Add mice schema

src/ethopy/config.py

@@ -59,6 +59,7 @@ def _set_defaults(self) -> None:
                 "behavior": "lab_behavior",
                 "interface": "lab_interface",
                 "recording": "lab_recordings",
+                "mice": "lab_mice",
             },
             "logging": {
                 "level": "INFO",

src/ethopy/core/logger.py

@@ -60,19 +60,21 @@ def _set_connection() -> None:
         behavior: The virtual module for behavior.
         interface: The virtual module for interface.
         recording: The virtual module for recording.
+        mice: The virtual module for the animal colony.
         public_conn: The connection object for public access.
 
     Returns:
         None
 
     """
-    global experiment, stimulus, behavior, interface, recording, public_conn
+    global experiment, stimulus, behavior, interface, recording, mice, public_conn
     virtual_modules, public_conn = create_virtual_modules(SCHEMATA)
     experiment = virtual_modules["experiment"]
     stimulus = virtual_modules["stimulus"]
     behavior = virtual_modules["behavior"]
     recording = virtual_modules["recording"]
     interface = virtual_modules["interface"]
+    mice = virtual_modules["mice"]
 
 
 _set_connection()

src/ethopy/core/mice.py

@@ -0,0 +1,233 @@
+"""Create tables for the lab_mice schema.
+
+Mirrors the animal colony schema hosted at `lab_mice`: animal identity, lines and
+genotypes, weights, surgeries/implants and location transfers. Importing this
+module declares any missing table in the schema mapped to ``mice`` in SCHEMATA.
+"""
+
+import datajoint as dj
+
+from ethopy.core.logger import mice  # noqa: F401
+
+
+@mice.schema
+class Lines(dj.Manual):
+    """Basic mouse line info."""
+
+    definition = """
+    # Basic mouse line info
+    line                 : varchar(100)                 # Mouse Line Abbreviation
+    ---
+    line_full            : varchar(100)                 # full line name
+    rec_strain           : varchar(20)                  # recipient strain
+    donor_strain         : varchar(20)                  # donor strain
+    n=null               : tinyint                      # minimum number of backcrosses to recipient strain
+    seq                  : varchar(5000)                # sequence of transgene, if available
+    line_notes           : varchar(4096)                # other comments
+    line_ts=CURRENT_TIMESTAMP : timestamp               # automatic
+    """
+
+
+@mice.schema
+class Mice(dj.Manual):
+    """Basic mouse info."""
+
+    definition = """
+    # Basic mouse info
+    animal_id            : int                          # id number
+    ---
+    other_id=''          : varchar(20)                  # alternative id number
+    dob=null             : date                         # animal's date of birth
+    dow=null             : date                         # animal's date of weaning
+    sex='unknown'        : enum('M','F','unknown')      # animal's sex
+    color='unknown'      : enum('Black','Brown','White','unknown') # animal's color
+    line=''              : varchar(255)                 # mouse line
+    genotype='unknown'   : enum('homozygous','heterozygous','hemizygous','positive','negative','wild type','unknown')
+    ear_punch='unknown'  : enum('None','R','L','RL','RR','LL','unknown') # animal's ear punch
+    owner='none'         : enum('manolis','maria','emina','Other','Available','none') # mouse's owner
+    fluo_test='unknown'  : enum('unknown','no','yes')   # fluorescence test result
+    mouse_notes=''       : varchar(4096)                # other comments and distinguishing features
+    facility='unknown'   : enum('TMF','Taub','Other','unknown') # animal's current facility
+    room='unknown'       : enum('VK3','VH1','T014','T057','T086D','Other','unknown','T027') # animal's current room
+    rack=null            : char(4)                      # animal's current rack
+    row=''               : char(1)                      # animal's current row
+    mouse_ts=CURRENT_TIMESTAMP : timestamp              # automatic
+    cage_id=''           : varchar(100)                 # animal's current cage
+    usage='unknown'      : enum('in use','available','euthanize','unknown') # availability
+    """
+
+
+@mice.schema
+class Death(dj.Manual):
+    """Info about each mouse's death."""
+
+    definition = """
+    # info about each mouse's death
+    -> Mice
+    ---
+    dod=null             : date                         # date of death
+    death_notes=''       : varchar(4096)                # other comments
+    death_ts=CURRENT_TIMESTAMP : timestamp              # automatic
+    """
+
+
+@mice.schema
+class Founders(dj.Manual):
+    """Additional info about founder mice."""
+
+    definition = """
+    # Additional info about founder mice
+    -> Mice
+    -> Lines
+    ---
+    source               : varchar(100)                 # source of mouse (lab, company)
+    doa=null             : date                         # date of arrival
+    founder_notes        : varchar(4096)                # other comments
+    founder_ts=CURRENT_TIMESTAMP : timestamp            # automatic
+    """
+
+
+@mice.schema
