Merge pull request #865 from cortex-lab/dev

Dev

alyx/actions/admin.py

@@ -244,15 +244,6 @@ def session_l(self, obj):
 
 
 class WaterRestrictionForm(forms.ModelForm):
-    implant_weight = forms.FloatField()
-
-    def save(self, commit=True):
-        implant_weight = self.cleaned_data.get('implant_weight')
-        subject = self.cleaned_data.get('subject', None)
-        if implant_weight:
-            subject.implant_weight = implant_weight
-            subject.save()
-        return super(WaterRestrictionForm, self).save(commit=commit)
 
     class Meta:
         model = WaterRestriction
@@ -272,22 +263,20 @@ def formfield_for_foreignkey(self, db_field, request, **kwargs):
     def get_form(self, request, obj=None, **kwargs):
         form = super(WaterRestrictionAdmin, self).get_form(request, obj, **kwargs)
         subject = getattr(obj, 'subject', None)
-        iw = getattr(subject, 'implant_weight', None)
         rw = subject.water_control.weight() if subject else None
-        form.base_fields['implant_weight'].initial = iw
         if self.has_change_permission(request, obj):
             form.base_fields['reference_weight'].initial = rw or 0
         return form
 
     form = WaterRestrictionForm
 
-    fields = ['subject', 'implant_weight', 'reference_weight',
-              'start_time', 'end_time', 'water_type', 'users', 'narrative']
+    fields = ['subject', 'reference_weight', 'start_time',
+              'end_time', 'water_type', 'users', 'narrative', 'implant_weight']
     list_display = ('subject_w', 'start_time_l', 'end_time_l', 'water_type', 'weight',
                     'weight_ref') + WaterControl._columns[3:] + ('projects',)
     list_select_related = ('subject',)
     list_display_links = ('start_time_l', 'end_time_l')
-    readonly_fields = ('weight',)  # WaterControl._columns[1:]
+    readonly_fields = ('weight', 'implant_weight')  # WaterControl._columns[1:]
     ordering = ['-start_time', 'subject__nickname']
     search_fields = ['subject__nickname', 'subject__projects__name']
     list_filter = [ResponsibleUserListFilter,
@@ -361,6 +350,12 @@ def given_water_total(self, obj):
         return '%.2f' % obj.subject.water_control.given_water_total()
     given_water_total.short_description = 'water tot'
 
+    def implant_weight(self, obj):
+        if not obj.subject:
+            return
+        return '%.2f' % (obj.subject.water_control.implant_weight() or 0.)
+    implant_weight.short_description = 'implant weight'
+
     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)
@@ -421,11 +416,19 @@ class WaterTypeAdmin(BaseActionAdmin):
     list_display_links = ('name',)
 
 
+class SurgeryActionForm(BaseActionForm):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.fields['implant_weight'].required = True
+
+
 class SurgeryAdmin(BaseActionAdmin):
-    list_display = ['subject_l', 'date', 'users_l', 'procedures_l', 'narrative', 'projects']
+    form = SurgeryActionForm
+    list_display = ['subject_l', 'date', 'users_l', 'procedures_l',
+                    'narrative', 'projects', 'implant_weight']
     list_select_related = ('subject',)
 
-    fields = BaseActionAdmin.fields + ['outcome_type']
+    fields = BaseActionAdmin.fields + ['outcome_type', 'implant_weight']
     list_display_links = ['date']
     search_fields = ('subject__nickname', 'subject__projects__name')
     list_filter = [SubjectAliveListFilter,

alyx/actions/migrations/0022_project_to_projects.py

@@ -6,6 +6,7 @@
 
 logger = logging.getLogger(__name__)
 
