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Granting/Updating Permission for Packages (#2)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#2
This commit is contained in:
jebus
2025-06-25 08:49:58 +12:00
parent 7c3bc69b38
commit 844d0708c9
9 changed files with 303 additions and 588 deletions
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66
epdb/logic.py
View File

@ -35,6 +35,11 @@ class UserManager(object):
def get_user(user_url): def get_user(user_url):
pass pass
@staticmethod
def get_user_lp(user_url: str):
uuid = user_url.strip().split('/')[-1]
return get_user_model().objects.get(uuid=uuid)
@staticmethod @staticmethod
def get_users(): def get_users():
return [] return []
@ -52,6 +57,11 @@ class GroupManager(object):
return g return g
@staticmethod
def get_group_lp(group_url: str):
uuid = group_url.strip().split('/')[-1]
return Group.objects.get(uuid=uuid)
@staticmethod @staticmethod
def get_group_by_url(user, group_url): def get_group_by_url(user, group_url):
return GroupManager.get_group_by_id(user, group_url.split('/')[-1]) return GroupManager.get_group_by_id(user, group_url.split('/')[-1])
@ -80,7 +90,7 @@ class PackageManager(object):
def readable(user, package): def readable(user, package):
# TODO Owner! # TODO Owner!
if UserPackagePermission.objects.filter(package=package, user=user).exists() or \ if UserPackagePermission.objects.filter(package=package, user=user).exists() or \
GroupPackagePermission.objects.filter(package=package, group__in=user.groups.all()) or \ GroupPackagePermission.objects.filter(package=package, group__in=GroupManager.get_groups(user)) or \
package.reviewed is True or \ package.reviewed is True or \
user.is_superuser: user.is_superuser:
return True return True
@ -91,7 +101,7 @@ class PackageManager(object):
def writable(user, package): def writable(user, package):
# TODO Owner! # TODO Owner!
if UserPackagePermission.objects.filter(package=package, user=user, permission=Permission.WRITE).exists() or \ if UserPackagePermission.objects.filter(package=package, user=user, permission=Permission.WRITE).exists() or \
GroupPackagePermission.objects.filter(package=package, group__in=user.groups.all(), GroupPackagePermission.objects.filter(package=package, group__in=GroupManager.get_groups(user),
permission=Permission.WRITE) or \ permission=Permission.WRITE) or \
user.is_superuser: user.is_superuser:
return True return True
@ -125,8 +135,12 @@ class PackageManager(object):
if user.is_superuser: if user.is_superuser:
qs = Package.objects.all() qs = Package.objects.all()
else: else:
up = UserPackagePermission.objects.filter(user=user).values('package').distinct() user_package_qs = Package.objects.filter(
qs = Package.objects.filter(id__in=up) id__in=UserPackagePermission.objects.filter(user=user).values('package').distinct())
group_package_qs = Package.objects.filter(
id__in=GroupPackagePermission.objects.filter(group__in=GroupManager.get_groups(user)).values(
'package').distinct())
qs = user_package_qs | group_package_qs
if include_reviewed: if include_reviewed:
qs |= Package.objects.filter(reviewed=True) qs |= Package.objects.filter(reviewed=True)
@ -142,9 +156,19 @@ class PackageManager(object):
if user.is_superuser: if user.is_superuser:
qs = Package.objects.all() qs = Package.objects.all()
else: else:
up = UserPackagePermission.objects.filter(user=user, permission=Permission.WRITE).values( write_user_packs = UserPackagePermission.objects.filter(user=user, permission=Permission.WRITE[0]).values('package').distinct()
'package').distinct() owner_user_packs = UserPackagePermission.objects.filter(user=user, permission=Permission.ALL[0]).values('package').distinct()
qs = Package.objects.filter(id__in=up)
user_packs = write_user_packs | owner_user_packs
user_package_qs = Package.objects.filter(id__in=user_packs)
write_group_packs = GroupPackagePermission.objects.filter(group__in=GroupManager.get_groups(user), permission=Permission.WRITE[0]).values( 'package').distinct()
owner_group_packs = GroupPackagePermission.objects.filter(group__in=GroupManager.get_groups(user), permission=Permission.ALL[0]).values( 'package').distinct()
group_packs = write_group_packs | owner_group_packs
group_package_qs = Package.objects.filter(id__in=group_packs)
qs = user_package_qs | group_package_qs
qs = qs.filter(reviewed=False) qs = qs.filter(reviewed=False)
@ -170,6 +194,34 @@ class PackageManager(object):
return p return p
@staticmethod
@transaction.atomic
def update_permissions(caller: User, package: Package, grantee: Union[User, Group], new_perm: Optional[str]):
if not PackageManager.writable(caller, package):
raise ValueError(f"User {caller} is not allowed to modify permissions on {package}")
data = {
'package': package,
}
if isinstance(grantee, User):
perm_cls = UserPackagePermission
data['user'] = grantee
else:
perm_cls = GroupPackagePermission
data['group'] = grantee
if new_perm is None:
qs = perm_cls.objects.filter(**data)
if qs.count() > 1:
raise ValueError("Got more Permission objects than expected!")
if qs.count() != 0:
logger.info(f"Deleting Perm {qs.first()}")
qs.delete()
else:
logger.debug(f"No Permission object for {perm_cls} with filter {data} found!")
else:
_ = perm_cls.objects.update_or_create(defaults={'permission': new_perm}, **data)
class SettingManager(object): class SettingManager(object):
setting_pattern = re.compile(r".*/setting/[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}$") setting_pattern = re.compile(r".*/setting/[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}$")

