Merge pull request #725 from cortex-lab/dev

Release 1.0.0

Author: oliche

.gitignore

@@ -31,3 +31,5 @@ alyx/alyx/settings_lab.py
 alyx/alyx/settings.py
 
 alyx/.idea/
+
+alyx.log

README.md

@@ -13,7 +13,7 @@ Alyx has only been tested on Ubuntu (16.04 / 18.04 / 20.04), the latest is recom
 this setup will work on other systems. Assumptions made are that you have sudo permissions under an account named
 `ubuntu`.
 
-## Install apache, wsgi module, and set group and acl permissions
+### Install apache, wsgi module, and set group and acl permissions
     sudo apt-get update    
     sudo apt-get install apache2 libapache2-mod-wsgi-py3 acl
     sudo a2enmod wsgi
@@ -78,6 +78,27 @@ Location of error logs for apache if it fails to start
 
     /var/log/apache2/
 
+### [Optional] Setup AWS Cloudwatch Agent logging
+
+If you are running alyx as an EC2 instance on AWS, you can easily add the AWS Cloudwatch agent to the server to ease log
+evaluation and alerting. This can also be done with a non-ec2 server, but is likely not worth it unless you are already 
+using Cloudwatch for other logs.
+
+To give an overview of the installation process for an EC2 instance:
+* Create an IAM role that enables the agent to collect metrics from the server and attach the role to the server.
+* Download the agent package to the instance.
+* Modify the CloudWatch agent configuration file, specify the metrics and the log files that you want to collect.
+* Install and start the agent on your server.
+* Verify in Cloudwatch 
+  * you are now able to generate alerts from the metrics of interest
+  * you are now shipping the logs files to your log group
+
+Follow the latest instructions from the official [AWS Cloudwatch Agent documentation](https://docs.aws.amazon.com/AmazonCloudWatch/latest/monitoring/Install-CloudWatch-Agent.html).
+
+Other useful references:
+* [IAM documentation](https://docs.aws.amazon.com/IAM/latest/UserGuide/access_policies_managed-vs-inline.html)
+* [EC2 metadata documentation](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/ec2-instance-metadata.html) 
+
 ---
 
 ### [macOS] Local installation of alyx

alyx/actions/admin.py

@@ -118,7 +118,9 @@ def __init__(self, *args, **kwargs):
             self.fields['users'].queryset = get_user_model().objects.all().order_by('username')
         if 'user' in self.fields:
             self.fields['user'].queryset = get_user_model().objects.all().order_by('username')
-        if 'subject' in self.fields:
+        # restricts the subject choices only to managed subjects
+        if 'subject' in self.fields and not (
+                self.current_user.is_stock_manager or self.current_user.is_superuser):
             inst = self.instance
             ids = [s.id for s in Subject.objects.filter(responsible_user=self.current_user,
                                                         cull__isnull=True).order_by('nickname')]
@@ -356,6 +358,14 @@ def given_water_total(self, obj):
         return '%.2f' % obj.subject.water_control.given_water_total()
     given_water_total.short_description = 'water tot'
 
+    def has_change_permission(self, request, obj=None):
+        # setting to override edition of water restrictions in the settings.lab file
+        override = getattr(settings, 'WATER_RESTRICTIONS_EDITABLE', False)
+        if override:
+            return True
+        else:
+            return super(WaterRestrictionAdmin, self).has_change_permission(request, obj=obj)
+
     def expected_water(self, obj):
         if not obj.subject:
             return

