forked from enviPath/enviPy
Merge branch 'develop' into enhancement/licenses
This commit is contained in:
32
epdb/context_processors.py
Normal file
32
epdb/context_processors.py
Normal file
@ -0,0 +1,32 @@
|
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"""
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Context processors for enviPy application.
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Context processors automatically make variables available to all templates.
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"""
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from .logic import PackageManager
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from .models import Package
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def package_context(request):
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"""
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Provides package data for the search modal which is included globally
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in framework_modern.html.
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Returns:
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dict: Context dictionary with reviewed and unreviewed packages
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"""
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current_user = request.user
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reviewed_package_qs = PackageManager.get_reviewed_packages()
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unreviewed_package_qs = Package.objects.none()
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# Only get user-specific packages if user is authenticated
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if current_user.is_authenticated:
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unreviewed_package_qs = PackageManager.get_all_readable_packages(current_user)
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return {
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"reviewed_packages": reviewed_package_qs,
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"unreviewed_packages": unreviewed_package_qs,
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}
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@ -4,6 +4,7 @@ import json
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from typing import Union, List, Optional, Set, Dict, Any
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from uuid import UUID
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import nh3
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from django.contrib.auth import get_user_model
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from django.db import transaction
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from django.conf import settings as s
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@ -185,6 +186,12 @@ class UserManager(object):
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def create_user(
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username, email, password, set_setting=True, add_to_group=True, *args, **kwargs
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):
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# Clean for potential XSS
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clean_username = nh3.clean(username).strip()
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clean_email = nh3.clean(email).strip()
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if clean_username != username or clean_email != email:
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# This will be caught by the try in view.py/register
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raise ValueError("Invalid username or password")
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# avoid circular import :S
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from .tasks import send_registration_mail
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@ -262,8 +269,9 @@ class GroupManager(object):
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@staticmethod
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def create_group(current_user, name, description):
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g = Group()
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g.name = name
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g.description = description
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# Clean for potential XSS
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g.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
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g.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
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g.owner = current_user
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g.save()
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@ -518,8 +526,13 @@ class PackageManager(object):
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@transaction.atomic
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def create_package(current_user, name: str, description: str = None):
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p = Package()
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p.name = name
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p.description = description
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|
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# Clean for potential XSS
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p.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
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|
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if description is not None and description.strip() != "":
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p.description = nh3.clean(description.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
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p.save()
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up = UserPackagePermission()
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@ -1094,28 +1107,29 @@ class SettingManager(object):
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model: EPModel = None,
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model_threshold: float = None,
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):
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s = Setting()
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s.name = name
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s.description = description
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s.max_nodes = max_nodes
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s.max_depth = max_depth
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s.model = model
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s.model_threshold = model_threshold
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new_s = Setting()
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# Clean for potential XSS
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new_s.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
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new_s.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
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new_s.max_nodes = max_nodes
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new_s.max_depth = max_depth
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new_s.model = model
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new_s.model_threshold = model_threshold
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|
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s.save()
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new_s.save()
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|
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if rule_packages is not None:
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for r in rule_packages:
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s.rule_packages.add(r)
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s.save()
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new_s.rule_packages.add(r)
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new_s.save()
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usp = UserSettingPermission()
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usp.user = user
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usp.setting = s
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usp.setting = new_s
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usp.permission = Permission.ALL[0]
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usp.save()
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return s
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return new_s
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@staticmethod
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def get_default_setting(user: User):
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@ -1542,7 +1556,9 @@ class SPathway(object):
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if sub.app_domain_assessment is None:
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if self.prediction_setting.model:
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if self.prediction_setting.model.app_domain:
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app_domain_assessment = self.prediction_setting.model.app_domain.assess(sub.smiles)
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app_domain_assessment = self.prediction_setting.model.app_domain.assess(
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sub.smiles
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)
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if self.persist is not None:
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n = self.snode_persist_lookup[sub]
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@ -1574,7 +1590,9 @@ class SPathway(object):
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app_domain_assessment = None
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if self.prediction_setting.model:
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if self.prediction_setting.model.app_domain:
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app_domain_assessment = (self.prediction_setting.model.app_domain.assess(c))
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app_domain_assessment = (
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self.prediction_setting.model.app_domain.assess(c)
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)
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self.smiles_to_node[c] = SNode(
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c, sub.depth + 1, app_domain_assessment
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190
epdb/models.py
190
epdb/models.py
@ -11,6 +11,7 @@ from typing import Union, List, Optional, Dict, Tuple, Set, Any
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from uuid import uuid4
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import math
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import joblib
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import nh3
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import numpy as np
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from django.conf import settings as s
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from django.contrib.auth.models import AbstractUser
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@ -28,8 +29,14 @@ from sklearn.metrics import precision_score, recall_score, jaccard_score
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from sklearn.model_selection import ShuffleSplit
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from utilities.chem import FormatConverter, ProductSet, PredictionResult, IndigoUtils
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from utilities.ml import RuleBasedDataset, ApplicabilityDomainPCA, EnsembleClassifierChain, RelativeReasoning, \
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EnviFormerDataset, Dataset
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from utilities.ml import (
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RuleBasedDataset,
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ApplicabilityDomainPCA,
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EnsembleClassifierChain,
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RelativeReasoning,
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EnviFormerDataset,
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Dataset,
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)
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logger = logging.getLogger(__name__)
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@ -804,14 +811,16 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
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c = Compound()
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c.package = package
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if name is None or name.strip() == "":
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if name is not None:
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# Clean for potential XSS
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name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
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if name is None or name == "":
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name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
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c.name = name
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# We have a default here only set the value if it carries some payload
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if description is not None and description.strip() != "":
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c.description = description.strip()
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c.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
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c.save()
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@ -983,11 +992,11 @@ class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdenti
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raise ValueError("Unpersisted Compound! Persist compound first!")
