Task protocol model

alyx/actions/admin.py

@@ -477,18 +477,18 @@ def _pass_narrative_templates(context):
 
 class SessionAdmin(BaseActionAdmin):
     list_display = ['subject_l', 'start_time', 'number', 'lab', 'dataset_count',
-                    'task_protocol', 'qc', 'user_list', 'project_']
+                    'task_protocol_', 'qc', 'user_list', 'project_']
     list_display_links = ['start_time']
     fields = BaseActionAdmin.fields + [
-        'repo_url', 'qc', 'extended_qc', 'projects', ('type', 'task_protocol', ), 'number',
+        'repo_url', 'qc', 'extended_qc', 'projects', ('type', 'task_protocols', ), 'number',
         'n_correct_trials', 'n_trials', 'weighing', 'auto_datetime']
     list_filter = [('users', RelatedDropdownFilter),
                    ('start_time', DateRangeFilter),
                    ('projects', RelatedDropdownFilter),
                    ('lab', RelatedDropdownFilter),
                    ]
     search_fields = ('subject__nickname', 'lab__name', 'projects__name', 'users__username',
-                     'task_protocol', 'pk')
+                     'task_protocol__name', 'pk')
     ordering = ('-start_time', 'task_protocol', 'lab')
     inlines = [WaterAdminInline, DatasetInline, NoteInline]
     readonly_fields = ['repo_url', 'task_protocol', 'weighing', 'qc', 'extended_qc',
@@ -520,6 +520,9 @@ def add_view(self, request, extra_context=None):
     def project_(self, obj):
         return [getattr(p, 'name', None) for p in obj.projects.all()]
 
+    def task_protocol_(self, obj):
+        return [getattr(p, 'name', None) for p in obj.task_protocols.all()]
+
     def repo_url(self, obj):
         url = settings.SESSION_REPO_URL.format(
             lab=obj.subject.lab.name,

alyx/actions/migrations/0019_session_task_protocols_alter_session_task_protocol.py

@@ -0,0 +1,24 @@
+# Generated by Django 4.1.5 on 2023-02-03 10:16
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('experiments', '0012_taskprotocol'),
+        ('actions', '0018_session_projects_alter_session_project'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='session',
+            name='task_protocols',
+            field=models.ManyToManyField(blank=True, to='experiments.taskprotocol', verbose_name='Session task protocols'),
+        ),
+        migrations.AlterField(
+            model_name='session',
+            name='task_protocol',
+            field=models.CharField(blank=True, default='old task protocol', max_length=1023),
+        ),
+    ]

alyx/actions/models.py

@@ -251,7 +251,9 @@ class Session(BaseAction):
                             help_text="User-defined session type (e.g. Base, Experiment)")
     number = models.IntegerField(null=True, blank=True,
                                  help_text="Optional session number for this level")
-    task_protocol = models.CharField(max_length=1023, blank=True, default='')
+    task_protocol = models.CharField(max_length=1023, blank=True, default='old task protocol')
+    task_protocols = models.ManyToManyField('experiments.TaskProtocol', blank=True,
+                                            verbose_name='Session task protocols')
     n_trials = models.IntegerField(blank=True, null=True)
     n_correct_trials = models.IntegerField(blank=True, null=True)
 

alyx/actions/serializers.py

@@ -10,11 +10,12 @@
 from data.models import Dataset, DatasetType
 from misc.models import LabLocation, Lab
 from experiments.serializers import ProbeInsertionListSerializer, FilterDatasetSerializer
+from experiments.models import TaskProtocol
 from misc.serializers import NoteSerializer
 
 
 SESSION_FIELDS = ('subject', 'users', 'location', 'procedures', 'lab', 'projects', 'type',
-                  'task_protocol', 'number', 'start_time', 'end_time', 'narrative',
+                  'task_protocols', 'number', 'start_time', 'end_time', 'narrative',
                   'parent_session', 'n_correct_trials', 'n_trials', 'url', 'extended_qc', 'qc',
                   'wateradmin_session_related', 'data_dataset_session_related',
                   'auto_datetime')
@@ -121,18 +122,23 @@ class SessionListSerializer(BaseActionSerializer):
                                             slug_field='name',
                                             queryset=Project.objects.all(),
                                             many=True)
+    task_protocols = serializers.SlugRelatedField(read_only=False,
+                                                  slug_field='name',
+                                                  queryset=TaskProtocol.objects.all(),
+                                                  many=True)
 
