Merge pull request #43 from kushalbakshi/main

Add injection schema

CHANGELOG.md

@@ -3,6 +3,11 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.2.0] - 2023-08-23
+
++ Add - `injection` schema
++ Update - docstrings, `linking_module` within each `activate` function
+
 ## [0.1.8] - 2023-06-20
 
 + Update - GitHub Actions workflows
@@ -58,6 +63,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Add - `subject` schema
 + Add - `genotyping` schema
 
+[0.2.0]: https://github.com/datajoint/element-animal/releases/tag/0.2.0
 [0.1.8]: https://github.com/datajoint/element-animal/releases/tag/0.1.8
 [0.1.7]: https://github.com/datajoint/element-animal/releases/tag/0.1.7
 [0.1.6]: https://github.com/datajoint/element-animal/releases/tag/0.1.6

docs/src/concepts.md

@@ -56,6 +56,10 @@ There are three modules in `element-animal`:
 
 ![Surgery schema diagram](https://raw.githubusercontent.com/datajoint/element-animal/main/images/surgery_diagram.svg)
 
+### Injection Diagram
+
+![Injection schema diagram](https://raw.githubusercontent.com/datajoint/element-animal/main/images/injection_diagram.svg)
+
 ## `subject` schema ([API docs](https://datajoint.com/docs/elements/element-animal/api/element_animal/subject))
 
 - Although not required, most choose to connect the `Session` table to a `Subject` table.
@@ -93,3 +97,12 @@ There are three modules in `element-animal`:
 | Hemisphere          | Brain region hemisphere                                        |
 | ImplantationType    | Type of implantation                                           |
 | Implantation        | Implantation of a device                                       |
+
+### `injection` schema ([API docs](https://datajoint.com/docs/elements/element-animal/api/element_animal/injection))
+
+| Table               | Description                                                    |
+| ------------------- | -------------------------------------------------------------- |
+| VirusSerotype       | Virus serotype                                                 |
+| InjectionProtocol   | Injection device protocol                                      |
+| VirusName           | Full virus name                                                |
+| Injection           | Information about the virus injection                          |

element_animal/genotyping.py

@@ -6,13 +6,14 @@
 from . import subject
 
 schema = dj.schema()
+_linking_module = None
 
 
 def activate(
-    genotyping_schema_name,
-    subject_schema_name=None,
-    create_schema=True,
-    create_tables=True,
+    genotyping_schema_name: str,
+    subject_schema_name: str = None,
+    create_schema: bool = True,
+    create_tables: bool = True,
     linking_module=None,
 ):
     """Activate this schema.
@@ -26,8 +27,8 @@ def activate(
                             database if it does not yet exist.
         create_tables (bool, optional): when True (default), create tables in the
                             database if they do not yet exist.
-        linking_module (bool, optional): a module name or a module containing the
-        required dependencies to activate the `subject` element:
+        linking_module (str): A module name or a module containing the required
+            dependencies to activate the `genotyping` module.
 
     Dependencies:
     Upstream tables:
@@ -56,7 +57,7 @@ def activate(
         genotyping_schema_name,
         create_schema=create_schema,
         create_tables=create_tables,
-        add_objects=linking_module.__dict__,
+        add_objects=_linking_module.__dict__,
     )
 
 

