {% endfor %}
-            </div>
-        </div>
 
+            <!-- Scenarios -->
+            {% if rule.scenarios.all %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="rule-scenario-link" data-toggle="collapse" data-parent="#rule-detail"
+                           href="#rule-scenario">Scenarios</a>
+                    </h4>
+                </div>
+                <div id="rule-scenario" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for s in rule.scenarios.all %}
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
+            <!-- Reactions -->
+            {% if rule.related_reactions %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="rule-reaction-link" data-toggle="collapse" data-parent="#rule-detail"
+                           href="#rule-reaction">Reactions</a>
+                    </h4>
+                </div>
+                <div id="rule-reaction" class="panel-collapse collapse">
+                    <div class="panel-body list-group-item">
+                        {% for r in rule.related_reactions %}
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
+            <!-- Pathways -->
+            {% if rule.related_pathways %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="rule-pathway-link" data-toggle="collapse" data-parent="#rule-detail"
+                           href="#rule-pathway">Pathways</a>
+                    </h4>
+                </div>
+                <div id="rule-pathway" class="panel-collapse collapse">
+                    <div class="panel-body list-group-item">
+                        {% for r in rule.related_pathways %}
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+        </div>
     </div>
-</div>
 {% endblock content %}

templates/objects/user.html

@@ -15,7 +15,7 @@
         <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
             {{ user.username }}
             <div id="actionsButton"
-                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;"
+                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
                                      aria-haspopup="true" aria-expanded="false"><span
                     class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span

templates/search.html

@@ -1,62 +1,160 @@
 {% extends "framework.html" %}
 {% load static %}
 {% block content %}
-<!--<script>-->
-<!--$(document).arrive(".selPackages", function() {-->
-<!--    // selectpicker triggers 'bootstrap-select' library-->
-<!--    $(this).selectpicker();-->
-<!--});-->
-<!--</script>-->
 
-<div id=searchContent>
+    <div id=searchContent>
-    <div id="packSelector">
+        <div id="packSelector">
-        <label>Select Packages</label><br>
+            <label>Select Packages</label><br>
-        <select id="selPackages" name="selPackages" data-actions-box='true' class="selPackages" multiple
+            <select id="selPackages" name="selPackages" data-actions-box='true' class="selPackages" multiple
-                data-width='100%'>
+                    data-width='100%'>
-            {% if unreviewed_objects %}
+                {% if unreviewed_objects %}
-            <option disabled>Reviewed Packages</option>
+                    <option disabled>Reviewed Packages</option>
-            {% endif %}
+                {% endif %}
-            {% for obj in reviewed_objects %}
+                {% for obj in reviewed_objects %}
-            <option value="{{ obj.url }}" selected>{{ obj.name }}</option>
+                    <option value="{{ obj.url }}" selected>{{ obj.name }}</option>
-            {% endfor %}
+                {% endfor %}
-            {% if unreviewed_objects %}
+                {% if unreviewed_objects %}
-            <option disabled>Unreviewed Packages</option>
+                    <option disabled>Unreviewed Packages</option>
-            {% endif %}
+                {% endif %}
-            {% for obj in unreviewed_objects %}
+                {% for obj in unreviewed_objects %}
-            <option value="{{ obj.url }}">{{ obj.name }}</option>
+                    <option value="{{ obj.url }}">{{ obj.name }}</option>
-            {% endfor %}
+                {% endfor %}
-        </select>
+            </select>
-    </div>
+        </div>
-    <p></p>
+        <p></p>
-    <div>
+        <div>
-        <label>Search Term</label><br>
+            <label>Search Term</label><br>
-        <div class="input-group" id="index-form-bar">
+            <div class="input-group" id="index-form-bar">
-            <input type="text" class="form-control" id='index-form-text-input' placeholder="Benfuracarb">
+                <input type="text" class="form-control" id='searchbar' placeholder="Benfuracarb">
-            <div class="input-group-btn">
+                <div class="input-group-btn">
-                <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown" id="action-button"
+                    <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown"
-                        aria-haspopup="true" aria-expanded="false">Text <span class="caret"></span></button>
+                            id="mode-button"
-                <ul class="dropdown-menu">
+                            aria-haspopup="true" aria-expanded="false">Text <span class="caret"></span></button>
-                    <li class="dropdown-header">Text</li>
+                    <ul class="dropdown-menu">
-                    <li><a id="dropdown-predict-text-text">Text</a></li>
+                        <li class="dropdown-header">Text</li>
-                    <li class="dropdown-header">SMILES</li>
+                        <li><a id="dropdown-predict-text-text">Text</a></li>
-                    <li><a id="dropdown-search-smiles-default" data-toggle="tooltip">Default</a></li>
+                        <li class="dropdown-header">SMILES</li>
-                    <li><a id="dropdown-search-smiles-canonical">Canonical</a></li>
+                        <li><a id="dropdown-search-smiles-default" data-toggle="tooltip">Default</a></li>
-                    <li><a id="dropdown-search-smiles-exact">Exact</a></li>
+                        <li><a id="dropdown-search-smiles-canonical">Canonical</a></li>
-                    <li class="dropdown-header">InChI</li>
+                        <li><a id="dropdown-search-smiles-exact">Exact</a></li>
-                    <li><a id="dropdown-search-inchi-inchikey">InChIKey</a></li>
+                        <li class="dropdown-header">InChI</li>
-                </ul>
+                        <li><a id="dropdown-search-inchi-inchikey">InChIKey</a></li>
-                <button class="btn" style="background-color:#222222;color:#9d9d9d" type="button" id="run-button">Go!
+                    </ul>
-                </button>
+                    <button class="btn" style="background-color:#222222;color:#9d9d9d" type="button" id="search-button">
+                        Go!
+                    </button>
+                </div>
             </div>
+            <p></p>
+            <div id="results"></div>
+            <p></p>
+            <div id="loading"></div>
         </div>
-        <div id="results">
-        </div>
-        <div id="loading"></div>
-
     </div>
     <script>
+        function modeDropdownClicked() {
+            var suffix = ' <span class="caret"></span>';
+            var dropdownVal = $(this).text();
+            $('#mode-button').html(dropdownVal + suffix);
+        }
 