2
epdb/management/commands/bootstrap.py
View File

@ -63,7 +63,7 @@ class Command(BaseCommand):
up = UserPackagePermission() up = UserPackagePermission()
up.user = owner up.user = owner
up.package = pack up.package = pack
up.permission = up.ALL up.permission = up.ALL[0]
up.save() up.save()
# Stores old_id to new_id # Stores old_id to new_id

571
epdb/migrations/0001_initial.py
View File

@ -1,571 +0,0 @@
# Generated by Django 5.2.1 on 2025-06-16 13:57
import datetime
import django.contrib.auth.models
import django.contrib.auth.validators
import django.contrib.postgres.fields
import django.db.models.deletion
import django.utils.timezone
import model_utils.fields
import uuid
from django.conf import settings
from django.db import migrations, models
class Migration(migrations.Migration):
initial = True
dependencies = [
('auth', '0012_alter_user_first_name_max_length'),
('contenttypes', '0002_remove_content_type_name'),
]
operations = [
migrations.CreateModel(
name='Compound',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
],
),
migrations.CreateModel(
name='EPModel',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
),
migrations.CreateModel(
name='Permission',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('permission', models.CharField(choices=[('read', 'Read'), ('write', 'Write'), ('all', 'All')], max_length=32)),
],
),
migrations.CreateModel(
name='Package',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
],
options={
'abstract': False,
},
),
migrations.CreateModel(
name='Rule',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
),
migrations.CreateModel(
name='User',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('password', models.CharField(max_length=128, verbose_name='password')),
('last_login', models.DateTimeField(blank=True, null=True, verbose_name='last login')),
('is_superuser', models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status')),
('username', models.CharField(error_messages={'unique': 'A user with that username already exists.'}, help_text='Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only.', max_length=150, unique=True, validators=[django.contrib.auth.validators.UnicodeUsernameValidator()], verbose_name='username')),
('first_name', models.CharField(blank=True, max_length=150, verbose_name='first name')),
('last_name', models.CharField(blank=True, max_length=150, verbose_name='last name')),
('is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
('is_active', models.BooleanField(default=True, help_text='Designates whether this user should be treated as active. Unselect this instead of deleting accounts.', verbose_name='active')),
('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
('email', models.EmailField(max_length=254, unique=True)),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('user_permissions', models.ManyToManyField(blank=True, help_text='Specific permissions for this user.', related_name='user_set', related_query_name='user', to='auth.permission', verbose_name='user permissions')),
],
options={
'verbose_name': 'user',
'verbose_name_plural': 'users',
'abstract': False,
},
managers=[
('objects', django.contrib.auth.models.UserManager()),
],
),
migrations.CreateModel(
name='APIToken',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('hashed_key', models.CharField(max_length=128, unique=True)),
('created', models.DateTimeField(auto_now_add=True)),
('expires_at', models.DateTimeField(blank=True, default=datetime.datetime(2025, 9, 14, 13, 57, 57, 138459, tzinfo=datetime.timezone.utc), null=True)),
('name', models.CharField(blank=True, help_text='Optional name for the token', max_length=100)),
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
],
),
migrations.CreateModel(
name='CompoundStructure',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('smiles', models.TextField(verbose_name='SMILES')),
('normalized_structure', models.BooleanField(default=False)),
('compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.compound')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='compound',
name='default_structure',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='compound_default_structure', to='epdb.compoundstructure', verbose_name='Default Structure'),
),
migrations.CreateModel(
name='Edge',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
),
migrations.CreateModel(
name='EnviFormer',
fields=[
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
('threshold', models.FloatField(default=0.5)),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.epmodel',),
),
migrations.CreateModel(
name='PluginModel',
fields=[
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.epmodel',),
),
migrations.CreateModel(
name='RuleBaseRelativeReasoning',
fields=[
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.epmodel',),
),
migrations.CreateModel(
name='Group',
fields=[
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
('name', models.TextField(verbose_name='Group name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('group_member', models.ManyToManyField(related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Group Owner')),
('user_member', models.ManyToManyField(related_name='users_in_group', to=settings.AUTH_USER_MODEL, verbose_name='User members')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='user',
name='default_group',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='default_group', to='epdb.group', verbose_name='Default Group'),
),
migrations.AddField(
model_name='user',
name='groups',
field=models.ManyToManyField(to='epdb.group', verbose_name='groups'),
),
migrations.CreateModel(
name='Node',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('depth', models.IntegerField(verbose_name='Node depth')),
('default_node_label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='default_node_structure', to='epdb.compoundstructure', verbose_name='Default Node Label')),
('node_labels', models.ManyToManyField(related_name='node_structures', to='epdb.compoundstructure', verbose_name='All Node Labels')),
('out_edges', models.ManyToManyField(to='epdb.edge', verbose_name='Outgoing Edges')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='edge',
name='end_nodes',
field=models.ManyToManyField(related_name='edge_products', to='epdb.node', verbose_name='End Nodes'),
),
migrations.AddField(
model_name='edge',
name='start_nodes',
field=models.ManyToManyField(related_name='edge_educts', to='epdb.node', verbose_name='Start Nodes'),
),
migrations.AddField(
model_name='epmodel',
name='package',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
),
migrations.AddField(
model_name='compound',
name='package',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
),
migrations.AddField(
model_name='user',