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cs = CompoundStructure()
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# Clean for potential XSS
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if name is not None:
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cs.name = name
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cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
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if description is not None:
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cs.description = description
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cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
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cs.smiles = smiles
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cs.compound = compound
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@ -1189,21 +1198,29 @@ class SimpleAmbitRule(SimpleRule):
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r = SimpleAmbitRule()
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r.package = package
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if name is None or name.strip() == "":
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if name is not None:
|
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name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
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if name is None or name == "":
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name = f"Rule {Rule.objects.filter(package=package).count() + 1}"
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r.name = name
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if description is not None and description.strip() != "":
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r.description = description
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r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
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r.smirks = smirks
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if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != "":
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r.reactant_filter_smarts = reactant_filter_smarts
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if not FormatConverter.is_valid_smarts(reactant_filter_smarts.strip()):
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raise ValueError(f'Reactant Filter SMARTS "{reactant_filter_smarts}" is invalid!')
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else:
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r.reactant_filter_smarts = reactant_filter_smarts.strip()
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|
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if product_filter_smarts is not None and product_filter_smarts.strip() != "":
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r.product_filter_smarts = product_filter_smarts
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if not FormatConverter.is_valid_smarts(product_filter_smarts.strip()):
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raise ValueError(f'Product Filter SMARTS "{product_filter_smarts}" is invalid!')
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else:
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r.product_filter_smarts = product_filter_smarts.strip()
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r.save()
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return r
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@ -1404,12 +1421,11 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
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r = Reaction()
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r.package = package
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# Clean for potential XSS
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if name is not None and name.strip() != "":
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||||
r.name = name
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||||
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r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
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if description is not None and name.strip() != "":
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r.description = description
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r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
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r.multi_step = multi_step
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@ -1717,14 +1733,15 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
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):
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pw = Pathway()
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pw.package = package
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|
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if name is None or name.strip() == "":
|
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if name is not None:
|
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# Clean for potential XSS
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name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
|
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if name is None or name == "":
|
||||
name = f"Pathway {Pathway.objects.filter(package=package).count() + 1}"
|
||||
|
||||
pw.name = name
|
||||
|
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if description is not None and description.strip() != "":
|
||||
pw.description = description
|
||||
pw.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
|
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pw.save()
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try:
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@ -2019,11 +2036,16 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
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for node in end_nodes:
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e.end_nodes.add(node)
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|
||||
if name is None:
|
||||
# Clean for potential XSS
|
||||
# Cleaning technically not needed as it is also done in Reaction.create, including it here for consistency
|
||||
if name is not None:
|
||||
name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
if name is None or name == "":
|
||||
name = f"Reaction {pathway.package.reactions.count() + 1}"
|
||||
|
||||
if description is None:
|
||||
description = s.DEFAULT_VALUES["description"]
|
||||
description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
r = Reaction.create(
|
||||
pathway.package,
|
||||
@ -2345,7 +2367,9 @@ class PackageBasedModel(EPModel):
|
||||
eval_reactions = list(
|
||||
Reaction.objects.filter(package__in=self.eval_packages.all()).distinct()
|
||||
)
|
||||
ds = RuleBasedDataset.generate_dataset(eval_reactions, self.applicable_rules, educts_only=True)
|
||||
ds = RuleBasedDataset.generate_dataset(
|
||||
eval_reactions, self.applicable_rules, educts_only=True
|
||||
)
|
||||
if isinstance(self, RuleBasedRelativeReasoning):
|
||||
X = ds.X(exclude_id_col=False, na_replacement=None).to_numpy()
|
||||
y = ds.y(na_replacement=np.nan).to_numpy()
|
||||
@ -2543,14 +2567,15 @@ class RuleBasedRelativeReasoning(PackageBasedModel):
|
||||
):
|
||||
rbrr = RuleBasedRelativeReasoning()
|
||||
rbrr.package = package
|
||||
|
||||
if name is None or name.strip() == "":
|
||||
if name is not None:
|
||||
# Clean for potential XSS
|
||||
name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
if name is None or name == "":
|
||||
name = f"RuleBasedRelativeReasoning {RuleBasedRelativeReasoning.objects.filter(package=package).count() + 1}"
|
||||
|
||||
rbrr.name = name
|
||||
|
||||
if description is not None and description.strip() != "":
|
||||
rbrr.description = description
|
||||
rbrr.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
if threshold is None or (threshold <= 0 or 1 <= threshold):
|
||||
raise ValueError("Threshold must be a float between 0 and 1.")