-        $(function() {
+        function handleSearchResponse(id, data) {
+            content = `
+                <div class='panel-group' id='search-accordion'>
+                    <div class='panel panel-default'>
+                        <div class='panel-heading' id='headingPanel' style='font-size:2rem;height: 46px'>
+                        Results
+                        </div>
+                        <div id='descDiv'></div>
+                    </div>`;
+
+            function makeContent(objs) {
+                links = "";
+                for (idx in objs) {
+                    obj = objs[idx];
+                    links += `<a class='list-group-item' href='${obj.url}'>${obj.name}</a>`
+                }
+                return links;
+            }
+
+            allEmpty = true;
+            for (key in data) {
+                if (data[key].length < 1) {
+                    continue;
+                }
+                allEmpty = false;
+                content += `
+                    <div class='panel panel-default panel-heading list-group-item' style='background-color:silver'>
+                        <h4 class='panel-title'>
+                            <a id='${key}_link' data-toggle='collapse' data-parent='#search-accordion' href='#${key}_panel'>
+                                ${key}
+                            </a>
+                        </h4>
+                    </div>
+                    <div id='${key}_panel' class='panel-collapse collapse in'>
+                        <div class='panel-body list-group-item'>
+                        ${makeContent(data[key])}
+                        </div>
+                    </div>
+
+        `;
+            }
+            if (allEmpty) {
+                $('#' + id).append('<div class="alert alert-danger" role="alert"><p>' + "No results..." + '</p></div>');
+            } else {
+                $('#' + id).append(content);
+            }
+        }
+
+        function search(e) {
+            e.preventDefault();
+
+            query = $("#searchbar").val()
+
+            if (!query) {
+                // Nothing to search...
+                console.log("Search phrase empty, won't do search")
+                return;
+            }
+
+            var selPacks = [];
+            $("#selPackages :selected").each(function () {
+                var id = this.value;
+                selPacks.push(id);
+            });
+
+            if (selPacks.length < 1) {
+                console.log("No package selected, won't do search")
+                return;
+            }
+
+            var mode = $('#mode-button').text().trim().toLowerCase();
+
+            var par = {};
+            par['packages'] = selPacks;
+            par['search'] = query;
+            par['mode'] = mode;
+
+            console.log(par);
+
+            var queryString = $.param(par, true);
+
+            makeLoadingGif("#loading", "{% static '/images/wait.gif' %}");
+
+            $("#results").empty();
+
+            $.getJSON("{{ SERVER_BASE }}/search?" + queryString, function (result) {
+                handleSearchResponse("results", result);
+                $("#loading").empty();
+            }).fail(function (d) {
+                $("#loading").empty();
+                console.log(d.responseText);
+                handleError(JSON.parse(d.responseText));
+            });
+        }
+
+
+        $(function () {
 