     @staticmethod
     def setup_eager_loading(queryset):
         """ Perform necessary eager loading of data to avoid horrible performance."""
         queryset = queryset.select_related('subject', 'lab')
         queryset = queryset.prefetch_related('projects')
+        queryset = queryset.prefetch_related('task_protocols')
         return queryset.order_by('-start_time')
 
     class Meta:
         model = Session
         fields = ('id', 'subject', 'start_time', 'number', 'lab', 'projects', 'url',
-                  'task_protocol')
+                  'task_protocols')
 
 
 class SessionDetailSerializer(BaseActionSerializer):
@@ -142,6 +148,9 @@ class SessionDetailSerializer(BaseActionSerializer):
     probe_insertion = ProbeInsertionListSerializer(read_only=True, many=True)
     projects = serializers.SlugRelatedField(read_only=False, slug_field='name', many=True,
                                             queryset=Project.objects.all(), required=False)
+    task_protocols = serializers.SlugRelatedField(
+        read_only=False, slug_field='name', many=True,
+        queryset=TaskProtocol.objects.all(), required=False)
     notes = NoteSerializer(read_only=True, many=True)
     qc = BaseSerializerEnumField(required=False)
 

alyx/actions/tests_rest.py

@@ -6,6 +6,7 @@
 from alyx import base
 from alyx.base import BaseTests
 from subjects.models import Subject, Project
+from experiments.models import TaskProtocol
 from misc.models import Lab, Note, ContentType
 from actions.models import Session, WaterType, WaterAdministration
 
@@ -21,6 +22,8 @@ def setUp(self):
         self.lab02 = Lab.objects.create(name='awesomelab')
         self.projectX = Project.objects.create(name='projectX')
         self.projectY = Project.objects.create(name='projectY')
+        self.protocolX = TaskProtocol.objects.create(name='ephysChoiceWorld')
+        self.protocolY = TaskProtocol.objects.create(name='passiveChoiceWorld')
         # Set an implant weight.
         self.subject.implant_weight = 4.56
         self.subject.save()
@@ -187,6 +190,45 @@ def test_sessions_projects(self):
         d = self.ar(self.client.get(reverse('session-list') + f'?projects={self.projectY.name}'))
         self.assertEqual(len(d), 1)
 
+    def test_sessions_protocols(self):
+        ses1dict = {'subject': self.subject.nickname,
+                    'users': [self.superuser.username],
+                    'projects': [self.projectX.name],
+                    'start_time': '2020-07-09T12:34:56',
+                    'end_time': '2020-07-09T12:34:57',
+                    'type': 'Base',
+                    'number': '1',
+                    'lab': self.lab01.name,
+                    'task_protocol': [self.protocolX]
+                    }
+        ses2dict = {'subject': self.subject.nickname,
+                    'users': [self.superuser.username, self.superuser2.username],
+                    'projects': [self.projectX.name],
+                    'start_time': '2020-07-09T12:34:56',
+                    'end_time': '2020-07-09T12:34:57',
+                    'type': 'Base',
+                    'number': '2',
+                    'lab': self.lab01.name,
+                    'task_protocol': [self.protocolX, self.protocolY]
+                    }
+        self.ar(self.post(reverse('session-list'), data=ses1dict), 201)
+        self.ar(self.post(reverse('session-list'), data=ses2dict), 201)
+        # Test the user filter, this should return 2 sessions
+        q = f'?task_protocols={self.protocolX.name}'
+        d = self.ar(self.client.get(reverse('session-list') + q))
+        self.assertEqual(len(d), 2)
+        # This should return only one session
+        q = f'?task_protocols={self.protocolY.name}'
+        d = self.ar(self.client.get(reverse('session-list') + q))
+        self.assertEqual(len(d), 1)
+        # test the legacy filter that should act in the same way
+        q = f'?task_protocol={self.protocolX.name}'
+        d = self.ar(self.client.get(reverse('session-list') + q))
+        self.assertEqual(len(d), 2)
+        q = f'?task_protocols={self.protocolY.name}'
+        d = self.ar(self.client.get(reverse('session-list') + q))
+        self.assertEqual(len(d), 1)
+
     def test_sessions(self):
         a_dict4json = {'String': 'this is not a JSON', 'Integer': 4, 'List': ['titi', 4]}
         ses_dict = {'subject': self.subject.nickname,
@@ -201,7 +243,7 @@ def test_sessions(self):
                     'lab': self.lab01.name,
                     'n_trials': 100,
                     'n_correct_trials': 75,
-                    'task_protocol': self.test_protocol,
+                    'task_protocol': [self.protocolX],
                     'json': a_dict4json}
         # Test the session creation
         r = self.post(reverse('session-list'), data=ses_dict)