name='default_package',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.package', verbose_name='Default Package'),
),
migrations.CreateModel(
name='SequentialRule',
fields=[
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.rule',),
),
migrations.CreateModel(
name='SimpleRule',
fields=[
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.rule',),
),
migrations.CreateModel(
name='Pathway',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='node',
name='pathway',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
),
migrations.AddField(
model_name='edge',
name='pathway',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
),
migrations.CreateModel(
name='Reaction',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('multi_step', models.BooleanField(verbose_name='Multistep Reaction')),
('medline_references', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), null=True, size=None, verbose_name='Medline References')),
('educts', models.ManyToManyField(related_name='reaction_educts', to='epdb.compoundstructure', verbose_name='Educts')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
('products', models.ManyToManyField(related_name='reaction_products', to='epdb.compoundstructure', verbose_name='Products')),
('rules', models.ManyToManyField(related_name='reaction_rule', to='epdb.rule', verbose_name='Rule')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='edge',
name='edge_label',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.reaction', verbose_name='Edge label'),
),
migrations.CreateModel(
name='Scenario',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('date', models.DateField(null=True, verbose_name='Study date')),
('type', models.CharField(default='Not specified', max_length=256)),
('additional_information', models.JSONField(verbose_name='Additional Information')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='rule',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='reaction',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='pathway',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='node',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='edge',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='compoundstructure',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='compound',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.CreateModel(
name='Setting',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('public', models.BooleanField(default=False)),
('global_default', models.BooleanField(default=False)),
('max_depth', models.IntegerField(default=5, verbose_name='Setting Max Depth')),
('max_nodes', models.IntegerField(default=30, verbose_name='Setting Max Number of Nodes')),
('model_threshold', models.FloatField(blank=True, default=0.25, null=True, verbose_name='Setting Model Threshold')),
('model', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.epmodel', verbose_name='Setting EPModel')),
('rule_packages', models.ManyToManyField(related_name='setting_rule_packages', to='epdb.package', verbose_name='Setting Rule Packages')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='user',
name='default_setting',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.setting', verbose_name='The users default settings'),
),
migrations.CreateModel(
name='MLRelativeReasoning',
fields=[
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
('threshold', models.FloatField(default=0.5)),
('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
('data_packages', models.ManyToManyField(related_name='data_packages', to='epdb.package', verbose_name='Data Packages')),
('eval_packages', models.ManyToManyField(related_name='eval_packages', to='epdb.package', verbose_name='Evaluation Packages')),
('rule_packages', models.ManyToManyField(related_name='rule_packages', to='epdb.package', verbose_name='Rule Packages')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.epmodel',),
),
migrations.CreateModel(
name='ApplicabilityDomain',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('num_neighbours', models.FloatField(default=5)),
('reliability_threshold', models.FloatField(default=0.5)),
('local_compatibilty_threshold', models.FloatField(default=0.5)),
('model', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.mlrelativereasoning')),
],
options={
'abstract': False,
},
),
migrations.CreateModel(
name='SimpleAmbitRule',
fields=[
('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
('smirks', models.TextField(verbose_name='SMIRKS')),
('reactant_filter_smarts', models.TextField(null=True, verbose_name='Reactant Filter SMARTS')),
('product_filter_smarts', models.TextField(null=True, verbose_name='Product Filter SMARTS')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.simplerule',),
),
migrations.CreateModel(
name='SimpleRDKitRule',
fields=[
('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
('reaction_smarts', models.TextField(verbose_name='SMIRKS')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.simplerule',),
),
migrations.CreateModel(
name='SequentialRuleOrdering',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('order_index', models.IntegerField()),
('sequential_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.sequentialrule')),
('simple_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.simplerule')),
],
),
migrations.AddField(
model_name='sequentialrule',
name='simple_rules',
field=models.ManyToManyField(through='epdb.SequentialRuleOrdering', to='epdb.simplerule', verbose_name='Simple rules'),
),
migrations.CreateModel(
name='ParallelRule',
fields=[
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
('simple_rules', models.ManyToManyField(to='epdb.simplerule', verbose_name='Simple rules')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.rule',),
),
migrations.AlterUniqueTogether(
name='compound',
unique_together={('uuid', 'package')},
),
migrations.CreateModel(
name='GroupPackagePermission',
fields=[
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
('group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.group', verbose_name='Permission to')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Permission on')),
],
options={
'unique_together': {('package', 'group')},
},
bases=('epdb.permission',),
),
migrations.CreateModel(
name='UserPackagePermission',
fields=[
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Permission on')),
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
],
options={
'unique_together': {('package', 'user')},
},
bases=('epdb.permission',),
),
migrations.CreateModel(
name='UserSettingPermission',
fields=[
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
('setting', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Permission on')),
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
],
options={
'unique_together': {('setting', 'user')},
},
bases=('epdb.permission',),
),
]