             tooltips = {
                 'dropdown-predict-text-text': 'The inserted pattern will be searched on all enviPath object names and descriptions',
@@ -71,44 +169,17 @@
                     placement: "top",
                     title: tooltips[key]
                 });
+
+                $('#' + key).on('click', modeDropdownClicked);
             });
 
             $("#selPackages").selectpicker();
+            $("#search-button").on("click", search);
 
-            $("#search-button").on("click", function(e) {
-                e.preventDefault();
-
-                if (!hasValue("searchbar")) {
-                    return;
-                }
-
-                var query = $("#searchbar").val();
-
-                selPackages = [];
-                var selPacks = $("#selPackages :selected");
-                selPacks.each(function () {
-                    var id = this.value;
-                    selPackages.push(id);
-                });
-
-                var par = {};
-                par['packages'] = selPackages;
-                par['search'] = query;
-                var queryString = $.param(par);
-
-                makeLoadingGif("#loading", "{% static '/images/wait.gif' %}");
-
-                $("#results").empty();
-
-                $.getJSON("{{ SERVER_BASE }}/search?" + queryString, function (result) {
-                    makeSearchList("#results", result);
-                    $("#loading").empty();
-                }).fail(function (d) {
-                    handleError(JSON.parse(d.responseText));
-                });
-            });
         });
-
+        {% if search_result %}
+            handleSearchResponse("results", {{ search_result|safe }});
+        {% endif %}
     </script>
 
-    {% endblock content %}
+{% endblock content %}

tests/test_compound_model.py

@@ -5,7 +5,7 @@ from epdb.models import Compound, User, CompoundStructure
 
 
 class CompoundTest(TestCase):
-    fixtures = ["test_fixture.json.gz"]
+    fixtures = ["test_fixture.cleaned.json"]
 
     def setUp(self):
         pass
@@ -53,6 +53,14 @@ class CompoundTest(TestCase):
                 description='No Desc'
             )
 
+        with self.assertRaises(ValueError):
+            _ = Compound.create(
+                self.package,
+                smiles='  ',
+                name='Afoxolaner',
+                description='No Desc'
+            )
+
     def test_smiles_are_trimmed(self):
         c = Compound.create(
             self.package,