alyx/actions/views.py

@@ -198,6 +198,8 @@ class SessionFilter(BaseFilterSet):
     date_range = django_filters.CharFilter(field_name='date_range', method=('filter_date_range'))
     type = django_filters.CharFilter(field_name='type', lookup_expr=('iexact'))
     lab = django_filters.CharFilter(field_name='lab__name', lookup_expr=('iexact'))
+    task_protocols = django_filters.CharFilter(field_name='task_protocols__name',
+                                               lookup_expr=('icontains'))
     task_protocol = django_filters.CharFilter(field_name='task_protocol',
                                               lookup_expr=('icontains'))
     qc = django_filters.CharFilter(method='enum_field_filter')

alyx/experiments/migrations/0012_taskprotocol.py

@@ -0,0 +1,27 @@
+# Generated by Django 4.1.5 on 2023-02-03 10:16
+
+from django.db import migrations, models
+import uuid
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('experiments', '0011_chronic_insertion'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='TaskProtocol',
+            fields=[
+                ('id', models.UUIDField(default=uuid.uuid4, editable=False, primary_key=True, serialize=False)),
+                ('json', models.JSONField(blank=True, help_text='Structured data, formatted in a user-defined way', null=True)),
+                ('name', models.CharField(max_length=255)),
+                ('version', models.CharField(help_text='The major version of the task protocol', max_length=255)),
+                ('description', models.CharField(blank=True, help_text='Description of the task protocol', max_length=1023)),
+            ],
+            options={
+                'unique_together': {('name', 'version')},
+            },
+        ),
+    ]

alyx/experiments/models.py

@@ -235,3 +235,16 @@ class Meta:
     def save(self, *args, **kwargs):
         super(Channel, self).save(*args, **kwargs)
         self.trajectory_estimate.save()  # this will bump the datetime auto-update of trajectory
+
+
+class TaskProtocol(BaseModel):
+    name = models.CharField(max_length=255)
+    version = models.CharField(max_length=255, help_text='The major version of the task protocol')
+    description = models.CharField(
+        max_length=1023, blank=True, help_text='Description of the task protocol')
+
+    class Meta:
+        unique_together = (('name', 'version'),)
+
+    def __str__(self):
+        return "<TaskProtocol %s>" % self.name

alyx/jobs/admin.py

@@ -11,9 +11,9 @@ class TaskAdmin(BaseAdmin):
     exclude = ['json']
     readonly_fields = ['session', 'log', 'parents']
     list_display = ['name', 'graph', 'status', 'version_str', 'level', 'datetime',
-                    'session_str', 'session_task_protocol', 'session_projects']
+                    'session_str', 'session_task_protocols', 'session_projects']
     search_fields = ('session__id', 'session__lab__name', 'session__subject__nickname',
-                     'log', 'version', 'session__task_protocol', 'session__projects__name')
+                     'log', 'version', 'session__task_protocols__name', 'session__projects__name')
     ordering = ('-session__start_time', 'level')
     list_editable = ('status', )
     list_filter = [('name', DropdownFilter),
@@ -32,9 +32,10 @@ def session_projects(self, obj):
             return obj.session.projects.name
     session_projects.short_description = 'projects'
 