12
epdb/models.py
View File

@ -83,8 +83,7 @@ class APIToken(models.Model):
class Group(TimeStampedModel): class Group(TimeStampedModel):
uuid = models.UUIDField(null=False, blank=False, verbose_name='UUID of this object', primary_key=True, uuid = models.UUIDField(null=False, blank=False, verbose_name='UUID of this object', unique=True, default=uuid4)
default=uuid4)
name = models.TextField(blank=False, null=False, verbose_name='Group name') name = models.TextField(blank=False, null=False, verbose_name='Group name')
owner = models.ForeignKey("User", verbose_name='Group Owner', on_delete=models.CASCADE) owner = models.ForeignKey("User", verbose_name='Group Owner', on_delete=models.CASCADE)
description = models.TextField(blank=False, null=False, verbose_name='Descriptions', default='no description') description = models.TextField(blank=False, null=False, verbose_name='Descriptions', default='no description')
@ -110,6 +109,15 @@ class Permission(TimeStampedModel):
] ]
permission = models.CharField(max_length=32, choices=PERMS, null=False) permission = models.CharField(max_length=32, choices=PERMS, null=False)
def has_read(self):
return self.permission in [p[0] for p in self.PERMS]
def has_write(self):
return self.permission in [self.WRITE[0], self.ALL[0]]
def has_all(self):
return self.permission == self.ALL[0]
class Meta: class Meta:
abstract: True abstract: True