+
 def project2projects(apps, schema_editor):
     """
     Find sessions where the project field (singular) value is not in the projects (plural) many-to-many

alyx/actions/migrations/0024_surgery_implant_weight.py

@@ -0,0 +1,24 @@
+# Generated by Django 4.2.10 on 2024-03-15 13:53
+
+import django.core.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('actions', '0023_remove_session_project'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='surgery',
+            name='implant_weight',
+            field=models.FloatField(blank=True, default=0, help_text='Implant weight in grams', validators=[django.core.validators.MinValueValidator(0)]),
+            preserve_default=False,
+        ),
+        migrations.AddConstraint(
+            model_name='surgery',
+            constraint=models.CheckConstraint(check=models.Q(('implant_weight__gte', 0)), name='implant_weight_gte_0'),
+        ),
+    ]

alyx/actions/migrations/0025_move_implant_weight.py

@@ -0,0 +1,71 @@
+# Generated by Django 4.2.10 on 2024-03-15 13:53
+"""
+In 2024-03 the Subject.implant_weight field was removed and the Surgery.implant_weight field
+was added.  This script 'saves' the non-zero implant weights to the Subject.JSON field and if
+unambiguous, saves the implant weight to the relevent surgery.
+"""
+import logging
+from pathlib import Path
+from datetime import datetime, timezone
+
+from django.db import migrations
+from django.core import serializers
+
+import alyx
+
+logger = logging.getLogger(__name__)
+
+
+def move_implant_weight(apps, schema_editor):
+    Subject = apps.get_model('subjects', 'Subject')
+    ProcedureType = apps.get_model('actions', 'ProcedureType')
+    try:
+        headplate_implant = ProcedureType.objects.get(name='Headplate implant')
+    except ProcedureType.DoesNotExist:
+        headplate_implant = None
+    query = Subject.objects.filter(implant_weight__gt=0)
+    now = datetime.now(timezone.utc).isoformat()
+    n = 0
+    for subject in query:
+        # Add implant weight to JSON field for prosperity
+        iw = subject.implant_weight
+        json = subject.json or {}
+        d = {'implant_weight': [{'value': iw, 'datetime': now}]}
+        if 'history' in json:
+            json['history'].update(d)
+        else:
+            json['history'] = d
+        subject.json = json
+        subject.save()
+        # If possible, add implant weight to previous surgery
+        surgeries = subject.actions_surgerys.filter(procedures__name__icontains='implant').distinct()
+        if surgeries.count() == 0:
+            # If no surgeries contain an implant procedure, attempt to find one surgery where
+            # implant or headplate are mentioned in the narrative
+            surgeries = subject.actions_surgerys.filter(narrative__iregex='.*(headplate|implant).*')
+        # If there is an unambiguous result, set the surgery implant weight
+        if surgeries.count() == 1:
+            surgery = surgeries.first()
+            surgery.implant_weight = iw
+            # If headplate is mentioned in the narrative, add Headplate implant procedure
+            # to the surgeries procedures list
+            if headplate_implant and 'headplate' in surgery.narrative.lower():
+                surgery.procedures.add(headplate_implant)
+            surgery.save()
+            n += 1
+
+    logger.info(f'implant weights: {query.count():,g} subjects; {n:,g} surgeries updated')
+    if query.count():
+        filename = now[:19].replace(':', '-') + '_subject-implant-weight.json'
+        filepath = Path(alyx.__file__).parents[2].joinpath('data', filename)
+        with open(filepath, 'w') as fp:
+            fp.write(serializers.serialize('json', query, fields=['implant_weight']))
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('actions', '0024_surgery_implant_weight'),
+    ]
+
+    operations = [migrations.RunPython(move_implant_weight)]

alyx/actions/models.py

@@ -203,9 +203,15 @@ class Surgery(BaseAction):
                                  default=_default_surgery_location,
                                  help_text="The physical location at which the surgery was "
                                  "performed")
+    implant_weight = models.FloatField(null=False, blank=True, validators=[MinValueValidator(0)],
+                                       help_text="Implant weight in grams")
 
     class Meta:
         verbose_name_plural = "surgeries"
+        constraints = [
+            models.CheckConstraint(
+                check=models.Q(implant_weight__gte=0), name="implant_weight_gte_0"),
+        ]
 