|
||||
@ -2647,14 +2672,15 @@ class MLRelativeReasoning(PackageBasedModel):
|
||||
):
|
||||
mlrr = MLRelativeReasoning()
|
||||
mlrr.package = package
|
||||
|
||||
if name is None or name.strip() == "":
|
||||
if name is not None:
|
||||
# Clean for potential XSS
|
||||
name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
if name is None or name == "":
|
||||
name = f"MLRelativeReasoning {MLRelativeReasoning.objects.filter(package=package).count() + 1}"
|
||||
|
||||
mlrr.name = name
|
||||
|
||||
if description is not None and description.strip() != "":
|
||||
mlrr.description = description
|
||||
mlrr.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
if threshold is None or (threshold <= 0 or 1 <= threshold):
|
||||
raise ValueError("Threshold must be a float between 0 and 1.")
|
||||
@ -2808,7 +2834,9 @@ class ApplicabilityDomain(EnviPathModel):
|
||||
else:
|
||||
smiles.append(structures)
|
||||
|
||||
assessment_ds, assessment_prods = ds.classification_dataset(structures, self.model.applicable_rules)
|
||||
assessment_ds, assessment_prods = ds.classification_dataset(
|
||||
structures, self.model.applicable_rules
|
||||
)
|
||||
|
||||
# qualified_neighbours_per_rule is a nested dictionary structured as:
|
||||
# {
|
||||
@ -2824,12 +2852,16 @@ class ApplicabilityDomain(EnviPathModel):
|
||||
qualified_neighbours_per_rule: Dict = {}
|
||||
|
||||
import polars as pl
|
||||
|
||||
# Select only the triggered columns
|
||||
for i, row in enumerate(assessment_ds[:, assessment_ds.triggered()].iter_rows(named=True)):
|
||||
# Find the rules the structure triggers. For each rule, filter the training dataset to rows that also
|
||||
# trigger that rule.
|
||||
train_trig = {trig_uuid.split("_")[-1]: ds.filter(pl.col(trig_uuid).eq(1))
|
||||
for trig_uuid, value in row.items() if value == 1}
|
||||
train_trig = {
|
||||
trig_uuid.split("_")[-1]: ds.filter(pl.col(trig_uuid).eq(1))
|
||||
for trig_uuid, value in row.items()
|
||||
if value == 1
|
||||
}
|
||||
qualified_neighbours_per_rule[i] = train_trig
|
||||
rule_to_i = {str(r.uuid): i for i, r in enumerate(self.model.applicable_rules)}
|
||||
preds = self.model.combine_products_and_probs(
|
||||
@ -2849,18 +2881,28 @@ class ApplicabilityDomain(EnviPathModel):
|
||||
# loop through rule indices together with the collected neighbours indices from train dataset
|
||||
for rule_uuid, train_instances in qualified_neighbours_per_rule[i].items():
|
||||
# compute tanimoto distance for all neighbours and add to dataset
|
||||
dists = self._compute_distances(assessment_ds[i, assessment_ds.struct_features()].to_numpy()[0],
|
||||
train_instances[:, train_instances.struct_features()].to_numpy())
|
||||
dists = self._compute_distances(
|
||||
assessment_ds[i, assessment_ds.struct_features()].to_numpy()[0],
|
||||
train_instances[:, train_instances.struct_features()].to_numpy(),
|
||||
)
|
||||
train_instances = train_instances.with_columns(dist=pl.Series(dists))
|
||||
|
||||
# sort them in a descending way and take at most `self.num_neighbours`
|
||||
# TODO: Should this be descending? If we want the most similar then we want values close to zero (ascending)
|
||||
train_instances = train_instances.sort("dist", descending=True)[:self.num_neighbours]
|
||||
train_instances = train_instances.sort("dist", descending=True)[
|
||||
: self.num_neighbours
|
||||
]
|
||||
# compute average distance
|
||||
rule_reliabilities[rule_uuid] = train_instances.select(pl.mean("dist")).fill_nan(0.0).item()
|
||||
rule_reliabilities[rule_uuid] = (
|
||||
train_instances.select(pl.mean("dist")).fill_nan(0.0).item()
|
||||
)
|
||||
# for local_compatibility we'll need the datasets for the indices having the highest similarity
|
||||
local_compatibilities[rule_uuid] = self._compute_compatibility(rule_uuid, train_instances)
|
||||
neighbours_per_rule[rule_uuid] = list(CompoundStructure.objects.filter(uuid__in=train_instances["structure_id"]))
|
||||
local_compatibilities[rule_uuid] = self._compute_compatibility(
|
||||
rule_uuid, train_instances
|
||||
)
|
||||
neighbours_per_rule[rule_uuid] = list(
|
||||
CompoundStructure.objects.filter(uuid__in=train_instances["structure_id"])
|
||||
)
|
||||
neighbor_probs_per_rule[rule_uuid] = train_instances[f"prob_{rule_uuid}"].to_list()
|
||||
|
||||
ad_res = {
|
||||
@ -2934,8 +2976,11 @@ class ApplicabilityDomain(EnviPathModel):
|
||||
def _compute_compatibility(self, rule_idx: int, neighbours: "RuleBasedDataset"):
|
||||
accuracy = 0.0
|
||||
import polars as pl
|
||||
obs_pred = neighbours.select(obs=pl.col(f"obs_{rule_idx}").cast(pl.Boolean),
|
||||
