forked from enviPath/enviPy
[Chore] Linted Files (#150)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#150
This commit is contained in:
@ -18,7 +18,7 @@ from .models import (
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Scenario,
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Setting,
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ExternalDatabase,
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ExternalIdentifier
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ExternalIdentifier,
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)
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@ -39,7 +39,7 @@ class GroupPackagePermissionAdmin(admin.ModelAdmin):
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class EPAdmin(admin.ModelAdmin):
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search_fields = ['name', 'description']
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search_fields = ["name", "description"]
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class PackageAdmin(EPAdmin):
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13
epdb/api.py
13
epdb/api.py
@ -21,7 +21,7 @@ class BearerTokenAuth(HttpBearer):
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def _anonymous_or_real(request):
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if request.user.is_authenticated and not request.user.is_anonymous:
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return request.user
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return get_user_model().objects.get(username='anonymous')
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return get_user_model().objects.get(username="anonymous")
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router = Router(auth=BearerTokenAuth())
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@ -85,7 +85,9 @@ def get_package(request, package_uuid):
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try:
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return PackageManager.get_package_by_id(request.auth, package_id=package_uuid)
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except ValueError:
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return 403, {'message': f'Getting Package with id {package_uuid} failed due to insufficient rights!'}
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return 403, {
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"message": f"Getting Package with id {package_uuid} failed due to insufficient rights!"
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}
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@router.get("/compound", response={200: List[CompoundSchema], 403: Error})
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@ -97,7 +99,9 @@ def get_compounds(request):
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return qs
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@router.get("/package/{uuid:package_uuid}/compound", response={200: List[CompoundSchema], 403: Error})
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@router.get(
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"/package/{uuid:package_uuid}/compound", response={200: List[CompoundSchema], 403: Error}
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)
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@paginate
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def get_package_compounds(request, package_uuid):
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try:
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@ -105,4 +109,5 @@ def get_package_compounds(request, package_uuid):
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return Compound.objects.filter(package=p)
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except ValueError:
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return 403, {
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'message': f'Getting Compounds for Package with id {package_uuid} failed due to insufficient rights!'}
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"message": f"Getting Compounds for Package with id {package_uuid} failed due to insufficient rights!"
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}
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@ -2,8 +2,8 @@ from django.apps import AppConfig
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class EPDBConfig(AppConfig):
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default_auto_field = 'django.db.models.BigAutoField'
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name = 'epdb'
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default_auto_field = "django.db.models.BigAutoField"
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name = "epdb"
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def ready(self):
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import epdb.signals # noqa: F401
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@ -1,5 +0,0 @@
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from django import forms
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class EmailLoginForm(forms.Form):
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email = forms.EmailField()
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File diff suppressed because it is too large
Load Diff
991
epdb/logic.py
991
epdb/logic.py
File diff suppressed because it is too large
Load Diff
@ -5,32 +5,49 @@ from django.core.management.base import BaseCommand
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from django.db import transaction
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from epdb.logic import UserManager, GroupManager, PackageManager, SettingManager
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from epdb.models import UserSettingPermission, MLRelativeReasoning, EnviFormer, Permission, User, ExternalDatabase
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from epdb.models import (
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UserSettingPermission,
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MLRelativeReasoning,
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EnviFormer,
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Permission,
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User,
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ExternalDatabase,
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)
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class Command(BaseCommand):
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def create_users(self):
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# Anonymous User
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if not User.objects.filter(email='anon@envipath.com').exists():
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anon = UserManager.create_user("anonymous", "anon@envipath.com", "SuperSafe",
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is_active=True, add_to_group=False, set_setting=False)
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if not User.objects.filter(email="anon@envipath.com").exists():
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anon = UserManager.create_user(
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"anonymous",
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"anon@envipath.com",
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"SuperSafe",
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is_active=True,
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add_to_group=False,
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set_setting=False,
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)
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else:
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anon = User.objects.get(email='anon@envipath.com')
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anon = User.objects.get(email="anon@envipath.com")
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# Admin User
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if not User.objects.filter(email='admin@envipath.com').exists():
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admin = UserManager.create_user("admin", "admin@envipath.com", "SuperSafe",
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is_active=True, add_to_group=False, set_setting=False)
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if not User.objects.filter(email="admin@envipath.com").exists():
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admin = UserManager.create_user(
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"admin",
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"admin@envipath.com",
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"SuperSafe",
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is_active=True,
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add_to_group=False,
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set_setting=False,
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)
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admin.is_staff = True
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admin.is_superuser = True
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admin.save()
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else:
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admin = User.objects.get(email='admin@envipath.com')
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admin = User.objects.get(email="admin@envipath.com")
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# System Group
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g = GroupManager.create_group(admin, 'enviPath Users', 'All enviPath Users')
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g = GroupManager.create_group(admin, "enviPath Users", "All enviPath Users")
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g.public = True
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g.save()
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@ -43,14 +60,20 @@ class Command(BaseCommand):
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admin.default_group = g
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admin.save()
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if not User.objects.filter(email='user0@envipath.com').exists():
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user0 = UserManager.create_user("user0", "user0@envipath.com", "SuperSafe",
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is_active=True, add_to_group=False, set_setting=False)
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if not User.objects.filter(email="user0@envipath.com").exists():
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user0 = UserManager.create_user(
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"user0",
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"user0@envipath.com",
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"SuperSafe",
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is_active=True,
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add_to_group=False,
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set_setting=False,
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)
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user0.is_staff = True