element_animal/injection.py

@@ -0,0 +1,153 @@
+import importlib
+import inspect
+
+import datajoint as dj
+
+from . import surgery
+
+schema = dj.Schema()
+_linking_module = None
+
+
+def activate(
+    injection_schema_name: str,
+    surgery_schema_name: str = None,
+    lab_schema_name: str = None,
+    *,
+    create_schema: bool = True,
+    create_tables: bool = True,
+    linking_module=None,
+):
+    """Activate this schema.
+
+    Args:
+        schema_name (str): schema name on the database server to activate the
+                        `subject` element
+        create_schema (bool): when True (default), create schema in the
+                            database if it does not yet exist.
+        create_tables (bool): when True (default), create tables in the
+                            database if they do not yet exist.
+        linking_module (str): A module name or a module containing the required
+            dependencies to activate the `injection` module.
+
+    Dependencies:
+    Upstream tables:
+        Device: table from `element-lab`.
+    """
+
+    if isinstance(linking_module, str):
+        linking_module = importlib.import_module(linking_module)
+    assert inspect.ismodule(
+        linking_module
+    ), "The argument 'linking_module' must be a module's name or a module"
+
+    global _linking_module
+    _linking_module = linking_module
+
+    surgery.activate(
+        surgery_schema_name,
+        create_schema=create_schema,
+        create_tables=create_tables,
+        linking_module=_linking_module,
+    )
+    schema.activate(
+        injection_schema_name,
+        create_schema=create_schema,
+        create_tables=create_tables,
+        add_objects=_linking_module.__dict__,
+    )
+
+
+@schema
+class VirusSerotype(dj.Lookup):
+    """Virus serotype.
+
+    Attributes:
+        virus_serotype (str): Virus serotype.
+    """
+
+    definition = """
+    virus_serotype: varchar(10)
+    """
+    contents = zip(
+        [
+            "AAV1",
+            "AAV2",
+            "AAV4",
+            "AAV5",
+            "AAV6",
+            "AAV7",
+            "AAV8",
+            "AAV9",
+            "AAV2/1",
+            "AAV2/5",
+            "AAV2/9",
+            "AAVrg",
+            "AAV/DJ",
+            "pAAV",
+        ]
+    )
+
+
+@schema
+class InjectionProtocol(dj.Manual):
+    """Injection device protocol.
+
+    Attributes:
+        protocol_id (int): Unique protocol ID.
+        lab.Device (foreign key): Primary key from lab.Device.
+        volume_per_pulse (float): Volume dispensed per microinjector pulse.
+        injection_rate (float): Rate at which injectate is dispensed.
+        interpulse_delay (float): Delay between injection pulses. Set to 0 if
+        injection is a single pulse.
+    """
+
+    definition = """
+    protocol_id         : int
+    ---
+    -> Device
+    volume_per_pulse    : float
+    injection_rate      : float
+    interpulse_delay    : float
+    """
+
+
+@schema
+class VirusName(dj.Manual):
+    """Full virus name.
+
+    Attributes:
+        virus_name (str): Full virus name. Ex: AAV1.CAG.Flex.ArchT.GFP.
+        VirusSerotype (foreign key, nullable): Primary key from VirusSerotype.
+    """
+
+    definition = """
+    virus_name: varchar(64)  # Full virus name. Ex: AAV1.CAG.Flex.ArchT.GFP.
+    ---
+    -> [nullable] VirusSerotype
+    """
+
+
+@schema
+class Injection(dj.Manual):
+    """Information about the virus injection.
+
+    Attributes:
+        surgery.Implantation (foreign key): Primary key from
+        surgery.Implantation.
+        VirusName (foreign key): Primary key from VirusName.
+        InjectionProtocol (foreign key): Primary key from InjectionProtocol.
+        titer (str): Titer of injectate at the current injection site.
+        total_volume (float): Total volume injected at the current injection site.
+        injection_comment (str): Comments about the virus injection.
+    """
+
+    definition = """
+    -> surgery.Implantation
+    -> VirusName
+    -> InjectionProtocol
+    ---
+    titer           : varchar(16)
+    total_volume    : float
+    injection_comment=''  : varchar(1024)
+    """

element_animal/subject.py

@@ -11,7 +11,7 @@ def activate(
     *,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module: bool = True,
+    linking_module=None,
 ):
     """Activate this schema.
 
@@ -22,8 +22,8 @@ def activate(
                             database if it does not yet exist.
         create_tables (bool): when True (default), create tables in the
                             database if they do not yet exist.
-        linking_module (bool): a module name or a module containing the
-        required dependencies to activate the `subject` element:
+        linking_module (str): A module name or a module containing the required
+            dependencies to activate the `subject` module.
 
     Dependencies:
     Upstream tables:
@@ -49,7 +49,7 @@ def activate(
         schema_name,
         create_schema=create_schema,
         create_tables=create_tables,
-        add_objects=linking_module.__dict__,
+        add_objects=_linking_module.__dict__,
     )
 
 
@@ -147,7 +147,7 @@ class Subject(dj.Manual):
 
     Attributes:
         subject ( varchar(8) ): Subject ID.
-        subject_nickname ( varchar(8) ): Subject nickname.
+        subject_nickname ( varchar(64) ): Subject nickname.
         sex (enum): 'M', 'F', or 'U'; Male, Female, or Unknown.
         subject_birth_date (date): Birth date of the subject.
         subject_description ( varchar(1024) ): Description of the subject.

element_animal/surgery.py

@@ -16,7 +16,7 @@ def activate(
     *,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module: bool = True,
+    linking_module=None,
 ):
     """Activate this schema.
 
@@ -27,8 +27,8 @@ def activate(
                             database if it does not yet exist.
         create_tables (bool): when True (default), create tables in the
                             database if they do not yet exist.
-        linking_module (bool): a module name or a module containing the
-        required dependencies to activate the `subject` element:
+        linking_module (str): A module name or a module containing the required
+            dependencies to activate the `surgery` module.
 
     Dependencies:
     Upstream tables:
@@ -54,7 +54,7 @@ def activate(
         surgery_schema_name,
         create_schema=create_schema,
         create_tables=create_tables,
-        add_objects=linking_module.__dict__,
+        add_objects=_linking_module.__dict__,
     )
 
 
@@ -132,21 +132,15 @@ class Implantation(dj.Manual):
     """Implantation of a device
 
     Attributes:
-        Session (foreign key): Session primary key
-        location_id (int): ID of of brain location
-        ap ( float ): In mm, Anterior/posterior; Anterior Positive
-        ap_reference (projected attribute): Coordinate reference
-        ml ( float ): In mm, medial axis; Right Positive
-        ml_reference (projected attribute): Coordinate reference
-        dv ( float ): In mm, dorso-ventral axis. Ventral negative
-        dv_reference (projected attribute): Coordinate reference
-        theta ( float, nullable ): Elevation in degrees.
-            Rotation about ml-axis [0, 180] relative to z-axis
-        phi ( float, nullable ): Azimuth in degrees.
-            Rotations about dv-axis [0, 360] relative to x-axis
-        beta ( float, nullable ): Rotation about shank in degrees.
-            Rotation about the shank [-180, 180]. Clockwise is increasing.
-            0 is the probe-front facing anterior
+        Subject (foreign key): Subject primary key.
+        implant_date (datetime): Date and time of implantation surgery.
+        ImplantationType (foreign key): ImplantationType primary key.
+        region_acronym ( projected attribute, varchar(32) ): Brain region
+        shorthand from BrainRegion.
+        hemisphere ( projected attribute, varchar(8) ): Brain region hemisphere
+        from Hemisphere.
+        user ( projected attribute, varchar(32) ): User who performed the surgery.
+        implant_comment ( varchar(1024), optional ): Comments about the implant.
     """
 
     definition = """
@@ -161,6 +155,22 @@ class Implantation(dj.Manual):
     """
 
     class Coordinate(dj.Part):
+        """Coordinates of the Implantation Device.
+
+        Attributes:
+            Implantation (foreign key): Primary keys from Implantation.
+            ap ( float ): In mm, Anterior/posterior; Anterior Positive.
+            ap_reference (projected attribute): Coordinate reference.
+            ml ( float ): In mm, medial axis; Right Positive.
+            ml_reference (projected attribute): Coordinate reference.
+            dv ( float ): In mm, dorso-ventral axis. Ventral negative.
+            dv_reference (projected attribute): Coordinate reference.
+            theta ( float, nullable ): Elevation in degrees. Rotation about ml-axis [0, 180] relative to z-axis.
+            phi ( float, nullable ): Azimuth in degrees. Rotations about dv-axis [0, 360] relative to x-axis.
+            beta ( float, nullable ): Rotation about shank in degrees. Rotation
+            about the shank [-180, 180]. Clockwise is increasing. 0 is the probe-front facing anterior.
+        """
+
         definition = """
         -> master
         ---

element_animal/version.py

@@ -1,2 +1,2 @@
 """Package metadata."""
-__version__ = "0.1.8"
+__version__ = "0.2.0"