pred=pl.col(f"prob_{rule_idx}") >= self.model.threshold)
|
||||
|
||||
obs_pred = neighbours.select(
|
||||
obs=pl.col(f"obs_{rule_idx}").cast(pl.Boolean),
|
||||
pred=pl.col(f"prob_{rule_idx}") >= self.model.threshold,
|
||||
)
|
||||
# Compute tp, tn, fp, fn using polars expressions
|
||||
tp = obs_pred.filter((pl.col("obs")) & (pl.col("pred"))).height
|
||||
tn = obs_pred.filter((~pl.col("obs")) & (~pl.col("pred"))).height
|
||||
@ -2962,14 +3007,15 @@ class EnviFormer(PackageBasedModel):
|
||||
):
|
||||
mod = EnviFormer()
|
||||
mod.package = package
|
||||
|
||||
if name is None or name.strip() == "":
|
||||
if name is not None:
|
||||
# Clean for potential XSS
|
||||
name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
if name is None or name == "":
|
||||
name = f"EnviFormer {EnviFormer.objects.filter(package=package).count() + 1}"
|
||||
|
||||
mod.name = name
|
||||
|
||||
if description is not None and description.strip() != "":
|
||||
mod.description = description
|
||||
mod.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
if threshold is None or (threshold <= 0 or 1 <= threshold):
|
||||
raise ValueError("Threshold must be a float between 0 and 1.")
|
||||
@ -3104,7 +3150,7 @@ class EnviFormer(PackageBasedModel):
|
||||
pred_dict = {}
|
||||
for k, pred in enumerate(predictions):
|
||||
pred_smiles, pred_proba = zip(*pred.items())
|
||||
reactant, true_product = test_ds[k, "educts"], test_ds[k, "products"]
|
||||
reactant, _ = test_ds[k, "educts"], test_ds[k, "products"]
|
||||
pred_dict.setdefault(reactant, {"predict": [], "scores": []})
|
||||
for smiles, proba in zip(pred_smiles, pred_proba):
|
||||
smiles = set(smiles.split("."))
|
||||
@ -3218,8 +3264,9 @@ class EnviFormer(PackageBasedModel):
|
||||
|
||||
# If there are eval packages perform single generation evaluation on them instead of random splits
|
||||
if self.eval_packages.count() > 0:
|
||||
ds = EnviFormerDataset.generate_dataset(Reaction.objects.filter(
|
||||
package__in=self.eval_packages.all()).distinct())
|
||||
ds = EnviFormerDataset.generate_dataset(
|
||||
Reaction.objects.filter(package__in=self.eval_packages.all()).distinct()
|
||||
)
|
||||
test_result = self.model.predict_batch(ds.X())
|
||||
single_gen_result = evaluate_sg(ds, test_result, self.threshold)
|
||||
self.eval_results = self.compute_averages([single_gen_result])
|
||||
@ -3237,7 +3284,9 @@ class EnviFormer(PackageBasedModel):
|
||||
train = ds[train_index]
|
||||
test = ds[test_index]
|
||||
start = datetime.now()
|
||||
model = fine_tune(train.X(), train.y(), s.MODEL_DIR, str(split_id), device=s.ENVIFORMER_DEVICE)
|
||||
model = fine_tune(
|
||||
train.X(), train.y(), s.MODEL_DIR, str(split_id), device=s.ENVIFORMER_DEVICE
|
||||
)
|
||||
end = datetime.now()
|
||||
logger.debug(
|
||||
f"EnviFormer finetuning took {(end - start).total_seconds():.2f} seconds"
|
||||
@ -3314,7 +3363,12 @@ class EnviFormer(PackageBasedModel):
|
||||
for pathway in train_pathways:
|
||||
for reaction in pathway.edges:
|
||||
reaction = reaction.edge_label
|
||||
if any([educt in test_educts for educt in reaction_to_educts[str(reaction.uuid)]]):
|
||||
if any(
|
||||
[
|
||||
educt in test_educts
|
||||
for educt in reaction_to_educts[str(reaction.uuid)]
|
||||
]
|
||||
):
|
||||
overlap += 1
|
||||
continue
|
||||
train_reactions.append(reaction)
|
||||
@ -3371,41 +3425,44 @@ class Scenario(EnviPathModel):
|
||||
scenario_type: str,
|
||||
additional_information: List["EnviPyModel"],
|
||||
):
|
||||
s = Scenario()
|
||||
s.package = package
|
||||
|
||||
if name is None or name.strip() == "":
|
||||
new_s = Scenario()
|
||||
new_s.package = package
|
||||
if name is not None:
|
||||
# Clean for potential XSS
|
||||
name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
if name is None or name == "":
|
||||
name = f"Scenario {Scenario.objects.filter(package=package).count() + 1}"
|
||||
|
||||
s.name = name
|
||||
new_s.name = name
|
||||
|
||||
if description is not None and description.strip() != "":
|
||||
s.description = description
|
||||
new_s.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
if scenario_date is not None and scenario_date.strip() != "":
|
||||
s.scenario_date = scenario_date
|
||||
new_s.scenario_date = nh3.clean(scenario_date).strip()
|
||||
|
||||
if scenario_type is not None and scenario_type.strip() != "":
|
||||
s.scenario_type = scenario_type
|
||||
new_s.scenario_type = scenario_type
|
||||
|
||||
add_inf = defaultdict(list)
|
||||
|
||||
for info in additional_information:
|
||||
cls_name = info.__class__.__name__
|
||||
ai_data = json.loads(info.model_dump_json())