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user0.is_superuser = True
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user0.save()
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else:
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user0 = User.objects.get(email='user0@envipath.com')
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user0 = User.objects.get(email="user0@envipath.com")
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g.user_member.add(user0)
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g.save()
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@ -61,18 +84,20 @@ class Command(BaseCommand):
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return anon, admin, g, user0
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def import_package(self, data, owner):
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return PackageManager.import_legacy_package(data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True)
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return PackageManager.import_legacy_package(
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data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
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)
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def create_default_setting(self, owner, packages):
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s = SettingManager.create_setting(
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owner,
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name='Global Default Setting',
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description='Global Default Setting containing BBD Rules and Max 30 Nodes and Max Depth of 8',
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name="Global Default Setting",
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description="Global Default Setting containing BBD Rules and Max 30 Nodes and Max Depth of 8",
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max_nodes=30,
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max_depth=5,
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rule_packages=packages,
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model=None,
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model_threshold=None
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model_threshold=None,
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)
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return s
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@ -84,54 +109,51 @@ class Command(BaseCommand):
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"""
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databases = [
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{
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'name': 'PubChem Compound',
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'full_name': 'PubChem Compound Database',
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'description': 'Chemical database of small organic molecules',
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'base_url': 'https://pubchem.ncbi.nlm.nih.gov',
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'url_pattern': 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'
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"name": "PubChem Compound",
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"full_name": "PubChem Compound Database",
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"description": "Chemical database of small organic molecules",
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"base_url": "https://pubchem.ncbi.nlm.nih.gov",
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"url_pattern": "https://pubchem.ncbi.nlm.nih.gov/compound/{id}",
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},
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{
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'name': 'PubChem Substance',
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'full_name': 'PubChem Substance Database',
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'description': 'Database of chemical substances',
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'base_url': 'https://pubchem.ncbi.nlm.nih.gov',
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'url_pattern': 'https://pubchem.ncbi.nlm.nih.gov/substance/{id}'
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"name": "PubChem Substance",
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"full_name": "PubChem Substance Database",
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"description": "Database of chemical substances",
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"base_url": "https://pubchem.ncbi.nlm.nih.gov",
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"url_pattern": "https://pubchem.ncbi.nlm.nih.gov/substance/{id}",
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},
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{
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'name': 'ChEBI',
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'full_name': 'Chemical Entities of Biological Interest',
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'description': 'Dictionary of molecular entities',
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'base_url': 'https://www.ebi.ac.uk/chebi',
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'url_pattern': 'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{id}'
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"name": "ChEBI",
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"full_name": "Chemical Entities of Biological Interest",
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"description": "Dictionary of molecular entities",
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"base_url": "https://www.ebi.ac.uk/chebi",
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"url_pattern": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{id}",
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},
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{
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'name': 'RHEA',
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'full_name': 'RHEA Reaction Database',
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'description': 'Comprehensive resource of biochemical reactions',
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'base_url': 'https://www.rhea-db.org',
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'url_pattern': 'https://www.rhea-db.org/rhea/{id}'
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"name": "RHEA",
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"full_name": "RHEA Reaction Database",
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"description": "Comprehensive resource of biochemical reactions",
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"base_url": "https://www.rhea-db.org",
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"url_pattern": "https://www.rhea-db.org/rhea/{id}",
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},
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{
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'name': 'KEGG Reaction',
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'full_name': 'KEGG Reaction Database',
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'description': 'Database of biochemical reactions',
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'base_url': 'https://www.genome.jp',
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'url_pattern': 'https://www.genome.jp/entry/{id}'
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"name": "KEGG Reaction",
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"full_name": "KEGG Reaction Database",
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"description": "Database of biochemical reactions",
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"base_url": "https://www.genome.jp",
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"url_pattern": "https://www.genome.jp/entry/{id}",
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},
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{
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'name': 'UniProt',
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'full_name': 'MetaCyc Metabolic Pathway Database',
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'description': 'UniProt is a freely accessible database of protein sequence and functional information',
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'base_url': 'https://www.uniprot.org',
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'url_pattern': 'https://www.uniprot.org/uniprotkb?query="{id}"'
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}
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"name": "UniProt",
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"full_name": "MetaCyc Metabolic Pathway Database",
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"description": "UniProt is a freely accessible database of protein sequence and functional information",
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"base_url": "https://www.uniprot.org",
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"url_pattern": 'https://www.uniprot.org/uniprotkb?query="{id}"',
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},
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]
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for db_info in databases:
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ExternalDatabase.objects.get_or_create(
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name=db_info['name'],
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defaults=db_info
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)
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ExternalDatabase.objects.get_or_create(name=db_info["name"], defaults=db_info)
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@transaction.atomic
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def handle(self, *args, **options):
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@ -142,20 +164,24 @@ class Command(BaseCommand):
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# Import Packages
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packages = [
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'EAWAG-BBD.json',
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'EAWAG-SOIL.json',
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'EAWAG-SLUDGE.json',
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'EAWAG-SEDIMENT.json',
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"EAWAG-BBD.json",
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"EAWAG-SOIL.json",
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"EAWAG-SLUDGE.json",
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"EAWAG-SEDIMENT.json",
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]
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mapping = {}
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for p in packages:
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print(f"Importing {p}...")