-    def session_task_protocol(self, obj):
-        return obj.session.task_protocol
-    session_task_protocol.short_description = 'task_protocol'
+    def session_task_protocols(self, obj):
+        if obj.session.task_protocols is not None:
+            return obj.session.task_protocols.name
+    session_task_protocols.short_description = 'task_protocols'
 
     def session_str(self, obj):
         url = get_admin_url(obj.session)

alyx/misc/management/commands/one_cache.py

@@ -311,12 +311,15 @@ def generate_sessions_frame(int_id=True, tags=None) -> pd.DataFrame:
     )
     """
     fields = ('id', 'lab__name', 'subject__nickname', 'start_time__date',
-              'number', 'task_protocol', 'all_projects')
+              'number', 'all_protocols', 'all_projects')
+    projects = ArrayAgg('projects__name')
+    protocols = ArrayAgg('task_protocols__name')
     query = (Session
              .objects
              .select_related('subject', 'lab')
              .prefetch_related('projects')
-             .annotate(all_projects=ArrayAgg('projects__name'))
+             .prefetch_related('task_protocols')
+             .annotate(all_projects=projects, all_protocols=protocols)
              .order_by('-start_time', 'subject__nickname', '-number'))  # FIXME Ignores nickname :(
     if tags:
         if not isinstance(tags, str):
@@ -327,16 +330,18 @@ def generate_sessions_frame(int_id=True, tags=None) -> pd.DataFrame:
     logger.debug(f'Raw session frame = {getsizeof(df) / 1024**2} MiB')
     # Rename, sort fields
     df['all_projects'] = df['all_projects'].map(lambda x: ','.join(filter(None, set(x))))
+    df['all_protocols'] = df['all_protocols'].map(lambda x: ','.join(filter(None, set(x))))
+    renames = {'start_time': 'date', 'all_projects': 'projects', 'all_protocols': 'task_protocols'}
     df = (
         (df
             .rename(lambda x: x.split('__')[0], axis=1)
-            .rename({'start_time': 'date', 'all_projects': 'projects'}, axis=1)
+            .rename(renames, axis=1)
             .dropna(subset=['number', 'date', 'subject', 'lab'])  # Remove dud or base sessions
             .sort_values(['date', 'subject', 'number'], ascending=False))
     )
     df['number'] = df['number'].astype(int)  # After dropping nans we can convert number to int
     # These columns may be empty; ensure None -> ''
-    for col in ('task_protocol', 'projects'):
+    for col in ('task_protocols', 'projects'):
         df[col] = df[col].astype(str)
 
     if int_id:

alyx/subjects/models.py

@@ -630,7 +630,11 @@ def new_litter_autoname(self):
     def new_subject_autoname(self):
         self.subject_autoname_index = self.subject_autoname_index + 1
         self.save()
-        return '%s_%04d' % (self.nickname, self.subject_autoname_index)
+        new_name = '%s_%04d' % (self.nickname, self.subject_autoname_index)
+        if Subject.objects.filter(nickname=new_name).count() > 0:
+            return self.new_subject_autoname()
+        assert Subject.objects.filter(nickname=new_name).count() == 0
+        return new_name
 
     def set_autoname(self, obj):
         if isinstance(obj, BreedingPair):

requirements_frozen.txt

@@ -1,7 +1,7 @@
 asgiref==3.6.0
 backports.zoneinfo==0.2.1
-boto3==1.26.51
-botocore==1.29.51
+boto3==1.26.56
+botocore==1.29.56
 certifi==2022.12.7
 cffi==1.15.1
 charset-normalizer==3.0.1
@@ -36,7 +36,7 @@ flake8==6.0.0
 fonttools==4.38.0
 globus-cli==3.10.1
 globus-sdk==3.15.0
-iblutil==1.4.0
+iblutil==1.5.0
 idna==3.4
 importlib-metadata==6.0.0
 itypes==1.2.0
@@ -51,9 +51,9 @@ matplotlib==3.6.3
 mccabe==0.7.0
 numba==0.56.4
 numpy==1.23.5
-ONE-api==1.18.0
+ONE-api==1.19.0
 packaging==23.0
-pandas==1.5.2
+pandas==1.5.3
 Pillow==9.4.0
 psycopg2-binary==2.9.5
 pyarrow==10.0.1