     def save(self, *args, **kwargs):
         # Issue #422.
@@ -336,6 +342,7 @@ def save(self, *args, **kwargs):
                 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)
+
         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)

alyx/actions/tests.py

@@ -7,7 +7,7 @@
 from actions.water_control import to_date
 from actions.models import (
     WaterAdministration, WaterRestriction, WaterType, Weighing,
-    Notification, NotificationRule, create_notification)
+    Notification, NotificationRule, create_notification, Surgery, ProcedureType)
 from actions.notifications import check_water_administration, check_weighed
 from misc.models import LabMember, LabMembership, Lab
 from subjects.models import Subject
@@ -40,6 +40,18 @@ def setUp(self):
         Lab.objects.create(name='zscore', reference_weight_pct=0, zscore_weight_pct=0.85)
         Lab.objects.create(name='rweigh', reference_weight_pct=0.85, zscore_weight_pct=0)
         Lab.objects.create(name='mixed', reference_weight_pct=0.425, zscore_weight_pct=0.425)
+        # create some surgeries to go with it (for testing implant weight in calculations)
+        date = self.start_date - datetime.timedelta(days=7)
+        surgery0 = Surgery.objects.create(subject=self.sub, implant_weight=4.56, start_time=date)
+        implant_proc, _ = ProcedureType.objects.get_or_create(name='Headplate implant')
+        surgery0.procedures.add(implant_proc.pk)
+        date = self.start_date + datetime.timedelta(days=10)
+        surgery1 = Surgery.objects.create(subject=self.sub, implant_weight=0., start_time=date)
+        date = self.start_date + datetime.timedelta(days=25)
+        surgery2 = Surgery.objects.create(subject=self.sub, implant_weight=7., start_time=date)
+        surgery2.procedures.add(implant_proc.pk)
+        self.surgeries = [surgery0, surgery1, surgery2]
+
         # Create an initial Water Restriction
         start_wr = self.start_date + datetime.timedelta(days=self.rwind)
         water_type = WaterType.objects.get(name='Hydrogel 5% Citric Acid')
@@ -68,29 +80,38 @@ def test_water_control_thresholds(self):
         self.sub.save()
         wc = self.sub.reinit_water_control()
         wc.expected_weight()
-        self.assertAlmostEqual(self.wei[self.rwind], wc.reference_weight())
-        self.assertAlmostEqual(self.wei[self.rwind], wc.expected_weight())
+        # expected weight should be different to reference weight as the implant weight changes
+        expected = self.wei[self.rwind] + (wc.implant_weights[1][1] - wc.implant_weights[0][1])
+        self.assertAlmostEqual(expected, wc.expected_weight())
+        expected = self.wei[self.rwind] - wc.implant_weights[0][1]
+        self.assertAlmostEqual(expected, wc.reference_weight())
+        # test implant weight values
+        self.assertEqual([4.56, 7.0], [x[1] for x in wc.implant_weights])
+        self.assertEqual(7.0, wc.implant_weight())
+        self.assertEqual(4.56, wc.implant_weight(self.start_date))
+        self.assertEqual(4.56, wc.reference_implant_weight_at())
         # test computation on zscore weight lab alone
         self.sub.lab = Lab.objects.get(name='zscore')
         self.sub.save()
         wc = self.sub.reinit_water_control()
-        wc.expected_weight()
-        self.assertAlmostEqual(self.wei[self.rwind], wc.reference_weight())
         zscore = wc.zscore_weight()
+        self.assertAlmostEqual(zscore, 31.04918367346939)
+        self.assertEqual(zscore + wc.implant_weights[1][1], wc.expected_weight())
         # test computation on mixed lab
         self.sub.lab = Lab.objects.get(name='mixed')
         self.sub.save()
         wc = self.sub.reinit_water_control()
-        self.assertAlmostEqual(self.wei[self.rwind], wc.reference_weight())
-        self.assertAlmostEqual(wc.expected_weight(), (wc.reference_weight() + zscore) / 2)
+        self.assertAlmostEqual(expected, wc.reference_weight())
+        expected_zscore = (wc.reference_weight() + zscore) / 2 + wc.implant_weights[1][1]
+        self.assertAlmostEqual(wc.expected_weight(), expected_zscore)
         # test that the thresholds are all above 70%
-        self.assertTrue(all([thrsh[0] > 0.4 for thrsh in wc.thresholds]))
+        self.assertTrue(all(thrsh[0] > 0.4 for thrsh in wc.thresholds))
         # if we change the reference weight of the water restriction, this should change in wc too
-        self.assertAlmostEqual(wc.reference_weight(), self.wr.reference_weight)
+        self.assertAlmostEqual(expected, wc.reference_weight())
         self.wr.reference_weight = self.wr.reference_weight + 1
         self.wr.save()
         wc = self.sub.reinit_water_control()
-        self.assertAlmostEqual(wc.reference_weight(), self.wr.reference_weight)
+        self.assertAlmostEqual(expected + 1, wc.reference_weight())
 