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package_data = json.loads(open(s.BASE_DIR / 'fixtures' / 'packages' / '2025-07-18' / p, encoding='utf-8').read())
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package_data = json.loads(
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open(
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s.BASE_DIR / "fixtures" / "packages" / "2025-07-18" / p, encoding="utf-8"
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).read()
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)
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imported_package = self.import_package(package_data, admin)
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mapping[p.replace('.json', '')] = imported_package
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mapping[p.replace(".json", "")] = imported_package
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setting = self.create_default_setting(admin, [mapping['EAWAG-BBD']])
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setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])
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setting.public = True
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setting.save()
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setting.make_global_default()
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@ -171,26 +197,28 @@ class Command(BaseCommand):
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usp.save()
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# Create Model Package
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pack = PackageManager.create_package(admin, "Public Prediction Models",
|
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"Package to make Prediction Models publicly available")
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pack = PackageManager.create_package(
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admin,
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"Public Prediction Models",
|
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"Package to make Prediction Models publicly available",
|
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)
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pack.reviewed = True
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pack.save()
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# Create RR
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ml_model = MLRelativeReasoning.create(
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package=pack,
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rule_packages=[mapping['EAWAG-BBD']],
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data_packages=[mapping['EAWAG-BBD']],
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rule_packages=[mapping["EAWAG-BBD"]],
|
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data_packages=[mapping["EAWAG-BBD"]],
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eval_packages=[],
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threshold=0.5,
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name='ECC - BBD - T0.5',
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description='ML Relative Reasoning',
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name="ECC - BBD - T0.5",
|
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description="ML Relative Reasoning",
|
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)
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|
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ml_model.build_dataset()
|
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ml_model.build_model()
|
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# ml_model.evaluate_model()
|
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|
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# If available, create EnviFormerModel
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if s.ENVIFORMER_PRESENT:
|
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enviFormer_model = EnviFormer.create(pack, 'EnviFormer - T0.5', 'EnviFormer Model with Threshold 0.5', 0.5)
|
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EnviFormer.create(pack, "EnviFormer - T0.5", "EnviFormer Model with Threshold 0.5", 0.5)
|
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|
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@ -12,11 +12,28 @@ class Command(BaseCommand):
|