tests/test_reaction_model.py

@@ -0,0 +1,196 @@
+from django.test import TestCase
+
+from epdb.logic import PackageManager
+from epdb.models import Compound, User, CompoundStructure, Reaction, Rule
+
+
+class ReactionTest(TestCase):
+    fixtures = ["test_fixture.cleaned.json"]
+
+    def setUp(self):
+        pass
+
+    @classmethod
+    def setUpClass(cls):
+        super(ReactionTest, cls).setUpClass()
+        cls.user = User.objects.get(username='anonymous')
+        cls.package = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')
+
+    @classmethod
+    def tearDownClass(cls):
+        pass
+
+    def tearDown(self):
+        pass
+
+    def test_smoke(self):
+        educt = Compound.create(
+            self.package,
+            smiles='C(CCl)Cl',
+            name='1,2-Dichloroethane',
+            description='Eawag BBD compound c0001'
+        ).default_structure
+
+        product = Compound.create(
+            self.package,
+            smiles='C(CO)Cl',
+            name='2-Chloroethanol',
+            description='Eawag BBD compound c0005'
+        ).default_structure
+
+        r = Reaction.create(
+            package=self.package,
+            name='Eawag BBD reaction r0001',
+            educts=[educt],
+            products=[product],
+            multi_step=False
+        )
+
+        self.assertEqual(r.smirks(), 'C(CCl)Cl>>C(CO)Cl')
+        self.assertEqual(r.name, 'Eawag BBD reaction r0001')
+        self.assertEqual(r.description, 'no description')
+
+
+
+    def test_string_educts_and_products(self):
+        r = Reaction.create(
+            package=self.package,
+            name='Eawag BBD reaction r0001',
+            educts=['C(CCl)Cl'],
+            products=['C(CO)Cl'],
+            multi_step=False
+        )
+
+        self.assertEqual(r.smirks(), 'C(CCl)Cl>>C(CO)Cl')
+
+    def test_missing_smiles(self):
+        educt = Compound.create(
+            self.package,
+            smiles='C(CCl)Cl',
+            name='1,2-Dichloroethane',
+            description='Eawag BBD compound c0001'
+        ).default_structure
+
+        product = Compound.create(
+            self.package,
+            smiles='C(CO)Cl',
+            name='2-Chloroethanol',
+            description='Eawag BBD compound c0005'
+        ).default_structure
+
+        with self.assertRaises(ValueError):
+            _ = Reaction.create(
+                package=self.package,
+                name='Eawag BBD reaction r0001',
+                educts=[educt],
+                products=[],
+                multi_step=False
+            )
+
+        with self.assertRaises(ValueError):
+            _ = Reaction.create(
+                package=self.package,
+                name='Eawag BBD reaction r0001',
+                educts=[],
+                products=[product],
+                multi_step=False
+            )
+
+        with self.assertRaises(ValueError):
+            _ = Reaction.create(
+                package=self.package,
+                name='Eawag BBD reaction r0001',
+                educts=[],
+                products=[],
+                multi_step=False
+            )
+
+    def test_empty_name_and_description_are_ignored(self):
+        r = Reaction.create(
+            package=self.package,
+            name='',
+            description='',
+            educts=['C(CCl)Cl'],
+            products=['C(CO)Cl'],
+            multi_step=False,
+        )
+
+        self.assertEqual(r.name, 'no name')
+        self.assertEqual(r.description, 'no description')
+
+    def test_deduplication(self):
+        rule = Rule.create(
+            package=self.package,
+            rule_type='SimpleAmbitRule',
+            name='bt0022-2833',
+            description='Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative',
+            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]',
+        )
+
+        r1 = Reaction.create(
+            package=self.package,
+            name='Eawag BBD reaction r0001',
+            educts=['C(CCl)Cl'],
+            products=['C(CO)Cl'],
+            rules=[rule],
+            multi_step=False
+        )
+
+        r2 = Reaction.create(
+            package=self.package,
+            name='Eawag BBD reaction r0001',
+            educts=['C(CCl)Cl'],
+            products=['C(CO)Cl'],
+            rules=[rule],
+            multi_step=False
+        )
+
+        # Check if create detects that this Compound already exist
+        # In this case the existing object should be returned
+        self.assertEqual(r1.pk, r2.pk)
+        self.assertEqual(len(self.package.reactions), 1)
+
+    def test_deduplication_without_rules(self):
+        r1 = Reaction.create(
+            package=self.package,
+            name='Eawag BBD reaction r0001',
+            educts=['C(CCl)Cl'],
+            products=['C(CO)Cl'],
+            multi_step=False
+        )
+
+        r2 = Reaction.create(
+            package=self.package,
+            name='Eawag BBD reaction r0001',
+            educts=['C(CCl)Cl'],
+            products=['C(CO)Cl'],
+            multi_step=False
+        )
+
+        # Check if create detects that this Compound already exist
+        # In this case the existing object should be returned
+        self.assertEqual(r1.pk, r2.pk)
+        self.assertEqual(len(self.package.reactions), 1)
+
+    def test_wrong_smiles(self):
+        with self.assertRaises(ValueError):
+            _ = Reaction.create(
+                package=self.package,
+                name='Eawag BBD reaction r0001',
+                educts=['ASDF'],
+                products=['C(CO)Cl'],
+                multi_step=False
+            )
+
+    def test_delete(self):
+        r = Reaction.create(
+            package=self.package,
+            name='Eawag BBD reaction r0001',
+            educts=['C(CCl)Cl'],
+            products=['C(CO)Cl'],
+            multi_step=False
+        )
+
+        r.delete()
+
+        self.assertEqual(Reaction.objects.filter(package=self.package).count(), 0)