|
||||
# Clean for potential XSS hidden in the additional information fields.
|
||||
ai_data = json.loads(nh3.clean(info.model_dump_json()).strip())
|
||||
ai_data["uuid"] = f"{uuid4()}"
|
||||
add_inf[cls_name].append(ai_data)
|
||||
|
||||
s.additional_information = add_inf
|
||||
new_s.additional_information = add_inf
|
||||
|
||||
s.save()
|
||||
new_s.save()
|
||||
|
||||
return s
|
||||
return new_s
|
||||
|
||||
@transaction.atomic
|
||||
def add_additional_information(self, data: "EnviPyModel"):
|
||||
cls_name = data.__class__.__name__
|
||||
ai_data = json.loads(data.model_dump_json())
|
||||
# Clean for potential XSS hidden in the additional information fields.
|
||||
ai_data = json.loads(nh3.clean(data.model_dump_json()).strip())
|
||||
ai_data["uuid"] = f"{uuid4()}"
|
||||
|
||||
if cls_name not in self.additional_information:
|
||||
@ -3440,7 +3497,8 @@ class Scenario(EnviPathModel):
|
||||
new_ais = defaultdict(list)
|
||||
for k, vals in data.items():
|
||||
for v in vals:
|
||||
ai_data = json.loads(v.model_dump_json())
|
||||
# Clean for potential XSS hidden in the additional information fields.
|
||||
ai_data = json.loads(nh3.clean(v.model_dump_json()).strip())
|
||||
if hasattr(v, "uuid"):
|
||||
ai_data["uuid"] = str(v.uuid)
|
||||
else:
|
||||
|
||||
@ -193,4 +193,13 @@ urlpatterns = [
|
||||
re_path(r"^jobs", v.jobs, name="jobs"),
|
||||
# OAuth Stuff
|
||||
path("o/userinfo/", v.userinfo, name="oauth_userinfo"),
|
||||
# Static Pages
|
||||
re_path(r"^terms$", v.static_terms_of_use, name="terms_of_use"),
|
||||
re_path(r"^privacy$", v.static_privacy_policy, name="privacy_policy"),
|
||||
re_path(r"^cookie-policy$", v.static_cookie_policy, name="cookie_policy"),
|
||||
re_path(r"^about$", v.static_about_us, name="about_us"),
|
||||
re_path(r"^contact$", v.static_contact_support, name="contact_support"),
|
||||
re_path(r"^careers$", v.static_careers, name="careers"),
|
||||
re_path(r"^cite$", v.static_cite, name="cite"),
|
||||
re_path(r"^legal$", v.static_legal, name="legal"),
|
||||
]
|
||||
|
||||
187
epdb/views.py
187
epdb/views.py
@ -10,6 +10,7 @@ from django.urls import reverse
|
||||
from django.views.decorators.csrf import csrf_exempt
|
||||
from envipy_additional_information import NAME_MAPPING
|
||||
from oauth2_provider.decorators import protected_resource
|
||||
import nh3
|
||||
|
||||
from utilities.chem import FormatConverter, IndigoUtils
|
||||
from utilities.decorators import package_permission_required
|
||||
@ -85,7 +86,11 @@ def login(request):
|
||||
from django.contrib.auth import authenticate
|
||||
from django.contrib.auth import login
|
||||
|
||||
username = request.POST.get("username")
|
||||
username = request.POST.get("username").strip()
|
||||
if username != request.POST.get("username"):
|
||||
context["message"] = "Login failed!"
|
||||
return render(request, "static/login.html", context)
|
||||
|
||||
password = request.POST.get("password")
|
||||
|
||||
# Get email for username and check if the account is active
|
||||
@ -100,6 +105,7 @@ def login(request):
|
||||
except get_user_model().DoesNotExist:
|
||||
context["message"] = "Login failed!"
|
||||
return render(request, "static/login.html", context)
|
||||
|
||||
try:
|
||||
user = authenticate(username=email, password=password)
|
||||
except Exception:
|
||||
@ -137,9 +143,14 @@ def register(request):
|
||||
context = get_base_context(request)
|
||||
|
||||
if request.method == "GET":
|
||||
context["title"] = "enviPath"
|
||||
context["next"] = request.GET.get("next", "")
|
||||
return render(request, "static/register.html", context)
|
||||
# Redirect to unified login page with signup tab
|
||||
next_url = request.GET.get("next", "")
|
||||
redirect_url = reverse("login") + "#signup"
|
||||
|
||||
if next_url:
|
||||
redirect_url += f"?next={next_url}"
|
||||
|
||||
return redirect(redirect_url)
|
||||
elif request.method == "POST":
|
||||
context["title"] = "enviPath"
|
||||
if next := request.POST.get("next"):
|
||||
@ -152,18 +163,18 @@ def register(request):
|
||||
|
||||
if not (username and email and password):
|
||||
context["message"] = "Invalid username/email/password"
|
||||
return render(request, "static/register.html", context)
|
||||
return render(request, "static/login.html", context)
|
||||
|
||||
if password != rpassword or password == "":
|
||||
context["message"] = "Registration failed, provided passwords differ!"