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the below command would be used:
|
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`python manage.py create_ml_models enviformer mlrr -d bbd soil -e sludge
|
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"""
|
||||
|
||||
def add_arguments(self, parser):
|
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parser.add_argument("model_names", nargs="+", type=str, help="The names of models to train. Options are: enviformer, mlrr")
|
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parser.add_argument("-d", "--data-packages", nargs="+", type=str, help="Packages for training")
|
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parser.add_argument("-e", "--eval-packages", nargs="*", type=str, help="Packages for evaluation", default=[])
|
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parser.add_argument("-r", "--rule-packages", nargs="*", type=str, help="Rule Packages mandatory for MLRR", default=[])
|
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parser.add_argument(
|
||||
"model_names",
|
||||
nargs="+",
|
||||
type=str,
|
||||
help="The names of models to train. Options are: enviformer, mlrr",
|
||||
)
|
||||
parser.add_argument(
|
||||
"-d", "--data-packages", nargs="+", type=str, help="Packages for training"
|
||||
)
|
||||
parser.add_argument(
|
||||
"-e", "--eval-packages", nargs="*", type=str, help="Packages for evaluation", default=[]
|
||||
)
|
||||
parser.add_argument(
|
||||
"-r",
|
||||
"--rule-packages",
|
||||
nargs="*",
|
||||
type=str,
|
||||
help="Rule Packages mandatory for MLRR",
|
||||
default=[],
|
||||
)
|
||||
|
||||
@transaction.atomic
|
||||
def handle(self, *args, **options):
|
||||
@ -28,7 +45,9 @@ class Command(BaseCommand):
|
||||
sludge = Package.objects.filter(name="EAWAG-SLUDGE")[0]
|
||||
sediment = Package.objects.filter(name="EAWAG-SEDIMENT")[0]
|
||||
except IndexError:
|
||||
raise IndexError("Can't find correct packages. They should be created with the bootstrap command")
|
||||
raise IndexError(
|
||||
"Can't find correct packages. They should be created with the bootstrap command"
|
||||
)
|
||||
|
||||
def decode_packages(package_list):
|
||||
"""Decode package strings into their respective packages"""
|
||||
@ -52,15 +71,27 @@ class Command(BaseCommand):
|
||||
data_packages = decode_packages(options["data_packages"])
|
||||
eval_packages = decode_packages(options["eval_packages"])
|
||||
rule_packages = decode_packages(options["rule_packages"])
|
||||
for model_name in options['model_names']:
|
||||
for model_name in options["model_names"]:
|
||||
model_name = model_name.lower()
|
||||
if model_name == "enviformer" and s.ENVIFORMER_PRESENT:
|
||||
model = EnviFormer.create(pack, data_packages=data_packages, eval_packages=eval_packages, threshold=0.5,
|
||||
name="EnviFormer - T0.5", description="EnviFormer transformer")
|
||||
model = EnviFormer.create(
|
||||
pack,
|
||||
data_packages=data_packages,
|
||||
eval_packages=eval_packages,
|
||||
threshold=0.5,
|
||||
name="EnviFormer - T0.5",
|
||||
description="EnviFormer transformer",
|
||||
)
|
||||
elif model_name == "mlrr":
|
||||
model = MLRelativeReasoning.create(package=pack, rule_packages=rule_packages,
|
||||
data_packages=data_packages, eval_packages=eval_packages, threshold=0.5,
|
||||
name='ECC - BBD - T0.5', description='ML Relative Reasoning')
|
||||
model = MLRelativeReasoning.create(
|
||||
package=pack,
|
||||
rule_packages=rule_packages,
|
||||
data_packages=data_packages,
|
||||
eval_packages=eval_packages,
|
||||
threshold=0.5,
|
||||
name="ECC - BBD - T0.5",
|
||||
description="ML Relative Reasoning",
|
||||
)
|
||||
else:
|
||||
raise ValueError(f"Cannot create model of type {model_name}, unknown model type")
|
||||
# Build the dataset for the model, train it, evaluate it and save it
|
||||
|
||||
@ -1,57 +1,58 @@
|
||||
from csv import DictReader
|
||||
|
||||
from django.core.management.base import BaseCommand
|
||||
from django.db import transaction
|
||||
|
||||
from epdb.models import *
|
||||
from epdb.models import Compound, CompoundStructure, Reaction, ExternalDatabase, ExternalIdentifier
|
||||
|
||||
|
||||
class Command(BaseCommand):
|
||||
STR_TO_MODEL = {
|
||||
'Compound': Compound,
|
||||
'CompoundStructure': CompoundStructure,
|
||||
'Reaction': Reaction,
|
||||
"Compound": Compound,
|
||||
"CompoundStructure": CompoundStructure,
|
||||
"Reaction": Reaction,
|
||||