49
epdb/views.py
View File

@ -10,7 +10,8 @@ from django.views.decorators.csrf import csrf_exempt
from utilities.chem import FormatConverter, IndigoUtils from utilities.chem import FormatConverter, IndigoUtils
from .logic import GroupManager, PackageManager, UserManager, SettingManager from .logic import GroupManager, PackageManager, UserManager, SettingManager
from .models import Package, GroupPackagePermission, Group, CompoundStructure, Compound, Reaction, Rule, Pathway, Node, \ from .models import Package, GroupPackagePermission, Group, CompoundStructure, Compound, Reaction, Rule, Pathway, Node, \
EPModel, EnviFormer, MLRelativeReasoning, RuleBaseRelativeReasoning, Scenario, SimpleAmbitRule, APIToken EPModel, EnviFormer, MLRelativeReasoning, RuleBaseRelativeReasoning, Scenario, SimpleAmbitRule, APIToken, \
UserPackagePermission, Permission
logger = logging.getLogger(__name__) logger = logging.getLogger(__name__)
@ -512,11 +513,30 @@ def package(request, package_uuid):
context['breadcrumbs'] = breadcrumbs(current_package) context['breadcrumbs'] = breadcrumbs(current_package)
context['package'] = current_package context['package'] = current_package
context['package_group'] = GroupPackagePermission.objects.filter(package=current_package, # context['package_group'] = GroupPackagePermission.objects.filter(package=current_package,
permission=GroupPackagePermission.ALL) # permission=GroupPackagePermission.ALL)
user_perms = UserPackagePermission.objects.filter(package=current_package)
users = get_user_model().objects.exclude(
id__in=UserPackagePermission.objects.filter(package=current_package).values_list('user_id', flat=True))
group_perms = GroupPackagePermission.objects.filter(package=current_package)
groups = Group.objects.exclude(
id__in=GroupPackagePermission.objects.filter(package=current_package).values_list('group_id', flat=True))
context['users'] = users
context['groups'] = groups
context['user_permissions'] = user_perms
context['group_permissions'] = group_perms
return render(request, 'objects/package.html', context) return render(request, 'objects/package.html', context)
elif request.method == 'POST': elif request.method == 'POST':
if s.DEBUG:
for k, v in request.POST.items():
print(k, v)
if hidden := request.POST.get('hidden', None): if hidden := request.POST.get('hidden', None):
if hidden == 'delete-package': if hidden == 'delete-package':
print(current_package.delete()) print(current_package.delete())
@ -527,6 +547,12 @@ def package(request, package_uuid):
new_package_name = request.POST.get('package-name') new_package_name = request.POST.get('package-name')
new_package_description = request.POST.get('package-description') new_package_description = request.POST.get('package-description')
grantee_url = request.POST.get('grantee')
read = request.POST.get('read') == 'on'
write = request.POST.get('write') == 'on'
owner = request.POST.get('owner') == 'on'
if new_package_name: if new_package_name:
current_package.name = new_package_name current_package.name = new_package_name
@ -536,6 +562,23 @@ def package(request, package_uuid):
if any([new_package_name, new_package_description]): if any([new_package_name, new_package_description]):
current_package.save() current_package.save()
return redirect(current_package.url) return redirect(current_package.url)
elif any([grantee_url, read, write, owner]):
if 'user' in grantee_url:
grantee = UserManager.get_user_lp(grantee_url)
else:
grantee = GroupManager.get_group_lp(grantee_url)
max_perm = None
if read:
max_perm = Permission.READ[0]
if write:
max_perm = Permission.WRITE[0]
if owner:
max_perm = Permission.ALL[0]
PackageManager.update_permissions(current_user, current_package, grantee, max_perm)
return redirect(current_package.url)
else: else:
return HttpResponseBadRequest() return HttpResponseBadRequest()