|
||||
return render(request, "static/register.html", context)
|
||||
return render(request, "static/login.html", context)
|
||||
|
||||
try:
|
||||
u = UserManager.create_user(username, email, password)
|
||||
logger.info(f"Created user {u.username} ({u.pk})")
|
||||
except Exception:
|
||||
context["message"] = "Registration failed! Couldn't create User Account."
|
||||
return render(request, "static/register.html", context)
|
||||
return render(request, "static/login.html", context)
|
||||
|
||||
if s.ADMIN_APPROVAL_REQUIRED:
|
||||
context["success_message"] = (
|
||||
@ -670,7 +681,7 @@ def search(request):
|
||||
|
||||
if request.method == "GET":
|
||||
package_urls = request.GET.getlist("packages")
|
||||
searchterm = request.GET.get("search")
|
||||
searchterm = request.GET.get("search", "").strip()
|
||||
mode = request.GET.get("mode")
|
||||
|
||||
# add HTTP_ACCEPT check to differentiate between index and ajax call
|
||||
@ -936,8 +947,14 @@ def package_model(request, package_uuid, model_uuid):
|
||||
else:
|
||||
return HttpResponseBadRequest()
|
||||
else:
|
||||
name = request.POST.get("model-name", "").strip()
|
||||
description = request.POST.get("model-description", "").strip()
|
||||
# TODO: Move cleaning to property updater
|
||||
name = request.POST.get("model-name")
|
||||
if name is not None:
|
||||
name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
description = request.POST.get("model-description")
|
||||
if description is not None:
|
||||
description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
if any([name, description]):
|
||||
if name:
|
||||
@ -1039,8 +1056,16 @@ def package(request, package_uuid):
|
||||
else:
|
||||
return HttpResponseBadRequest()
|
||||
|
||||
# TODO: Move cleaning to property updater
|
||||
new_package_name = request.POST.get("package-name")
|
||||
if new_package_name is not None:
|
||||
new_package_name = nh3.clean(new_package_name, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
new_package_description = request.POST.get("package-description")
|
||||
if new_package_description is not None:
|
||||
new_package_description = nh3.clean(
|
||||
new_package_description, tags=s.ALLOWED_HTML_TAGS
|
||||
).strip()
|
||||
|
||||
grantee_url = request.POST.get("grantee")
|
||||
read = request.POST.get("read") == "on"
|
||||
@ -1189,8 +1214,16 @@ def package_compound(request, package_uuid, compound_uuid):
|
||||
|
||||
return JsonResponse({"success": current_compound.url})
|
||||
|
||||
new_compound_name = request.POST.get("compound-name", "").strip()
|
||||
new_compound_description = request.POST.get("compound-description", "").strip()
|
||||
# TODO: Move cleaning to property updater
|
||||
new_compound_name = request.POST.get("compound-name")
|
||||
if new_compound_name is not None:
|
||||
new_compound_name = nh3.clean(new_compound_name, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
new_compound_description = request.POST.get("compound-description")
|
||||
if new_compound_description is not None:
|
||||
new_compound_description = nh3.clean(
|
||||
new_compound_description, tags=s.ALLOWED_HTML_TAGS
|
||||
).strip()
|
||||
|
||||
if new_compound_name:
|
||||
current_compound.name = new_compound_name
|
||||
@ -1255,7 +1288,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
|
||||
|
||||
elif request.method == "POST":
|
||||
structure_name = request.POST.get("structure-name")
|
||||
structure_smiles = request.POST.get("structure-smiles")
|
||||
structure_smiles = request.POST.get("structure-smiles").strip()
|
||||
structure_description = request.POST.get("structure-description")
|
||||
|
||||
try:
|
||||
@ -1326,8 +1359,16 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
|
||||
else:
|
||||
return HttpResponseBadRequest()
|
||||
|
||||
new_structure_name = request.POST.get("compound-structure-name", "").strip()
|
||||
new_structure_description = request.POST.get("compound-structure-description", "").strip()
|
||||
# TODO: Move cleaning to property updater
|
||||
new_structure_name = request.POST.get("compound-structure-name")
|
||||
if new_structure_name is not None:
|
||||
new_structure_name = nh3.clean(new_structure_name, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
new_structure_description = request.POST.get("compound-structure-description")
|
||||
if new_structure_description is not None:
|
||||
new_structure_description = nh3.clean(
|
||||
new_structure_description, tags=s.ALLOWED_HTML_TAGS
|
||||
).strip()
|
||||
|
||||
if new_structure_name:
|
||||
current_structure.name = new_structure_name
|
||||
@ -1429,11 +1470,11 @@ 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["smirks"] = request.POST.get("rule-smirks").strip()
|
||||
params["reactant_filter_smarts"] = request.POST.get("rule-reactant-smarts")