}
|
||||
|
||||
STR_TO_DATABASE = {
|
||||
'ChEBI': ExternalDatabase.objects.get(name='ChEBI'),
|
||||
'RHEA': ExternalDatabase.objects.get(name='RHEA'),
|
||||
'KEGG Reaction': ExternalDatabase.objects.get(name='KEGG Reaction'),
|
||||
'PubChem Compound': ExternalDatabase.objects.get(name='PubChem Compound'),
|
||||
'PubChem Substance': ExternalDatabase.objects.get(name='PubChem Substance'),
|
||||
"ChEBI": ExternalDatabase.objects.get(name="ChEBI"),
|
||||
"RHEA": ExternalDatabase.objects.get(name="RHEA"),
|
||||
"KEGG Reaction": ExternalDatabase.objects.get(name="KEGG Reaction"),
|
||||
"PubChem Compound": ExternalDatabase.objects.get(name="PubChem Compound"),
|
||||
"PubChem Substance": ExternalDatabase.objects.get(name="PubChem Substance"),
|
||||
}
|
||||
|
||||
def add_arguments(self, parser):
|
||||
parser.add_argument(
|
||||
'--data',
|
||||
"--data",
|
||||
type=str,
|
||||
help='Path of the ID Mapping file.',
|
||||
help="Path of the ID Mapping file.",
|
||||
required=True,
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
'--replace-host',
|
||||
"--replace-host",
|
||||
type=str,
|
||||
help='Replace https://envipath.org/ with this host, e.g. http://localhost:8000/',
|
||||
help="Replace https://envipath.org/ with this host, e.g. http://localhost:8000/",
|
||||
)
|
||||
|
||||
@transaction.atomic
|
||||
def handle(self, *args, **options):
|
||||
with open(options['data']) as fh:
|
||||
with open(options["data"]) as fh:
|
||||
reader = DictReader(fh)
|
||||
for row in reader:
|
||||
clz = self.STR_TO_MODEL[row['model']]
|
||||
clz = self.STR_TO_MODEL[row["model"]]
|
||||
|
||||
url = row['url']
|
||||
if options['replace_host']:
|
||||
url = url.replace('https://envipath.org/', options['replace_host'])
|
||||
url = row["url"]
|
||||
if options["replace_host"]:
|
||||
url = url.replace("https://envipath.org/", options["replace_host"])
|
||||
|
||||
instance = clz.objects.get(url=url)
|
||||
db = self.STR_TO_DATABASE[row['identifier_type']]
|
||||
db = self.STR_TO_DATABASE[row["identifier_type"]]
|
||||
|
||||
ExternalIdentifier.objects.create(
|
||||
content_object=instance,
|
||||
database=db,
|
||||
identifier_value=row['identifier_value'],
|
||||
url=db.url_pattern.format(id=row['identifier_value']),
|
||||
is_primary=False
|
||||
identifier_value=row["identifier_value"],
|
||||
url=db.url_pattern.format(id=row["identifier_value"]),
|
||||
is_primary=False,
|
||||
)
|
||||
|
||||
@ -1,27 +1,29 @@
|
||||
import json
|
||||
|
||||
from django.core.management.base import BaseCommand
|
||||
from django.db import transaction
|
||||
|
||||
from epdb.logic import PackageManager
|
||||
from epdb.models import *
|
||||
from epdb.models import User
|
||||
|
||||
|
||||
class Command(BaseCommand):
|
||||
|
||||
def add_arguments(self, parser):
|
||||
parser.add_argument(
|
||||
'--data',
|
||||
"--data",
|
||||
type=str,
|
||||
help='Path of the Package to import.',
|
||||
help="Path of the Package to import.",
|
||||
required=True,
|
||||
)
|
||||
parser.add_argument(
|
||||
'--owner',
|
||||
"--owner",
|
||||
type=str,
|
||||
help='Username of the desired Owner.',
|
||||
help="Username of the desired Owner.",
|
||||
required=True,
|
||||
)
|
||||
|
||||
@transaction.atomic
|
||||
def handle(self, *args, **options):
|
||||
owner = User.objects.get(username=options['owner'])
|
||||
package_data = json.load(open(options['data']))
|
||||
owner = User.objects.get(username=options["owner"])
|
||||
package_data = json.load(open(options["data"]))
|
||||
PackageManager.import_legacy_package(package_data, owner)
|
||||
|
||||
@ -6,46 +6,45 @@ from django.db.models.functions import Replace
|
||||
|
||||
|
||||
class Command(BaseCommand):
|
||||
|
||||
def add_arguments(self, parser):
|
||||
parser.add_argument(
|
||||
'--old',
|
||||
"--old",
|
||||
type=str,
|
||||
help='Old Host, most likely https://envipath.org/',
|
||||
help="Old Host, most likely https://envipath.org/",
|
||||
required=True,
|
||||
)
|
||||
parser.add_argument(
|
||||
'--new',
|
||||
"--new",
|
||||
type=str,
|
||||
help='New Host, most likely http://localhost:8000/',
|
||||
help="New Host, most likely http://localhost:8000/",
|
||||
required=True,
|
||||
)
|
||||
|
||||
def handle(self, *args, **options):
|
||||
MODELS = [
|
||||
'User',
|
||||
'Group',
|
||||
'Package',
|
||||
'Compound',
|
||||
'CompoundStructure',
|
||||
'Pathway',
|
||||
'Edge',
|
||||
'Node',
|
||||
'Reaction',
|
||||
'SimpleAmbitRule',