alyx/actions/migrations/0017_alter_chronicrecording_subject_and_more.py

@@ -0,0 +1,45 @@
+# Generated by Django 4.0.3 on 2022-03-30 15:46
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('subjects', '0010_auto_20210624_1253'),
+        ('actions', '0016_chronicrecording'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='chronicrecording',
+            name='subject',
+            field=models.ForeignKey(help_text='The subject on which this action was performed', on_delete=django.db.models.deletion.CASCADE, related_name='%(app_label)s_%(class)ss', to='subjects.subject'),
+        ),
+        migrations.AlterField(
+            model_name='otheraction',
+            name='subject',
+            field=models.ForeignKey(help_text='The subject on which this action was performed', on_delete=django.db.models.deletion.CASCADE, related_name='%(app_label)s_%(class)ss', to='subjects.subject'),
+        ),
+        migrations.AlterField(
+            model_name='session',
+            name='subject',
+            field=models.ForeignKey(help_text='The subject on which this action was performed', on_delete=django.db.models.deletion.CASCADE, related_name='%(app_label)s_%(class)ss', to='subjects.subject'),
+        ),
+        migrations.AlterField(
+            model_name='surgery',
+            name='subject',
+            field=models.ForeignKey(help_text='The subject on which this action was performed', on_delete=django.db.models.deletion.CASCADE, related_name='%(app_label)s_%(class)ss', to='subjects.subject'),
+        ),
+        migrations.AlterField(
+            model_name='virusinjection',
+            name='subject',
+            field=models.ForeignKey(help_text='The subject on which this action was performed', on_delete=django.db.models.deletion.CASCADE, related_name='%(app_label)s_%(class)ss', to='subjects.subject'),
+        ),
+        migrations.AlterField(
+            model_name='waterrestriction',
+            name='subject',
+            field=models.ForeignKey(help_text='The subject on which this action was performed', on_delete=django.db.models.deletion.CASCADE, related_name='%(app_label)s_%(class)ss', to='subjects.subject'),
+        ),
+    ]

alyx/actions/models.py

@@ -209,16 +209,20 @@ class Meta:
 
     def save(self, *args, **kwargs):
         # Issue #422.
-        if self.subject.protocol_number == '1':
-            self.subject.protocol_number = '3'
-        # Change from mild to moderate.
+        output = super(Surgery, self).save(*args, **kwargs)
+        self.subject.set_protocol_number()
         if self.subject.actual_severity == 2:
             self.subject.actual_severity = 3
-
         if self.outcome_type == 'a' and self.start_time:
             self.subject.death_date = self.start_time
         self.subject.save()
-        return super(Surgery, self).save(*args, **kwargs)
+        return output
+
+    def delete(self, *args, **kwargs):
+        output = super(Surgery, self).delete(*args, **kwargs)
+        self.subject.set_protocol_number()
+        self.subject.save()
+        return output
 
 
 class Session(BaseAction):
@@ -314,14 +318,28 @@ class WaterRestriction(BaseAction):
     def is_active(self):
         return self.start_time is not None and self.end_time is None
 
+    def delete(self, *args, **kwargs):
+        output = super(WaterRestriction, self).delete(*args, **kwargs)
+        self.subject.reinit_water_control()
+        self.subject.set_protocol_number()
+        self.subject.save()
+        return output
+
     def save(self, *args, **kwargs):
         if not self.reference_weight and self.subject:
             w = self.subject.water_control.last_weighing_before(self.start_time)
             if w:
                 self.reference_weight = w[1]
                 # makes sure the closest weighing is one week around, break if not
                 assert(abs(w[0] - self.start_time) < timedelta(days=7))
-        return super(WaterRestriction, self).save(*args, **kwargs)
+        output = super(WaterRestriction, self).save(*args, **kwargs)
+        # When creating a water restriction, the subject's protocol number should be changed to 3
+        # (request by Charu in 03/2022)
+        if self.subject:
+            self.subject.reinit_water_control()
+            self.subject.set_protocol_number()
+            self.subject.save()
+        return output
 
 
 class OtherAction(BaseAction):
@@ -543,13 +561,13 @@ def save(self, *args, **kwargs):
             self.subject.cull_method = str(self.cull_method)
             subject_change = True
         if subject_change:
-            self.subject.save()
             # End all open water restrictions.
             for wr in WaterRestriction.objects.filter(
                     subject=self.subject, start_time__isnull=False, end_time__isnull=True):
                 wr.end_time = self.date
                 logger.debug("Ending water restriction %s.", wr)
                 wr.save()
+            self.subject.save()
         return super(Cull, self).save(*args, **kwargs)
 
     def delete(self, *args, **kwargs):

alyx/actions/views.py

@@ -12,11 +12,11 @@
 from django.views.generic.list import ListView
 
 import django_filters
-from rest_framework import generics, permissions
+from rest_framework import generics
 from rest_framework.response import Response
 from rest_framework.views import APIView
 