6
fixtures/EAWAG-BBD.json
View File

@ -93740,7 +93740,7 @@
"scenarios" : [ "scenarios" : [
{ "id" : "http://localhost:8080/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/9e51c3f0-699e-4e4d-b443-6bcc436a1ea6" } { "id" : "http://localhost:8080/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/9e51c3f0-699e-4e4d-b443-6bcc436a1ea6" }
] , ] ,
"smirks" : "[#7:7]\\[#6:1](-[#7:8])=[#7]\\?[#7+](-[#8-])=O>>[#7:8]-[#6:1](-[#7:7])=O" "smirks" : "[#7:7]\\[#6:1](-[#7:8])=[#7]\\[#7+](-[#8-])=O>>[#7:8]-[#6:1](-[#7:7])=O"
}, { }, {
"aliases" : [ ] , "aliases" : [ ] ,
"creationDate" : "2015-11-18 11:33:12.221" , "creationDate" : "2015-11-18 11:33:12.221" ,
@ -93777,7 +93777,7 @@
"scenarios" : [ "scenarios" : [
{ "id" : "http://localhost:8080/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/9e51c3f0-699e-4e4d-b443-6bcc436a1ea6" } { "id" : "http://localhost:8080/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/9e51c3f0-699e-4e4d-b443-6bcc436a1ea6" }
] , ] ,
"smirks" : "[#7:7]\\[#6:1](-[#7:8])=[#7]\\?[#7+](-[#8-])=O>>[#7:8]-[#6:1](-[#7:7])=O" "smirks" : "[#7:7]\\[#6:1](-[#7:8])=[#7]\\[#7+](-[#8-])=O>>[#7:8]-[#6:1](-[#7:7])=O"
} , } ,
{ {
"aliases" : [ ] , "aliases" : [ ] ,
@ -439312,4 +439312,4 @@
] , ] ,
"scenarios" : [ ] "scenarios" : [ ]
}] }]
} }

2
templates/modals/objects/edit_package_modal.html
View File

@ -4,7 +4,7 @@
<div class="modal-dialog"> <div class="modal-dialog">
<div class="modal-content"> <div class="modal-content">
<div class="modal-header"> <div class="modal-header">
<h5 class="modal-title">Create a Package</h5> <h5 class="modal-title">Update Package</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close"> <button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span> <span aria-hidden="true">&times;</span>
</button> </button>

182
templates/modals/objects/edit_package_permissions_modal.html Normal file
View File