|
||||
'SimpleRDKitRule',
|
||||
'ParallelRule',
|
||||
'SequentialRule',
|
||||
'Scenario',
|
||||
'Setting',
|
||||
'MLRelativeReasoning',
|
||||
'RuleBasedRelativeReasoning',
|
||||
'EnviFormer',
|
||||
'ApplicabilityDomain',
|
||||
"User",
|
||||
"Group",
|
||||
"Package",
|
||||
"Compound",
|
||||
"CompoundStructure",
|
||||
"Pathway",
|
||||
"Edge",
|
||||
"Node",
|
||||
"Reaction",
|
||||
"SimpleAmbitRule",
|
||||
"SimpleRDKitRule",
|
||||
"ParallelRule",
|
||||
"SequentialRule",
|
||||
"Scenario",
|
||||
"Setting",
|
||||
"MLRelativeReasoning",
|
||||
"RuleBasedRelativeReasoning",
|
||||
"EnviFormer",
|
||||
"ApplicabilityDomain",
|
||||
]
|
||||
for model in MODELS:
|
||||
obj_cls = apps.get_model("epdb", model)
|
||||
print(f"Localizing urls for {model}")
|
||||
obj_cls.objects.update(
|
||||
url=Replace(F('url'), Value(options['old']), Value(options['new']))
|
||||
url=Replace(F("url"), Value(options["old"]), Value(options["new"]))
|
||||
)
|
||||
|
||||
@ -3,22 +3,25 @@ from django.shortcuts import redirect
|
||||
from django.urls import reverse
|
||||
from urllib.parse import quote
|
||||
|
||||
|
||||
class LoginRequiredMiddleware:
|
||||
def __init__(self, get_response):
|
||||
self.get_response = get_response
|
||||
self.exempt_urls = [
|
||||
reverse('login'),
|
||||
reverse('logout'),
|
||||
reverse('admin:login'),
|
||||
reverse('admin:index'),
|
||||
] + getattr(settings, 'LOGIN_EXEMPT_URLS', [])
|
||||
reverse("login"),
|
||||
reverse("logout"),
|
||||
reverse("admin:login"),
|
||||
reverse("admin:index"),
|
||||
] + getattr(settings, "LOGIN_EXEMPT_URLS", [])
|
||||
|
||||
def __call__(self, request):
|
||||
if not request.user.is_authenticated:
|
||||
path = request.path_info
|
||||
if not any(path.startswith(url) for url in self.exempt_urls):
|
||||
if request.method == 'GET':
|
||||
if request.get_full_path() and request.get_full_path() != '/':
|
||||
return redirect(f"{settings.LOGIN_URL}?next={quote(request.get_full_path())}")
|
||||
if request.method == "GET":
|
||||
if request.get_full_path() and request.get_full_path() != "/":
|
||||
return redirect(
|
||||
f"{settings.LOGIN_URL}?next={quote(request.get_full_path())}"
|
||||
)
|
||||
return redirect(settings.LOGIN_URL)
|
||||
return self.get_response(request)
|
||||
|
||||
1684
epdb/models.py
1684
epdb/models.py
File diff suppressed because it is too large
Load Diff
@ -2,55 +2,57 @@ import logging
|
||||
from typing import Optional
|
||||
|
||||
from celery import shared_task
|
||||
from epdb.models import Pathway, Node, Edge, EPModel, Setting
|
||||
from epdb.models import Pathway, Node, EPModel, Setting
|
||||
from epdb.logic import SPathway
|
||||
|
||||
|
||||
logger = logging.getLogger(__name__)
|
||||
|
||||
|
||||
@shared_task(queue='background')
|
||||
@shared_task(queue="background")
|
||||
def mul(a, b):
|
||||
return a * b
|
||||
|
||||
|
||||
@shared_task(queue='predict')
|
||||
@shared_task(queue="predict")
|
||||
def predict_simple(model_pk: int, smiles: str):
|
||||
mod = EPModel.objects.get(id=model_pk)
|
||||
res = mod.predict(smiles)
|
||||
return res
|
||||
|
||||
|
||||
@shared_task(queue='background')
|
||||
@shared_task(queue="background")
|
||||
def send_registration_mail(user_pk: int):
|
||||
pass
|
||||
|
||||
|
||||
@shared_task(queue='model')
|
||||
@shared_task(queue="model")
|
||||
def build_model(model_pk: int):
|
||||
mod = EPModel.objects.get(id=model_pk)
|
||||
mod.build_dataset()
|
||||
mod.build_model()
|
||||
|
||||
|
||||
@shared_task(queue='model')
|
||||
@shared_task(queue="model")
|
||||
def evaluate_model(model_pk: int):
|
||||
mod = EPModel.objects.get(id=model_pk)
|
||||
mod.evaluate_model()
|
||||
|
||||
|
||||
@shared_task(queue='model')
|
||||
@shared_task(queue="model")
|
||||
def retrain(model_pk: int):
|
||||
mod = EPModel.objects.get(id=model_pk)
|
||||
mod.retrain()
|
||||
|
||||
|
||||
@shared_task(queue='predict')
|
||||
def predict(pw_pk: int, pred_setting_pk: int, limit: Optional[int] = None, node_pk: Optional[int] = None) -> Pathway:
|
||||
@shared_task(queue="predict")
|
||||
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)
|
||||
|
||||
pw.kv.update(**{'status': 'running'})
|
||||
pw.kv.update(**{"status": "running"})
|
||||
pw.save()
|
||||
|
||||
try:
|
||||
@ -74,12 +76,10 @@ def predict(pw_pk: int, pred_setting_pk: int, limit: Optional[int] = None, node_
|
||||
else:
|
||||
raise ValueError("Neither limit nor node_pk given!")