+class Genotypes(dj.Manual):
+    """Info about each mouse's genotype."""
+
+    definition = """
+    # info about each mouse's genotype
+    -> Mice
+    -> Lines
+    ---
+    genotype='unknown'   : enum('homozygous','heterozygous','hemizygous','positive','negative','wild type','unknown') # animal's genotype
+    genotype_notes=null  : varchar(4096)                # other comments
+    genotype_ts=CURRENT_TIMESTAMP : timestamp           # automatic
+    """
+
+
+@mice.schema
+class Parents(dj.Manual):
+    """Parent-child relationships between mice."""
+
+    definition = """
+    # parent-child relationships between mice
+    -> Mice
+    parent_id            : varchar(20)                  # id number of parent
+    ---
+    relation_notes=''    : varchar(4096)                # other comments
+    relation_ts=CURRENT_TIMESTAMP : timestamp           # automatic
+    """
+
+
+@mice.schema
+class Transfers(dj.Manual):
+    """Completed transfers."""
+
+    definition = """
+    # completed transfers
+    -> Mice
+    dot                  : date                         # date of transfer
+    ---
+    from_owner='none'    : enum('alex','manolis','Other','Available','none') # previous owner
+    to_owner='none'      : enum('alex','manolis','Other','Available','none') # new owner
+    from_facility='unknown' : enum('TMF','Taub','Other','unknown') # animal's previous facility
+    to_facility='unknown' : enum('TMF','Taub','Other','unknown')   # animal's new facility
+    from_room='unknown'  : enum('VD4','T014','T057','T086D','Other','unknown','VK3','T027','VH1') # animal's previous room
+    to_room='unknown'    : enum('VD4','T014','T057','T086D','Other','unknown','VK3','T027','VH1') # animal's new room
+    from_rack=null       : char(4)                      # animal's previous rack
+    to_rack=null         : char(4)                      # animal's new rack
+    from_row=''          : char(1)                      # animal's previous row
+    to_row=''            : char(1)                      # animal's new row
+    transfer_notes=''    : varchar(4096)                # other comments
+    transfer_ts=CURRENT_TIMESTAMP : timestamp           # automatic
+    """
+
+
+@mice.schema
+class MouseWeight(dj.Manual):
+    """Weight measurements, logged by the setup at session start."""
+
+    definition = """
+    animal_id            : int unsigned                 # id number
+    timestamp=CURRENT_TIMESTAMP : timestamp             # timestamp of weight
+    ---
+    weight               : double(5,2)                  # weight in grams
+    """
+
+
+@mice.schema
+class GrowthCurve(dj.Lookup):
+    """Reference weight per age, sex and genotype."""
+
+    definition = """
+    age                  : int                          # in weeks
+    gender               : enum('male','female')
+    genotype             : enum('C57BL/6J')
+    ---
+    weight=null          : double                       # in grams
+    std=null             : double                       # standard deviation
+    """
+
+
+@mice.schema
+class SurgeryType(dj.Lookup):
+    """Surgery types."""
+
+    definition = """
+    # Surgery types
+    surgery              : varchar(16)                  # aim
+    ---
+    description=''       : varchar(2048)                # description
+    """
+
+
+@mice.schema
+class Surgery(dj.Manual):
+    """Surgery information."""
+
+    definition = """
+    # Surgery information
+    animal_id            : smallint unsigned            # animal id
+    timestamp            : datetime                     # timestamp
+    ---
+    user_name            : varchar(16)                  # user performing the surgery
+    -> SurgeryType
+    note=null            : varchar(2048)                # surgery notes
+    """
+
+
+@mice.schema
+class Implants(dj.Manual):
+    """Implant information."""
+
+    definition = """
+    animal_id            : int unsigned                 # id number
+    doi                  : date                         # date of implantation
+    ---
+    experimenter='Other' : varchar(64)                  # name of experimenter
+    anesthesia='Other'   : enum('isoflurane','ketamine/xylazine mix','Other') # anesthesia method
+    comments=null        : varchar(100)
+    """
+
+
+@mice.schema
+class Handling(dj.Manual):
+    """Handling sessions."""
+
+    definition = """
+    animal_id            : int unsigned                 # id number
+    timestamp            : datetime                     # date of handling
+    ---
+    experimenter='Other' : varchar(64)                  # name of experimenter
+    type='Touch'         : enum('Touch','Other')        # handling method
+    comments=null        : varchar(100)
+    """
+
+
+@mice.schema
+class Person(dj.Manual):
+    """People in the lab."""
+
+    definition = """
+    # people in the lab
+    person               : varchar(12)                  # person's short name
+    ---
+    full_name            : varchar(64)                  # person's full name
+    """

src/ethopy/experiments/calibrate.py

@@ -134,8 +134,9 @@ def cleanup(self):
                 if hasattr(self, "menu"):
                     self.menu.disable()
 