|
||||
params["product_filter_smarts"] = request.POST.get("rule-product-smarts")
|
||||
elif rule_type == "SimpleRDKitRule":
|
||||
params["reaction_smarts"] = request.POST.get("rule-reaction-smarts")
|
||||
params["reaction_smarts"] = request.POST.get("rule-reaction-smarts").strip()
|
||||
elif rule_type == "ParallelRule":
|
||||
pass
|
||||
elif rule_type == "SequentialRule":
|
||||
@ -1534,8 +1575,14 @@ def package_rule(request, package_uuid, rule_uuid):
|
||||
|
||||
return JsonResponse({"success": current_rule.url})
|
||||
|
||||
rule_name = request.POST.get("rule-name", "").strip()
|
||||
rule_description = request.POST.get("rule-description", "").strip()
|
||||
# TODO: Move cleaning to property updater
|
||||
rule_name = request.POST.get("rule-name")
|
||||
if rule_name is not None:
|
||||
rule_name = nh3.clean(rule_name, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
rule_description = request.POST.get("rule-description")
|
||||
if rule_description is not None:
|
||||
rule_description = nh3.clean(rule_description, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
if rule_name:
|
||||
current_rule.name = rule_name
|
||||
@ -1624,8 +1671,7 @@ def package_reactions(request, package_uuid):
|
||||
elif request.method == "POST":
|
||||
reaction_name = request.POST.get("reaction-name")
|
||||
reaction_description = request.POST.get("reaction-description")
|
||||
reactions_smirks = request.POST.get("reaction-smirks")
|
||||
|
||||
reactions_smirks = request.POST.get("reaction-smirks").strip()
|
||||
educts = reactions_smirks.split(">>")[0].split(".")
|
||||
products = reactions_smirks.split(">>")[1].split(".")
|
||||
|
||||
@ -1686,8 +1732,16 @@ def package_reaction(request, package_uuid, reaction_uuid):
|
||||
|
||||
return JsonResponse({"success": current_reaction.url})
|
||||
|
||||
new_reaction_name = request.POST.get("reaction-name", "").strip()
|
||||
new_reaction_description = request.POST.get("reaction-description", "").strip()
|
||||
# TODO: Move cleaning to property updater
|
||||
new_reaction_name = request.POST.get("reaction-name")
|
||||
if new_reaction_name is not None:
|
||||
new_reaction_name = nh3.clean(new_reaction_name, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
new_reaction_description = request.POST.get("reaction-description")
|
||||
if new_reaction_description is not None:
|
||||
new_reaction_description = nh3.clean(
|
||||
new_reaction_description, tags=s.ALLOWED_HTML_TAGS
|
||||
).strip()
|
||||
|
||||
if new_reaction_name:
|
||||
current_reaction.name = new_reaction_name
|
||||
@ -1764,8 +1818,9 @@ def package_pathways(request, package_uuid):
|
||||
|
||||
name = request.POST.get("name")
|
||||
description = request.POST.get("description")
|
||||
pw_mode = request.POST.get("predict", "predict").strip()
|
||||
|
||||
smiles = request.POST.get("smiles", "").strip()
|
||||
pw_mode = request.POST.get("predict", "predict").strip()
|
||||
|
||||
if "smiles" in request.POST and smiles == "":
|
||||
return error(
|
||||
@ -1774,8 +1829,6 @@ def package_pathways(request, package_uuid):
|
||||
"Pathway prediction failed due to missing or empty SMILES",
|
||||
)
|
||||
|
||||
smiles = smiles.strip()
|
||||
|
||||
try:
|
||||
stand_smiles = FormatConverter.standardize(smiles)
|
||||
except ValueError:
|
||||
@ -1934,8 +1987,14 @@ def package_pathway(request, package_uuid, pathway_uuid):
|
||||
|
||||
return JsonResponse({"success": current_pathway.url})
|
||||
|
||||
# TODO: Move cleaning to property updater
|
||||
pathway_name = request.POST.get("pathway-name")
|
||||
if pathway_name is not None:
|
||||
pathway_name = nh3.clean(pathway_name, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
pathway_description = request.POST.get("pathway-description")
|
||||
if pathway_description is not None:
|
||||
pathway_description = nh3.clean(pathway_description, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
|
||||
if any([pathway_name, pathway_description]):
|
||||
if pathway_name is not None and pathway_name.strip() != "":
|
||||
@ -2023,8 +2082,8 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
|
||||
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")
|
||||
|
||||
node_smiles = request.POST.get("node-smiles").strip()
|
||||
current_pathway.add_node(node_smiles, name=node_name, description=node_description)
|
||||
|
||||
return redirect(current_pathway.url)
|
||||
@ -2189,6 +2248,7 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
|
||||
|
||||
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")
|
||||
|
||||
@ -2275,7 +2335,7 @@ def package_scenarios(request, package_uuid):
|
||||
"all", False
|
||||
):
|
||||
scens = Scenario.objects.filter(package=current_package).order_by("name")
|
||||