-from alyx.base import base_json_filter, BaseFilterSet
+from alyx.base import base_json_filter, BaseFilterSet, rest_permission_classes
 from subjects.models import Subject
 from experiments.views import _filter_qs_with_brain_regions
 from .water_control import water_control, to_date
@@ -332,7 +332,8 @@ class SessionAPIList(generics.ListCreateAPIView):
     """
     queryset = Session.objects.all()
     queryset = SessionListSerializer.setup_eager_loading(queryset)
-    permission_classes = (permissions.IsAuthenticated,)
+    permission_classes = rest_permission_classes()
+
     filter_class = SessionFilter
 
     def get_serializer_class(self):
@@ -351,14 +352,14 @@ class SessionAPIDetail(generics.RetrieveUpdateDestroyAPIView):
     queryset = Session.objects.all().order_by('-start_time')
     queryset = SessionDetailSerializer.setup_eager_loading(queryset)
     serializer_class = SessionDetailSerializer
-    permission_classes = (permissions.IsAuthenticated,)
+    permission_classes = rest_permission_classes()
 
 
 class WeighingAPIListCreate(generics.ListCreateAPIView):
     """
     Lists or creates a new weighing.
     """
-    permission_classes = (permissions.IsAuthenticated,)
+    permission_classes = rest_permission_classes()
     serializer_class = WeighingDetailSerializer
     queryset = Weighing.objects.all()
     queryset = WeighingDetailSerializer.setup_eager_loading(queryset)
@@ -369,23 +370,23 @@ class WeighingAPIDetail(generics.RetrieveDestroyAPIView):
     """
     Allows viewing of full detail and deleting a weighing.
     """
-    permission_classes = (permissions.IsAuthenticated,)
+    permission_classes = rest_permission_classes()
     serializer_class = WeighingDetailSerializer
     queryset = Weighing.objects.all()
 
 
 class WaterTypeList(generics.ListCreateAPIView):
     queryset = WaterType.objects.all()
     serializer_class = WaterTypeDetailSerializer
-    permission_classes = (permissions.IsAuthenticated,)
+    permission_classes = rest_permission_classes()
     lookup_field = 'name'
 
 
 class WaterAdministrationAPIListCreate(generics.ListCreateAPIView):
     """
     Lists or creates a new water administration.
     """
-    permission_classes = (permissions.IsAuthenticated,)
+    permission_classes = rest_permission_classes()
     serializer_class = WaterAdministrationDetailSerializer
     queryset = WaterAdministration.objects.all()
     queryset = WaterAdministrationDetailSerializer.setup_eager_loading(queryset)
@@ -396,7 +397,7 @@ class WaterAdministrationAPIDetail(generics.RetrieveUpdateDestroyAPIView):
     """
     Allows viewing of full detail and deleting a water administration.
     """
-    permission_classes = (permissions.IsAuthenticated,)
+    permission_classes = rest_permission_classes()
     serializer_class = WaterAdministrationDetailSerializer
     queryset = WaterAdministration.objects.all()
 
@@ -413,7 +414,7 @@ def _merge_lists_dicts(la, lb, key):
 
 
 class WaterRequirement(APIView):
-    permission_classes = (permissions.IsAuthenticated,)
+    permission_classes = rest_permission_classes()
 
     def get(self, request, format=None, nickname=None):
         assert nickname
@@ -439,7 +440,7 @@ class WaterRestrictionList(generics.ListAPIView):
     """
     queryset = WaterRestriction.objects.all().order_by('-end_time', '-start_time')
     serializer_class = WaterRestrictionListSerializer
-    permission_classes = (permissions.IsAuthenticated,)
+    permission_classes = rest_permission_classes()
     filter_class = WaterRestrictionFilter
 