+                # Not pygame.quit(): it frees fonts still cached by
+                # pygame_menu, segfaulting the next menu built.
                 pygame.display.quit()
-                pygame.quit()
             except Exception as e:
                 log.warning(f"Error during pygame cleanup: {e}")
 
@@ -151,6 +152,47 @@ def cleanup(self):
             except Exception as e:
                 log.warning(f"Error updating logger status: {e}")
 
+    def _clear_menu(self):
+        """Clear the menu and re-add the always-available Abort button.
+
+        Every step rebuilds the menu from scratch, so the button has to be
+        re-added after each clear. It floats, so it does not shift the layout
+        of the widgets added after it.
+        """
+        self.menu.clear()
+        self.menu.add.button(
+            "Abort",
+            self.abort,
+            align=pygame_menu.locals.ALIGN_LEFT,
+            float=True,
+            padding=(5, 10, 5, 10),
+            background_color=(153, 0, 0),
+            font_size=25,
+        ).translate(650, 350)
+
+    def abort(self):
+        """Stop the calibration immediately.
+
+        Measurements already written by log_pulse_weight are left untouched;
+        only the remaining pulses and weight prompts are skipped.
+        """
+        log.warning("Calibration aborted by user")
+        try:
+            self.menu.clear()
+            self.menu.add.label(
+                "Calibration aborted!", float=True, font_size=30
+            ).translate(20, 80)
+            try:
+                self.menu.draw(self.screen)
+                pygame.display.flip()
+                time.sleep(2)
+            except pygame.error:
+                pass  # Display might already be quit
+        except Exception as e:
+            log.warning(f"Error during abort: {e}")
+        finally:
+            self.stop = True
+
     def exit(self):
         """exit _summary_
 
@@ -176,15 +218,15 @@ def exit(self):
 
     def create_pressure_menu(self):
         """The First menu in Calibration where is definde the air pressure in PSI"""
-        self.menu.clear()
+        self._clear_menu()
         self.button_input("Enter air pressure (PSI)", self.create_pulsenum_menu)
 
     def create_pulsenum_menu(self):
         """Before start pulses show a label in screen to place a pad under the ports"""
         self.pressure = self.curr
         self.curr = ""
         if self.cal_idx < len(self.session_params["pulsenum"]):
-            self.menu.clear()
+            self._clear_menu()
             self.menu.add.label(
                 "Place zero-weighted pad under the port", float=True, font_size=30
             ).translate(20, 80)
@@ -206,7 +248,7 @@ def create_pulse_num(self):
         """
         self.pulse = 0
         msg = f"Pulse {self.pulse + 1}/{self.session_params['pulsenum'][self.cal_idx]}"
-        self.menu.clear()
+        self._clear_menu()
         pulses_label = self.menu.add.label(
             msg,
             float=True,
@@ -224,6 +266,12 @@ def run_pulses(self, widget, menu):
             widget (_type_): The widget that uses the function
             menu (_type_): The current menu
         """
+        # run() calls menu.update() and menu.draw() in the same iteration, so an
+        # Abort pressed during update would otherwise still deliver one more round
+        # of pulses when this draw callback fires.
+        if self.stop:
+            return
+
         if self.pulse < self.session_params["pulsenum"][self.cal_idx]:
             self.msg = f"Pulse {self.pulse + 1}/{self.session_params['pulsenum'][self.cal_idx]}"
             log.info(f"\r{self.msg}")
@@ -251,10 +299,10 @@ def run_pulses(self, widget, menu):
 
     def create_port_weight(self):
         """A menu with numpad for defining the water in every port"""
-        self.menu.clear()
+        self._clear_menu()
         cal_idx = self.cal_idx - 1
         if self.session_params["save"]:
-            self.menu.clear()
+            self._clear_menu()
             if len(self.ports) != 0:
                 if len(self.ports) != len(self.session_params["ports"]):
                     self.log_pulse_weight(

src/ethopy/setup_db.py

@@ -280,6 +280,7 @@ def createschema() -> None:
         ("core/interface", "from ethopy.core.interface import *"),
         ("core/behavior", "from ethopy.core.behavior import *"),
         ("core/recordings", "from ethopy.core.recordings import *"),
+        ("core/mice", "from ethopy.core.mice import *"),
         ("stimuli", "from ethopy.stimuli import *"),
         ("behaviors", "from ethopy.behaviors import *"),
         ("experiments", "from ethopy.experiments import *"),