|
||||
|
||||
|
||||
|
||||
except Exception as e:
|
||||
pw.kv.update({'status': 'failed'})
|
||||
pw.kv.update({"status": "failed"})
|
||||
pw.save()
|
||||
raise e
|
||||
|
||||
pw.kv.update(**{'status': 'completed'})
|
||||
pw.save()
|
||||
pw.kv.update(**{"status": "completed"})
|
||||
pw.save()
|
||||
|
||||
@ -2,6 +2,7 @@ from django import template
|
||||
|
||||
register = template.Library()
|
||||
|
||||
|
||||
@register.filter
|
||||
def classname(obj):
|
||||
return obj.__class__.__name__
|
||||
return obj.__class__.__name__
|
||||
|
||||
@ -1,3 +0,0 @@
|
||||
from django.test import TestCase
|
||||
|
||||
# Create your tests here.
|
||||
228
epdb/urls.py
228
epdb/urls.py
@ -3,97 +3,177 @@ from django.contrib.auth import views as auth_views
|
||||
|
||||
from . import views as v
|
||||
|
||||
UUID = '[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}'
|
||||
UUID = "[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}"
|
||||
|
||||
urlpatterns = [
|
||||
# Home
|
||||
re_path(r'^$', v.index, name='index'),
|
||||
|
||||
re_path(r"^$", v.index, name="index"),
|
||||
# Login
|
||||
re_path(r'^login', v.login, name='login'),
|
||||
re_path(r'^logout', v.logout, name='logout'),
|
||||
re_path(r'^register', v.register, name='register'),
|
||||
|
||||
# Built In views
|
||||
path('password_reset/', auth_views.PasswordResetView.as_view(
|
||||
template_name='static/password_reset_form.html'
|
||||
), name='password_reset'),
|
||||
|
||||
path('password_reset/done/', auth_views.PasswordResetDoneView.as_view(
|
||||
template_name='static/password_reset_done.html'
|
||||
), name='password_reset_done'),
|
||||
|
||||
path('reset/<uidb64>/<token>/', auth_views.PasswordResetConfirmView.as_view(
|
||||
template_name='static/password_reset_confirm.html'
|
||||
), name='password_reset_confirm'),
|
||||
|
||||
path('reset/done/', auth_views.PasswordResetCompleteView.as_view(
|
||||
template_name='static/password_reset_complete.html'
|
||||
), name='password_reset_complete'),
|
||||
|
||||
|
||||
re_path(r"^login", v.login, name="login"),
|
||||
re_path(r"^logout", v.logout, name="logout"),
|
||||
re_path(r"^register", v.register, name="register"),
|
||||
# Built-In views
|
||||
path(
|
||||
"password_reset/",
|
||||
auth_views.PasswordResetView.as_view(template_name="static/password_reset_form.html"),
|
||||
name="password_reset",
|
||||
),
|
||||
path(
|
||||
"password_reset/done/",
|
||||
auth_views.PasswordResetDoneView.as_view(template_name="static/password_reset_done.html"),
|
||||
name="password_reset_done",
|
||||
),
|
||||
path(
|
||||
"reset/<uidb64>/<token>/",
|
||||
auth_views.PasswordResetConfirmView.as_view(
|
||||
template_name="static/password_reset_confirm.html"
|
||||
),
|
||||
name="password_reset_confirm",
|
||||
),
|
||||
path(
|
||||
"reset/done/",
|
||||
auth_views.PasswordResetCompleteView.as_view(
|
||||
template_name="static/password_reset_complete.html"
|
||||
),
|
||||
name="password_reset_complete",
|
||||
),
|
||||
# Top level urls
|
||||
re_path(r'^package$', v.packages, name='packages'),
|
||||
re_path(r'^compound$', v.compounds, name='compounds'),
|
||||
re_path(r'^rule$', v.rules, name='rules'),
|
||||
re_path(r'^reaction$', v.reactions, name='reactions'),
|
||||
re_path(r'^pathway$', v.pathways, name='pathways'),
|
||||
re_path(r'^scenario$', v.scenarios, name='scenarios'),
|
||||
re_path(r'^model$', v.models, name='model'),
|
||||
re_path(r'^user$', v.users, name='users'),
|
||||
re_path(r'^group$', v.groups, name='groups'),
|
||||
re_path(r'^search$', v.search, name='search'),
|
||||
|
||||
|
||||
re_path(r"^package$", v.packages, name="packages"),
|
||||
re_path(r"^compound$", v.compounds, name="compounds"),
|
||||
re_path(r"^rule$", v.rules, name="rules"),
|
||||
re_path(r"^reaction$", v.reactions, name="reactions"),
|
||||
re_path(r"^pathway$", v.pathways, name="pathways"),
|
||||
re_path(r"^scenario$", v.scenarios, name="scenarios"),
|
||||
re_path(r"^model$", v.models, name="model"),
|
||||
re_path(r"^user$", v.users, name="users"),
|
||||
re_path(r"^group$", v.groups, name="groups"),
|
||||
re_path(r"^search$", v.search, name="search"),
|
||||
# User Detail
|
||||
re_path(rf'^user/(?P<user_uuid>{UUID})', v.user, name='user'),
|
||||
re_path(rf"^user/(?P<user_uuid>{UUID})", v.user, name="user"),
|
||||
# Group Detail
|
||||
re_path(rf'^group/(?P<group_uuid>{UUID})$', v.group, name='group detail'),
|
||||
|
||||
re_path(rf"^group/(?P<group_uuid>{UUID})$", v.group, name="group detail"),
|
||||
# "in package" urls
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})$', v.package, name='package detail'),
|
||||
re_path(rf"^package/(?P<package_uuid>{UUID})$", v.package, name="package detail"),
|
||||
# Compound
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/compound$', v.package_compounds, name='package compound list'),
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})$', v.package_compound, name='package compound detail'),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/compound$",
|
||||
v.package_compounds,
|
||||
name="package compound list",