 
@@ -449,14 +450,14 @@ class LabLocationList(generics.ListAPIView):
     """
     queryset = LabLocation.objects.all()
     serializer_class = LabLocationSerializer
-    permission_classes = (permissions.IsAuthenticated,)
+    permission_classes = rest_permission_classes()
 
 
 class LabLocationAPIDetails(generics.RetrieveUpdateAPIView):
     """
     Allows viewing of full detail and deleting a water administration.
     """
-    permission_classes = (permissions.IsAuthenticated,)
+    permission_classes = rest_permission_classes()
     serializer_class = LabLocationSerializer
     queryset = LabLocation.objects.all()
     lookup_field = 'name'
@@ -468,4 +469,4 @@ class SurgeriesList(generics.ListAPIView):
     """
     queryset = Surgery.objects.all()
     serializer_class = SurgerySerializer
-    permission_classes = (permissions.IsAuthenticated,)
+    permission_classes = rest_permission_classes()

alyx/alyx/__init__.py

@@ -0,0 +1,2 @@
+__version__ = '1.0.0'
+VERSION = __version__  # synonym

alyx/alyx/base.py

@@ -24,9 +24,10 @@
 from django_filters.rest_framework import FilterSet
 from rest_framework.views import exception_handler
 
+from rest_framework import permissions
 from dateutil.parser import parse
 from reversion.admin import VersionAdmin
-
+from alyx import __version__ as version
 
 logger = structlog.get_logger(__name__)
 
@@ -316,13 +317,28 @@ def changelist_view(self, request, extra_context=None):
                                      for model in category_list[0].models]
         return super(BaseAdmin, self).changelist_view(request, extra_context=extra_context)
 
+    def has_add_permission(self, request, *args, **kwargs):
+        if request.user.is_public_user:
+            return False
+        else:
+            return super(BaseAdmin, self).has_add_permission(request, *args, **kwargs)
+
     def has_change_permission(self, request, obj=None):
+        if request.user.is_public_user:
+            return False
         if not obj:
             return True
         if request.user.is_superuser:
             return True
-        # Subject associated to the object.
-        subj = obj if hasattr(obj, 'responsible_user') else getattr(obj, 'subject', None)
+        # Find subject associated to the object.
+        if hasattr(obj, 'responsible_user'):
+            subj = obj
+        elif getattr(obj, 'session', None):
+            subj = obj.session.subject
+        elif getattr(obj, 'subject', None):
+            subj = obj.subject
+        else:
+            return False
         resp_user = getattr(subj, 'responsible_user', None)
         # List of allowed users for the subject.
         allowed = getattr(resp_user, 'allowed_users', None)
@@ -562,11 +578,29 @@ def rest_filters_exception_handler(exc, context):
     return response
 
 
+class BaseRestPublicPermission(permissions.BasePermission):
+    """
+    The purpose is to prevent public users from interfering in any way using writable methods
+    """
+    def has_permission(self, request, view):
+        if request.method == 'GET':
+            return True
+        elif request.user.is_public_user:
+            return False
+        else:
+            return True
+
+
+def rest_permission_classes():
+    permission_classes = (permissions.IsAuthenticated & BaseRestPublicPermission,)
+    return permission_classes
+
+
 mysite = MyAdminSite()
 mysite.site_header = 'Alyx'
 mysite.site_title = 'Alyx'
 mysite.site_url = None
-mysite.index_title = 'Welcome to Alyx'
+mysite.index_title = f'Welcome to Alyx {version}'
 mysite.enable_nav_sidebar = False
 
 admin.site = mysite

alyx/alyx/settings_lab_template.py

@@ -12,6 +12,7 @@
 STOCK_MANAGERS = ('root',)
 WEIGHT_THRESHOLD = 0.75
 DEFAULT_LAB_NAME = 'defaultlab'
+WATER_RESTRICTIONS_EDITABLE = False  # if set to True, all users can edit water restrictions
 DEFAULT_LAB_PK = '4027da48-7be3-43ec-a222-f75dffe36872'
 SESSION_REPO_URL = \
     "http://ibl.flatironinstitute.org/{lab}/Subjects/{subject}/{date}/{number:03d}/"