res = [{"name": s.name, "url": s.url, "uuid": s.uuid} for s in scens]
|
||||
res = [{"name": s_.name, "url": s_.url, "uuid": s_.uuid} for s_ in scens]
|
||||
return JsonResponse(res, safe=False)
|
||||
|
||||
context = get_base_context(request)
|
||||
@ -2323,21 +2383,21 @@ def package_scenarios(request, package_uuid):
|
||||
"name": "soil",
|
||||
"widgets": [
|
||||
HTMLGenerator.generate_html(ai, prefix=f"soil_{0}")
|
||||
for ai in [x for s in SOIL_ADDITIONAL_INFORMATION.values() for x in s]
|
||||
for ai in [x for sv in SOIL_ADDITIONAL_INFORMATION.values() for x in sv]
|
||||
],
|
||||
},
|
||||
"Sludge Data": {
|
||||
"name": "sludge",
|
||||
"widgets": [
|
||||
HTMLGenerator.generate_html(ai, prefix=f"sludge_{0}")
|
||||
for ai in [x for s in SLUDGE_ADDITIONAL_INFORMATION.values() for x in s]
|
||||
for ai in [x for sv in SLUDGE_ADDITIONAL_INFORMATION.values() for x in sv]
|
||||
],
|
||||
},
|
||||
"Water-Sediment System Data": {
|
||||
"name": "sediment",
|
||||
"widgets": [
|
||||
HTMLGenerator.generate_html(ai, prefix=f"sediment_{0}")
|
||||
for ai in [x for s in SEDIMENT_ADDITIONAL_INFORMATION.values() for x in s]
|
||||
for ai in [x for sv in SEDIMENT_ADDITIONAL_INFORMATION.values() for x in sv]
|
||||
],
|
||||
},
|
||||
}
|
||||
@ -2352,6 +2412,7 @@ def package_scenarios(request, package_uuid):
|
||||
|
||||
scenario_name = request.POST.get("scenario-name")
|
||||
scenario_description = request.POST.get("scenario-description")
|
||||
|
||||
scenario_date_year = request.POST.get("scenario-date-year")
|
||||
scenario_date_month = request.POST.get("scenario-date-month")
|
||||
scenario_date_day = request.POST.get("scenario-date-day")
|
||||
@ -2365,9 +2426,9 @@ def package_scenarios(request, package_uuid):
|
||||
scenario_type = request.POST.get("scenario-type")
|
||||
|
||||
additional_information = HTMLGenerator.build_models(request.POST.dict())
|
||||
additional_information = [x for s in additional_information.values() for x in s]
|
||||
additional_information = [x for sv in additional_information.values() for x in sv]
|
||||
|
||||
s = Scenario.create(
|
||||
new_scen = Scenario.create(
|
||||
current_package,
|
||||
name=scenario_name,
|
||||
description=scenario_description,
|
||||
@ -2376,7 +2437,7 @@ def package_scenarios(request, package_uuid):
|
||||
additional_information=additional_information,
|
||||
)
|
||||
|
||||
return redirect(s.url)
|
||||
return redirect(new_scen.url)
|
||||
else:
|
||||
return HttpResponseNotAllowed(
|
||||
[
|
||||
@ -2676,6 +2737,7 @@ def settings(request):
|
||||
|
||||
name = request.POST.get("prediction-setting-name")
|
||||
description = request.POST.get("prediction-setting-description")
|
||||
|
||||
new_default = request.POST.get("prediction-setting-new-default", "off") == "on"
|
||||
|
||||
max_nodes = min(
|
||||
@ -2826,3 +2888,60 @@ def userinfo(request):
|
||||
"email_verified": user.is_active,
|
||||
}
|
||||
return JsonResponse(res)
|
||||
|
||||
|
||||
# Static Pages
|
||||
def static_terms_of_use(request):
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - Terms of Use"
|
||||
context["public_mode"] = True
|
||||
return render(request, "static/terms_of_use.html", context)
|
||||
|
||||
|
||||
def static_privacy_policy(request):
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - Privacy Policy"
|
||||
context["public_mode"] = True
|
||||
return render(request, "static/privacy_policy.html", context)
|
||||
|
||||
|
||||
def static_cookie_policy(request):
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - Cookie Policy"
|
||||
context["public_mode"] = True
|
||||
return render(request, "static/cookie_policy.html", context)
|
||||
|
||||
|
||||
def static_about_us(request):
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - About Us"
|
||||
context["public_mode"] = True
|
||||
return render(request, "static/about_us.html", context)
|
||||
|
||||
|
||||
def static_contact_support(request):
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - Contact & Support"
|
||||
context["public_mode"] = True
|
||||
return render(request, "static/contact.html", context)
|
||||
|
||||
|
||||
def static_careers(request):
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - Careers"
|
||||
context["public_mode"] = True
|
||||
return render(request, "static/careers.html", context)
|
||||
|
||||
|
||||
def static_cite(request):
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - How to Cite"
|
||||
context["public_mode"] = True
|
||||
return render(request, "static/cite.html", context)
|
||||
|
||||
|
||||
def static_legal(request):
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - Legal Information"
|
||||
context["public_mode"] = True
|
||||
return render(request, "static/legal.html", context)
|
||||
|
||||
Reference in New Issue
Block a user