@ -0,0 +1,182 @@
{% load static %}
<!-- Edit Package Permission -->
<div id="edit_package_permissions_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Grant or Revoke Permissions</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
<p>
Modify permissions for this package. Note that if you give <code>write</code>
permissions to a user or group, <code>read</code> permissions will be granted automatically.
<br>
To allow users to perform destructive actions, such as deleting the package, <code>owner</code>
permissions must be granted.
</p>
<div class="row">
<div class="col-xs-4">
<legend>User or Group</legend>
</div>
<div class="col-xs-2">
<legend>Read</legend>
</div>
<div class="col-xs-2">
<legend>Write</legend>
</div>
<div class="col-xs-2">
<legend>Owner</legend>
</div>
</div>
<div class="row">
<form id="modal-form-permissions" class="form-inline" role="form" accept-charset="UTF-8" action=""
data-remote="true" method="post">
{% csrf_token %}
<div class="col-xs-4">
<select id="select_grantee" name="grantee" data-actions-box='true'
class="selPackages" data-width='100%'>
<option disabled selected>User</option>
{% for u in users %}
<option value="{{ u.url }}">{{ u.username }}</option>
{% endfor %}
<option disabled>Groups</option>
{% for g in groups %}
<option value="{{ g.url }}">{{ g.name }}</option>
{% endfor %}
</select>
</div>
<div class="col-xs-2">
<input type="checkbox" name="read" id="read_new"/>
</div>
<div class="col-xs-2">
<input type="checkbox" name="write" id="write_new"/>
</div>
<div class="col-xs-2">
<input type="checkbox" name="owner" id="owner_new"/>
</div>
<div class="col-xs-2">
<button type="submit" style="width:60%;" class="btn col-xs-2 modify-perm-button">
<span class="glyphicon glyphicon-plus"></span>
</button>
</div>
</form>
</div>
{% for up in user_permissions %}
<div class="row">
<form id="modal-form-permissions_{{ up.user.uuid }}" class="form-inline" role="form"
accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<div class="col-xs-4">
{{ up.user.username }}
<input type="hidden" name="grantee" value="{{ up.user.url }}"/>
</div>
<div class="col-xs-2">
<input type="checkbox" name="read" id="read_{{ up.user.uuid }}" {% if up.has_read %} checked {% endif %}/>
</div>
<div class="col-xs-2">
<input type="checkbox" name="write" id="write_{{ up.user.uuid }}" {% if up.has_write %} checked {% endif %}/>
</div>
<div class="col-xs-2">
<input type="checkbox" name="owner" id="owner_{{ up.user.uuid }}" {% if up.has_all %} checked {% endif %}/>
</div>
<div class="col-xs-2">
<button type="submit" style="width:60%;" class="btn col-xs-2 modify-perm-button">
<span class="glyphicon glyphicon-ok"></span>
</button>
</div>
</form>
</div>
{% endfor %}
{% for gp in group_permissions %}
<div class="row">
<form id="modal-form-permissions_{{ gp.user.uuid }}" class="form-inline" role="form"
accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<div class="col-xs-4">
{{ gp.group.name }}
<input type="hidden" name="grantee" value="{{ gp.group.url }}"/>
</div>
<div class="col-xs-2">
<input type="checkbox" name="read" id="read_{{ gp.group.uuid }}" {% if gp.has_read %} checked {% endif %}/>
</div>
<div class="col-xs-2">
<input type="checkbox" name="write" id="write_{{ gp.group.uuid }}" {% if gp.has_write %} checked {% endif %}/>
</div>
<div class="col-xs-2">
<input type="checkbox" name="owner" id="owner_{{ gp.group.uuid }}" {% if gp.has_all %} checked {% endif %}/>
</div>
<div class="col-xs-2">
<button type="submit" style="width:60%;" class="btn col-xs-2 modify-perm-button">
<span class="glyphicon glyphicon-ok"></span>
</button>
</div>
</form>
</div>
{% endfor %}
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
<button type="button" class="btn btn-primary" id="edit-package-modal-submit">Update</button>
</div>
</div>
</div>
</div>
<script>
function checkboxClick() {
// id looks like read_3cadef24-220e-4587-9fa5-0e9a17aca2da
parts = this.id.split('_');
perm = parts[0];
id = parts[1];
readbox = '#read_' + id;
writebox = '#write_' + id;
ownerbox = '#owner_' + id;
if (perm == 'read' && !$(readbox).prop("checked")) {
$(writebox).prop("checked", false);
$(ownerbox).prop("checked", false);
}
if (perm == 'write') {
if ($(writebox).prop("checked")) {
$(readbox).prop("checked", true);
}
if (!$(writebox).prop("checked")) {
$(ownerbox).prop("checked", false);
}
}
if (perm == 'owner') {
if ($(ownerbox).prop("checked")) {
$(readbox).prop("checked", true);
$(writebox).prop("checked", true);
}
}
}
$(function() {
$('#edit-package-modal-submit').click(function(e){
e.preventDefault();
$('#edit-package-modal-form').submit();
});
$("#select_grantee").selectpicker();
// Add click functions to permission checkboxes
$('[id^="read_"]').on('click', checkboxClick);
$('[id^="write_"]').on('click', checkboxClick);
$('[id^="owner_"]').on('click', checkboxClick);
})
</script>

1
templates/objects/package.html
View File

@ -4,6 +4,7 @@
{% block action_modals %} {% block action_modals %}
{% include "modals/objects/edit_package_modal.html" %} {% include "modals/objects/edit_package_modal.html" %}
{% include "modals/objects/edit_package_permissions_modal.html" %}
{% include "modals/objects/delete_package_modal.html" %} {% include "modals/objects/delete_package_modal.html" %}
{% endblock action_modals %} {% endblock action_modals %}