Merge branch 'master' into dev

alyx/actions/fixtures/actions.proceduretype.json

@@ -286,5 +286,14 @@
   "json": null,
   "description": "This term covers:\r\n- Induction and maintenance of general/local/regional anaesthesia by use of agents and by routes suitable for the species, nature and duration of the procedure - Inhalation.\r\n- Subcutaneous injection under anesthesia\r\n- Intramuscular injection under anesthesia\r\n- Administration of substances topically to the skin or conjunctiva with anaesthesia.\r\n- Placement of head in atraumatic headholder  (via atraumatic ear and eye bars) OR Head bolt clamp to a fixation bar (head bolt already in place and fully healed)\r\n- Craniotomy\r\n- Implantation of cannula"
  }
+},
+{
+ "model": "actions.proceduretype",
+ "pk": "a00737fa-7ec1-48c1-ad7c-08529712adcb",
+ "fields": {
+  "name": "Fiber photometry",
+  "json": null,
+  "description": ""
+ }
 }
 ]

alyx/data/fixtures/data.datasettype.json

@@ -1656,7 +1656,7 @@
       "json": null,
       "name": "photometry.ROIs",
       "created_by": null,
-      "description": "ROI integer for associateing with trajectory.",
+      "description": "ROI integer for associating with trajectory.",
       "filename_pattern": "*photometry.ROIs*"
     }
   },
@@ -1678,7 +1678,7 @@
       "json": null,
       "name": "fpData.raw",
       "created_by": null,
-      "description": "Raw FP data dataframe containing fluorescence data for every active channel (max: isosbestic, red and green) as well as information of coactive components with each frame (E.g TTL syncing pulse).",
+      "description": "Raw fiber photometry dataframe containing fluorescence data for every active channel (max: isosbestic, red and green) as well as information of coactive components with each frame (E.g TTL syncing pulse).",
       "filename_pattern": "_*_fpData.raw*"
     }
   },
@@ -1689,7 +1689,7 @@
       "json": null,
       "name": "fpData.channels",
       "created_by": null,
-      "description": "Frame flag value for each LED channel [OFF, L415, L470, L560].  Each row corresponds to a different labelled condition.  See user manual at https://neurophotometrics.com/documentation",
+      "description": "Frame flag value for each LED fiber photometry channel [OFF, L415, L470, L560].  Each row corresponds to a different labelled condition.  See user manual at https://neurophotometrics.com/documentation",
       "filename_pattern": "*fpData.channels.*"
     }
   },
@@ -2319,5 +2319,16 @@
       "description": "The raw frame exposure times.",
       "filename_pattern": ""
     }
+  },
+  {
+    "model": "data.datasettype",
+    "pk": "4c86d4e1-9365-41d2-97cf-cf88c8817bc3",
+    "fields": {
+      "json": null,
+      "name": "fpData.digitalInputs",
+      "created_by": null,
+      "description": "",
+      "filename_pattern": "*digitalInputs.raw*"
+    }
   }
 ]

alyx/misc/management/commands/homeoffice.py

@@ -40,14 +40,29 @@ def genotyped(start_date, end_date):
     return Q(genotype_date__gte=start_date, genotype_date__lte=end_date)
 
 
+# Filters
+
+# Do not have surgery
 def not_used(query):
     return query.filter(Q(actions_surgerys__isnull=True)).distinct()
 
 
+# Have surgery
 def used(query):
     return query.filter(actions_surgerys__isnull=False).distinct()
 
 
+# Protocol 2 or 3
+def used_2_3(query):
+    return Q(protocol_number__in=['2', '3'])
+
+
+# Have water restriction
+def restricted(query):
+    return query.filter(actions_waterrestrictions__isnull=False).distinct()
+
+
+# Transgenic
 def transgenic(query):
     return query.exclude(line__nickname='C57')
 
@@ -65,14 +80,23 @@ def display(title, query, start_date=None, end_date=None):
     if start_date:
         title = title % (start_date, end_date)
     path = 'homeoffice/%s.txt' % title
+
+    # Compute sex ratio.
+    males = sum(subj.sex == 'M' for subj in query)
+    total = sum(subj.sex in ('M', 'F') for subj in query)
+    sexratio = males / total
+
     with open(path, 'w') as f:
         with redirect_stdout(f):
-            print("%s: %d subjects." % (title, len(query)))
+            print("%s: %d subjects (%.1f%% males)." % (title, len(query), sexratio * 100))
             print('\t'.join(('#   ', 'user       ', 'prot.',
                              'born     ',
                              'genotyped',
                              'died     ',
-                             'EM', 'nickname')))
+                             'EM',
+                             'nickname',
+                             'sex',
+                             )))
             for i, subj in enumerate(query):
                 print('\t'.join(('%04d' % (i + 1),
                                  '{0: <12}'.format(subj.responsible_user.username),
@@ -82,6 +106,7 @@ def display(title, query, start_date=None, end_date=None):
                                  str(subj.death_date or ' ' * 10),
                                  subj.ear_mark,
                                  subj.nickname,
+                                 subj.sex,
                                  )))
             print('\n\n')
     os.system('expand -t 4 "%s" | sponge "%s"' % (path, path))
@@ -125,3 +150,13 @@ def handle(self, *args, **options):
 
         tkng = transgenic(k).exclude(genotyped('2000-01-01', '2100-01-01'))
         display("Transgenic killed and not genotyped %s - %s", tkng, start_date, end_date)
+
+        # Sex bias (cf email from Charu to Cyrille on 2024-07-23)
+        # Birth date.
+        sexbias = s.filter(born(start_date, '2100-01-01'))
+        sexbias = sexbias.filter(
+            Q(protocol_number__in=['2', '3']) |  # 1. protocol 2 or 3
+            Q(actions_surgerys__isnull=False) |  # 2. have a surgery
+            Q(actions_waterrestrictions__isnull=False)  # 3. have a water restriction
+        )
+        display("Sex bias %s - %s", sexbias, start_date, end_date)