|
||||
),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})$",
|
||||
v.package_compound,
|
||||
name="package compound detail",
|
||||
),
|
||||
# Compound Structure
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure$', v.package_compound_structures, name='package compound structure list'),
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure/(?P<structure_uuid>{UUID})$', v.package_compound_structure, name='package compound structure detail'),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure$",
|
||||
v.package_compound_structures,
|
||||
name="package compound structure list",
|
||||
),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure/(?P<structure_uuid>{UUID})$",
|
||||
v.package_compound_structure,
|
||||
name="package compound structure detail",
|
||||
),
|
||||
# Rule
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/rule$', v.package_rules, name='package rule list'),
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
|
||||
re_path(rf"^package/(?P<package_uuid>{UUID})/rule$", v.package_rules, name="package rule list"),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})$",
|
||||
v.package_rule,
|
||||
name="package rule detail",
|
||||
),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})$",
|
||||
v.package_rule,
|
||||
name="package rule detail",
|
||||
),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$",
|
||||
v.package_rule,
|
||||
name="package rule detail",
|
||||
),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$",
|
||||
v.package_rule,
|
||||
name="package rule detail",
|
||||
),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$",
|
||||
v.package_rule,
|
||||
name="package rule detail",
|
||||
),
|
||||
# Reaction
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/reaction$', v.package_reactions, name='package reaction list'),
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/reaction/(?P<reaction_uuid>{UUID})$', v.package_reaction, name='package reaction detail'),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/reaction$",
|
||||
v.package_reactions,
|
||||
name="package reaction list",
|
||||
),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/reaction/(?P<reaction_uuid>{UUID})$",
|
||||
v.package_reaction,
|
||||
name="package reaction detail",
|
||||
),
|
||||
# # Pathway
|
||||
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'),
|
||||
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$', v.package_pathway_nodes, name='package pathway node list'),
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node/(?P<node_uuid>{UUID})$', v.package_pathway_node, name='package pathway node detail'),
|
||||
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$', v.package_pathway_edges, name='package pathway edge list'),
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge/(?P<edge_uuid>{UUID})$', v.package_pathway_edge, name='package pathway edge detail'),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge$",
|
||||
v.package_pathway_edges,
|
||||
name="package pathway edge list",
|
||||
),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge/(?P<edge_uuid>{UUID})$",
|
||||
v.package_pathway_edge,
|
||||
name="package pathway edge detail",
|
||||
),
|
||||
# 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'),
|
||||
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",
|
||||
),
|
||||
# Model
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/model$', v.package_models, name='package model list'),
|
||||
re_path(rf'^package/(?P<package_uuid>{UUID})/model/(?P<model_uuid>{UUID})$', v.package_model,name='package model detail'),
|
||||
|
||||
re_path(r'^setting$', v.settings, name='settings'),
|
||||
re_path(rf'^setting/(?P<setting_uuid>{UUID})', v.setting, name='setting'),
|
||||
|
||||
re_path(r'^indigo/info$', v.indigo, name='indigo_info'),
|
||||
re_path(r'^indigo/aromatize$', v.aromatize, name='indigo_aromatize'),
|
||||
re_path(r'^indigo/dearomatize$', v.dearomatize, name='indigo_dearomatize'),
|
||||
re_path(r'^indigo/layout$', v.layout, name='indigo_layout'),
|
||||
|
||||
re_path(r'^depict$', v.depict, name='depict'),
|
||||
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/model$", v.package_models, name="package model list"
|
||||
),
|
||||
re_path(
|
||||
rf"^package/(?P<package_uuid>{UUID})/model/(?P<model_uuid>{UUID})$",
|
||||
v.package_model,
|
||||
name="package model detail",
|
||||
),
|
||||
re_path(r"^setting$", v.settings, name="settings"),
|
||||
re_path(rf"^setting/(?P<setting_uuid>{UUID})", v.setting, name="setting"),
|
||||
re_path(r"^indigo/info$", v.indigo, name="indigo_info"),
|
||||
re_path(r"^indigo/aromatize$", v.aromatize, name="indigo_aromatize"),
|
||||
re_path(r"^indigo/dearomatize$", v.dearomatize, name="indigo_dearomatize"),
|
||||
re_path(r"^indigo/layout$", v.layout, name="indigo_layout"),
|
||||
re_path(r"^depict$", v.depict, name="depict"),
|
||||
# OAuth Stuff
|
||||
path("o/userinfo/", v.userinfo, name="oauth_userinfo"),
|
||||
]
|
||||
|
||||
2167
epdb/views.py
2167
epdb/views.py
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user