 
 class NotificationTests(TestCase):

alyx/actions/tests_rest.py

@@ -7,7 +7,7 @@
 from alyx.base import BaseTests
 from subjects.models import Subject, Project
 from misc.models import Lab, Note, ContentType
-from actions.models import Session, WaterType, WaterAdministration
+from actions.models import Session, WaterType, WaterAdministration, Surgery, ProcedureType
 from data.models import Dataset, DatasetType
 
 
@@ -22,10 +22,13 @@ def setUp(self):
         self.lab02 = Lab.objects.create(name='awesomelab')
         self.projectX = Project.objects.create(name='projectX')
         self.projectY = Project.objects.create(name='projectY')
-        # Set an implant weight.
-        self.subject.implant_weight = 4.56
-        self.subject.save()
         self.test_protocol = 'test_passoire'
+        # Create a surgery with an implant weight.
+        self.surgery = Surgery.objects.create(
+            subject=self.subject, implant_weight=4.56, start_time=now() - timedelta(days=7))
+        implant_proc, _ = ProcedureType.objects.get_or_create(name='Headplate implant')
+        self.surgery.procedures.add(implant_proc.pk)
+        self.subject.save()
 
     def tearDown(self):
         base.DISABLE_MAIL = False
@@ -305,9 +308,9 @@ def test_surgeries(self):
         sr = self.ar(self.client.get(reverse('surgeries-list',)))
         self.assertTrue(ns > 0)
         self.assertTrue(len(sr) == ns)
-        self.assertTrue(set(sr[0].keys()) == set(
-            ['id', 'subject', 'name', 'json', 'narrative', 'start_time', 'end_time',
-             'outcome_type', 'lab', 'location', 'users', 'procedures']))
+        self.assertTrue(set(sr[0].keys()) == {
+            'id', 'subject', 'name', 'json', 'narrative', 'start_time', 'end_time',
+            'outcome_type', 'lab', 'location', 'users', 'procedures', 'implant_weight'})
 
     def test_list_retrieve_water_restrictions(self):
         url = reverse('water-restriction-list')

alyx/actions/views.py

@@ -1,4 +1,4 @@
-from datetime import timedelta, date
+from datetime import timedelta, date, datetime
 from operator import itemgetter
 
 from one.alf.spec import QC
@@ -457,7 +457,9 @@ def get(self, request, format=None, nickname=None):
         end_date = request.query_params.get('end_date', None)
         subject = Subject.objects.get(nickname=nickname)
         records = subject.water_control.to_jsonable(start_date=start_date, end_date=end_date)
-        data = {'subject': nickname, 'implant_weight': subject.implant_weight,
+        date_str = datetime.strptime(start_date, '%Y-%m-%d') if start_date else None
+        ref_iw = subject.water_control.reference_implant_weight_at(date_str)
+        data = {'subject': nickname, 'implant_weight': ref_iw,
                 'reference_weight_pct': subject.water_control.reference_weight_pct,
                 'zscore_weight_pct': subject.water_control.zscore_weight_pct,
                 'records': records}