tests/test_rule_model.py

@@ -0,0 +1,116 @@
+from django.test import TestCase
+
+from epdb.logic import PackageManager
+from epdb.models import Rule, User
+
+
+class RuleTest(TestCase):
+    fixtures = ["test_fixture.cleaned.json"]
+
+    def setUp(self):
+        pass
+
+    @classmethod
+    def setUpClass(cls):
+        super(RuleTest, cls).setUpClass()
+        cls.user = User.objects.get(username='anonymous')
+        cls.package = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')
+
+    @classmethod
+    def tearDownClass(cls):
+        pass
+
+    def tearDown(self):
+        pass
+
+    def test_smoke(self):
+        r = Rule.create(
+            rule_type='SimpleAmbitRule',
+            package=self.package,
+            name='bt0022-2833',
+            description='Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative',
+            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(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(r.name, 'bt0022-2833')
+        self.assertEqual(r.description,
+                         'Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative')
+
+    def test_smirks_are_trimmed(self):
+        r = Rule.create(
+            rule_type='SimpleAmbitRule',
+            package=self.package,
+            name='bt0022-2833',
+            description='Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative',
+            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(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]')
+
+    def test_name_and_description_optional(self):
+        r = Rule.create(
+            rule_type='SimpleAmbitRule',
+            package=self.package,
+            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.assertRegex(r.name, 'Rule \\d+')
+        self.assertEqual(r.description, 'no description')
+
+    def test_empty_name_and_description_are_ignored(self):
+        r = Rule.create(
+            rule_type='SimpleAmbitRule',
+            package=self.package,
+            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]',
+            name='',
+            description='',
+        )
+
+        self.assertRegex(r.name, 'Rule \\d+')
+        self.assertEqual(r.description, 'no description')
+
+    def test_deduplication(self):
+        r1 = Rule.create(
+            rule_type='SimpleAmbitRule',
+            package=self.package,
+            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]',
+            name='',
+            description='',
+        )
+
+        r2 = Rule.create(
+            rule_type='SimpleAmbitRule',
+            package=self.package,
+            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]',
+            name='',
+            description='',
+        )
+
+        self.assertEqual(r1.pk, r2.pk)
+        self.assertEqual(len(self.package.rules), 1)
+
+    def test_valid_smirks(self):
+        with self.assertRaises(ValueError):
+            r = Rule.create(
+                rule_type='SimpleAmbitRule',
+                package=self.package,
+                smirks='This is not a valid SMIRKS',
+                name='',
+                description='',
+            )
+
+    def test_delete(self):
+        r = Rule.create(
+            rule_type='SimpleAmbitRule',
+            package=self.package,
+            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]',
+            name='',
+            description='',
+        )
+
+        r.delete()
+
+        self.assertEqual(Rule.objects.filter(package=self.package).count(), 0)

utilities/chem.py

@@ -228,6 +228,14 @@ class FormatConverter(object):
     #
     #     return list(res)
 
+    @staticmethod
+    def is_valid_smirks(smirks: str) -> bool:
+        try:
+            rdChemReactions.ReactionFromSmarts(smirks)
+            return True
+        except:
+            return False
+
     @staticmethod
     def apply(smiles: str, smirks: str, preprocess_smiles: bool = True, bracketize: bool = False,
               standardize: bool = True, kekulize: bool = True) -> List['ProductSet']: