From 129945d1189da4c80d59c555384a223e2e2b2835 Mon Sep 17 00:00:00 2001
From: kushalbakshi <kushalbakshi@gmail.com>
Date: Mon, 14 Aug 2023 17:01:38 -0500
Subject: [PATCH 01/13] Edit existing docstrings + add injection schema

---
 element_animal/injection.py | 129 ++++++++++++++++++++++++++++++++++++
 element_animal/subject.py   |   2 +-
 element_animal/surgery.py   |  40 ++++++-----
 3 files changed, 155 insertions(+), 16 deletions(-)
 create mode 100644 element_animal/injection.py

diff --git a/element_animal/injection.py b/element_animal/injection.py
new file mode 100644
index 0000000..4b60aa7
--- /dev/null
+++ b/element_animal/injection.py
@@ -0,0 +1,129 @@
+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,
+    *,
+    create_schema: bool = True,
+    create_tables: bool = True,
+    linking_module: bool = True,
+):
+    """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 (bool): a module name or a module containing the
+        required dependencies to activate the `subject` element:
+
+    Dependencies:
+    Upstream tables:
+        User: the who conducted a particular surgery/implantation
+    """
+
+    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 AAVSerotype(dj.Lookup):
+    definition = """
+    aav_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 MicroInjectionDevice(dj.Lookup):
+    definition = """
+    micro_injection_device: varchar(12)
+    """
+    contents = zip(
+        [
+            "Nanoject",
+            "Picospritzer",
+        ]
+    )
+
+
+@schema
+class InjectionProtocol(dj.Manual):
+    definition = """
+    -> MicroInjectionDevice
+    protocol_id         : int
+    ---
+    volume_per_pulse    : float
+    injection_rate      : float
+    interpulse_delay    : float
+    """
+
+
+@schema
+class VirusName(dj.Manual):
+    definition = """
+    virus_name: varchar(64)  # Full virus name. Ex: AAV1.CAG.Flex.ArchT.GFP. 
+    """
+
+
+@schema
+class Injection(dj.Manual):
+    definition = """
+    -> surgery.Implantation
+    -> VirusName
+    -> surgery.BrainRegion
+    ---
+    -> [nullable] AAVSerotype
+    -> [nullable] InjectionProtocol
+    titer           : varchar(16)
+    total_volume    : float
+    """
diff --git a/element_animal/subject.py b/element_animal/subject.py
index f706105..d258df3 100644
--- a/element_animal/subject.py
+++ b/element_animal/subject.py
@@ -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.
diff --git a/element_animal/surgery.py b/element_animal/surgery.py
index d3e8ae2..62ca7f3 100644
--- a/element_animal/surgery.py
+++ b/element_animal/surgery.py
@@ -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): ID of brain location.
+        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) ): 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
         ---

From 56b2109ba6d6b2ae80fc1d6a32a7d8bce92ba88b Mon Sep 17 00:00:00 2001
From: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
Date: Wed, 23 Aug 2023 15:07:46 -0500
Subject: [PATCH 02/13] Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_animal/injection.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/element_animal/injection.py b/element_animal/injection.py
index 4b60aa7..5793b8a 100644
--- a/element_animal/injection.py
+++ b/element_animal/injection.py
@@ -59,9 +59,9 @@ def activate(
 
 
 @schema
-class AAVSerotype(dj.Lookup):
+class VirusSerotype(dj.Lookup):
     definition = """
-    aav_serotype: varchar(10)
+    virus_serotype: varchar(10)
     """
     contents = zip(
         [
@@ -99,9 +99,9 @@ class MicroInjectionDevice(dj.Lookup):
 @schema
 class InjectionProtocol(dj.Manual):
     definition = """
-    -> MicroInjectionDevice
     protocol_id         : int
     ---
+    -> MicroInjectionDevice
     volume_per_pulse    : float
     injection_rate      : float
     interpulse_delay    : float
@@ -112,6 +112,8 @@ class InjectionProtocol(dj.Manual):
 class VirusName(dj.Manual):
     definition = """
     virus_name: varchar(64)  # Full virus name. Ex: AAV1.CAG.Flex.ArchT.GFP. 
+    ---
+    -> VirusSerotype
     """
 
 
@@ -120,10 +122,9 @@ class Injection(dj.Manual):
     definition = """
     -> surgery.Implantation
     -> VirusName
-    -> surgery.BrainRegion
+    -> InjectionProtocol
     ---
-    -> [nullable] AAVSerotype
-    -> [nullable] InjectionProtocol
     titer           : varchar(16)
     total_volume    : float
+    injection_comment=''  : varchar(1024)
     """

From 679540158c920e05435dca5533ceb0961f023daf Mon Sep 17 00:00:00 2001
From: kushalbakshi <kushalbakshi@gmail.com>
Date: Wed, 23 Aug 2023 16:27:31 -0500
Subject: [PATCH 03/13] Update docstrings, requirements, docs, version

---
 CHANGELOG.md                 |   5 +
 docs/src/concepts.md         |  13 +++
 element_animal/injection.py  |  58 ++++++++---
 element_animal/version.py    |   2 +-
 images/injection_diagram.svg | 187 +++++++++++++++++++++++++++++++++++
 requirements.txt             |   1 +
 6 files changed, 251 insertions(+), 15 deletions(-)
 create mode 100644 images/injection_diagram.svg

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 893dab6..a2abfe8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 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
+
 ## [0.1.8] - 2023-06-20
 
 + Update - GitHub Actions workflows
@@ -58,6 +62,7 @@ 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
diff --git a/docs/src/concepts.md b/docs/src/concepts.md
index 52f772e..38e00c9 100644
--- a/docs/src/concepts.md
+++ b/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                          |
diff --git a/element_animal/injection.py b/element_animal/injection.py
index 5793b8a..1e57dd2 100644
--- a/element_animal/injection.py
+++ b/element_animal/injection.py
@@ -3,6 +3,7 @@
 
 import datajoint as dj
 
+from element_lab import lab
 from . import surgery
 
 schema = dj.Schema()
@@ -13,6 +14,7 @@
 def activate(
     injection_schema_name: str,
     surgery_schema_name: str = None,
+    lab_schema_name: str = None,
     *,
     create_schema: bool = True,
     create_tables: bool = True,
@@ -44,6 +46,11 @@ def activate(
     global _linking_module
     _linking_module = linking_module
 
+    lab.activate(
+        lab_schema_name,
+        create_schema=create_schema,
+        create_tables=create_tables,
+    )
     surgery.activate(
         surgery_schema_name,
         create_schema=create_schema,
@@ -60,6 +67,12 @@ def activate(
 
 @schema
 class VirusSerotype(dj.Lookup):
+    """Virus serotype.
+
+    Attributes:
+        virus_serotype (str): Virus serotype.
+    """
+
     definition = """
     virus_serotype: varchar(10)
     """
@@ -84,24 +97,22 @@ class VirusSerotype(dj.Lookup):
 
 
 @schema
-class MicroInjectionDevice(dj.Lookup):
-    definition = """
-    micro_injection_device: varchar(12)
+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.
     """
-    contents = zip(
-        [
-            "Nanoject",
-            "Picospritzer",
-        ]
-    )
-
 
-@schema
-class InjectionProtocol(dj.Manual):
     definition = """
     protocol_id         : int
     ---
-    -> MicroInjectionDevice
+    -> lab.Device
     volume_per_pulse    : float
     injection_rate      : float
     interpulse_delay    : float
@@ -110,15 +121,34 @@ class InjectionProtocol(dj.Manual):
 
 @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. 
     ---
-    -> VirusSerotype
+    -> [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
diff --git a/element_animal/version.py b/element_animal/version.py
index 10bc5c5..8667345 100644
--- a/element_animal/version.py
+++ b/element_animal/version.py
@@ -1,2 +1,2 @@
 """Package metadata."""
-__version__ = "0.1.8"
+__version__ = "0.2.0"
diff --git a/images/injection_diagram.svg b/images/injection_diagram.svg
new file mode 100644
index 0000000..1e11c50
--- /dev/null
+++ b/images/injection_diagram.svg
@@ -0,0 +1,187 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="668pt" height="256pt" viewBox="0.00 0.00 668.00 256.00">
+<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 252)">
+<title>%3</title>
+<polygon fill="white" stroke="none" points="-4,4 -4,-252 664,-252 664,4 -4,4"/>
+<!-- 28 -->
+<g id="node1" class="node"><title>28</title>
+<ellipse fill="#ff8800" fill-opacity="0.501961" stroke="#ff8800" stroke-opacity="0.501961" cx="71" cy="-88.5" rx="2" ry="2"/>
+<text text-anchor="middle" x="71" y="-88.2" font-family="arial" font-size="1.00" fill="#ff8800">28</text>
+</g>
+<!-- surgery.Implantation.Coordinate -->
+<g id="node15" class="node"><title>surgery.Implantation.Coordinate</title>
+<g id="a_node15"><a xlink:title="→ surgery.Implantation
------------------------------
ap=null              
→ [nullable] surgery.CoordinateReference.proj(ap_ref=&quot;reference&quot;)
ml=null              
→ [nullable] surgery.CoordinateReference.proj(ml_ref=&quot;reference&quot;)
dv=null              
→ [nullable] surgery.CoordinateReference.proj(dv_ref=&quot;reference&quot;)
theta=null           
phi=null             
beta=null            
">
+<polygon fill="none" stroke="none" points="263,-27 109,-27 109,-8 263,-8 263,-27"/>
+<text text-anchor="middle" x="186" y="-15" font-family="arial" font-size="10.00">surgery.Implantation.Coordinate</text>
+</a>
+</g>
+</g>
+<!-- 28&#45;&gt;surgery.Implantation.Coordinate -->
+<g id="edge1" class="edge"><title>28-&gt;surgery.Implantation.Coordinate</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M71.9037,-86.5169C74.4241,-83.8112 81.8184,-76.1163 89,-71 114.421,-52.8895 146.795,-36.5575 166.961,-27.0814"/>
+</g>
+<!-- 24 -->
+<g id="node2" class="node"><title>24</title>
+<ellipse fill="#ff8800" fill-opacity="0.501961" stroke="#ff8800" stroke-opacity="0.501961" cx="349" cy="-159.5" rx="2" ry="2"/>
+<text text-anchor="middle" x="349" y="-159.2" font-family="arial" font-size="1.00" fill="#ff8800">24</text>
+</g>
+<!-- surgery.Implantation -->
+<g id="node14" class="node"><title>surgery.Implantation</title>
+<g id="a_node14"><a xlink:title="→ subject.Subject
implant_date         
→ surgery.ImplantationType
→ surgery.BrainRegion.proj(target_region=&quot;region_acronym&quot;)
→ surgery.Hemisphere.proj(target_hemisphere=&quot;hemisphere&quot;)
------------------------------
→ `kushalbakshi_`.`#user`.proj(surgeon=&quot;user&quot;)
implant_comment=&quot;&quot;   
">
+<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="290,-106 170,-106 170,-71 290,-71 290,-106"/>
+<text text-anchor="start" x="178" y="-86.4" font-family="arial" text-decoration="underline" font-size="12.00" fill="darkgreen">surgery.Implantation</text>
+</a>
+</g>
+</g>
+<!-- 24&#45;&gt;surgery.Implantation -->
+<g id="edge2" class="edge"><title>24-&gt;surgery.Implantation</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M348.038,-157.518C345.357,-154.815 337.504,-147.126 330,-142 309.923,-128.286 285.833,-115.54 266.329,-106.042"/>
+</g>
+<!-- 29 -->
+<g id="node3" class="node"><title>29</title>
+<ellipse fill="#ff8800" fill-opacity="0.501961" stroke="#ff8800" stroke-opacity="0.501961" cx="107" cy="-88.5" rx="2" ry="2"/>
+<text text-anchor="middle" x="107" y="-88.2" font-family="arial" font-size="1.00" fill="#ff8800">29</text>
+</g>
+<!-- 29&#45;&gt;surgery.Implantation.Coordinate -->
+<g id="edge3" class="edge"><title>29-&gt;surgery.Implantation.Coordinate</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M107.966,-86.5949C110.645,-84.0885 118.408,-76.8559 125,-71 142.55,-55.411 163.336,-37.6727 175.553,-27.3197"/>
+</g>
+<!-- 25 -->
+<g id="node4" class="node"><title>25</title>
+<ellipse fill="#ff8800" fill-opacity="0.501961" stroke="#ff8800" stroke-opacity="0.501961" cx="169" cy="-159.5" rx="2" ry="2"/>
+<text text-anchor="middle" x="169" y="-159.2" font-family="arial" font-size="1.00" fill="#ff8800">25</text>
+</g>
+<!-- 25&#45;&gt;surgery.Implantation -->
+<g id="edge4" class="edge"><title>25-&gt;surgery.Implantation</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M169.862,-157.525C174.728,-152.021 199.107,-124.445 215.292,-106.137"/>
+</g>
+<!-- 27 -->
+<g id="node5" class="node"><title>27</title>
+<ellipse fill="#ff8800" fill-opacity="0.501961" stroke="#ff8800" stroke-opacity="0.501961" cx="143" cy="-88.5" rx="2" ry="2"/>
+<text text-anchor="middle" x="143" y="-88.2" font-family="arial" font-size="1.00" fill="#ff8800">27</text>
+</g>
+<!-- 27&#45;&gt;surgery.Implantation.Coordinate -->
+<g id="edge5" class="edge"><title>27-&gt;surgery.Implantation.Coordinate</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M143.608,-86.5246C147.589,-80.1364 170.102,-44.0113 180.604,-27.1581"/>
+</g>
+<!-- injection.VirusSerotype -->
+<g id="node6" class="node"><title>injection.VirusSerotype</title>
+<g id="a_node6"><a xlink:title="virus_serotype       
">
+<polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="493.5,-177 376.5,-177 376.5,-142 493.5,-142 493.5,-177"/>
+<text text-anchor="start" x="384.5" y="-158" font-family="arial" text-decoration="underline" font-size="10.00">injection.VirusSerotype</text>
+</a>
+</g>
+</g>
+<!-- injection.VirusName -->
+<g id="node11" class="node"><title>injection.VirusName</title>
+<g id="a_node11"><a xlink:title="virus_name           
------------------------------
→ injection.VirusSerotype
">
+<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="493.5,-106 372.5,-106 372.5,-71 493.5,-71 493.5,-106"/>
+<text text-anchor="start" x="380.5" y="-86.4" font-family="arial" text-decoration="underline" font-size="12.00" fill="darkgreen">injection.VirusName</text>
+</a>
+</g>
+</g>
+<!-- injection.VirusSerotype&#45;&gt;injection.VirusName -->
+<g id="edge6" class="edge"><title>injection.VirusSerotype-&gt;injection.VirusName</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M434.516,-141.797C434.201,-130.949 433.793,-116.867 433.48,-106.049"/>
+</g>
+<!-- injection.MicroInjectionDevice -->
+<g id="node7" class="node"><title>injection.MicroInjectionDevice</title>
+<g id="a_node7"><a xlink:title="micro_injection_device 
">
+<polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="658,-177 514,-177 514,-142 658,-142 658,-177"/>
+<text text-anchor="start" x="522" y="-158" font-family="arial" text-decoration="underline" font-size="10.00">injection.MicroInjectionDevice</text>
+</a>
+</g>
+</g>
+<!-- injection.InjectionProtocol -->
+<g id="node12" class="node"><title>injection.InjectionProtocol</title>
+<g id="a_node12"><a xlink:title="protocol_id          
------------------------------
→ injection.MicroInjectionDevice
volume_per_pulse     
injection_rate       
interpulse_delay     
">
+<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="660,-106 512,-106 512,-71 660,-71 660,-106"/>
+<text text-anchor="start" x="520" y="-86.4" font-family="arial" text-decoration="underline" font-size="12.00" fill="darkgreen">injection.InjectionProtocol</text>
+</a>
+</g>
+</g>
+<!-- injection.MicroInjectionDevice&#45;&gt;injection.InjectionProtocol -->
+<g id="edge7" class="edge"><title>injection.MicroInjectionDevice-&gt;injection.InjectionProtocol</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M586,-141.797C586,-130.949 586,-116.867 586,-106.049"/>
+</g>
+<!-- surgery.Hemisphere -->
+<g id="node8" class="node"><title>surgery.Hemisphere</title>
+<g id="a_node8"><a xlink:title="hemisphere           
">
+<polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="221,-248 117,-248 117,-213 221,-213 221,-248"/>
+<text text-anchor="start" x="125" y="-229" font-family="arial" text-decoration="underline" font-size="10.00">surgery.Hemisphere</text>
+</a>
+</g>
+</g>
+<!-- surgery.Hemisphere&#45;&gt;25 -->
+<g id="edge8" class="edge"><title>surgery.Hemisphere-&gt;25</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M169,-212.797C169,-194.929 169,-168.29 169,-161.91"/>
+</g>
+<!-- surgery.BrainRegion -->
+<g id="node9" class="node"><title>surgery.BrainRegion</title>
+<g id="a_node9"><a xlink:title="region_acronym       
------------------------------
region_name          
">
+<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="410.5,-248 287.5,-248 287.5,-213 410.5,-213 410.5,-248"/>
+<text text-anchor="start" x="295.5" y="-228.4" font-family="arial" text-decoration="underline" font-size="12.00" fill="darkgreen">surgery.BrainRegion</text>
+</a>
+</g>
+</g>
+<!-- surgery.BrainRegion&#45;&gt;24 -->
+<g id="edge9" class="edge"><title>surgery.BrainRegion-&gt;24</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M349,-212.797C349,-194.929 349,-168.29 349,-161.91"/>
+</g>
+<!-- surgery.ImplantationType -->
+<g id="node10" class="node"><title>surgery.ImplantationType</title>
+<g id="a_node10"><a xlink:title="implant_type         
------------------------------
implant_description  
">
+<polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="321.5,-177 196.5,-177 196.5,-142 321.5,-142 321.5,-177"/>
+<text text-anchor="start" x="204.5" y="-158" font-family="arial" text-decoration="underline" font-size="10.00">surgery.ImplantationType</text>
+</a>
+</g>
+</g>
+<!-- surgery.ImplantationType&#45;&gt;surgery.Implantation -->
+<g id="edge10" class="edge"><title>surgery.ImplantationType-&gt;surgery.Implantation</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M251.98,-141.797C247.42,-130.949 241.502,-116.867 236.955,-106.049"/>
+</g>
+<!-- injection.Injection -->
+<g id="node16" class="node"><title>injection.Injection</title>
+<g id="a_node16"><a xlink:title="→ surgery.Implantation
→ injection.VirusName
→ injection.InjectionProtocol
------------------------------
titer                
total_volume         
injection_comment=&quot;&quot; 
">
+<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="485,-35 381,-35 381,-0 485,-0 485,-35"/>
+<text text-anchor="middle" x="433" y="-14.4" font-family="arial" font-size="12.00" fill="darkgreen">injection.Injection</text>
+</a>
+</g>
+</g>
+<!-- injection.VirusName&#45;&gt;injection.Injection -->
+<g id="edge11" class="edge"><title>injection.VirusName-&gt;injection.Injection</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M433,-70.797C433,-59.9485 433,-45.8669 433,-35.0492"/>
+</g>
+<!-- injection.InjectionProtocol&#45;&gt;injection.Injection -->
+<g id="edge12" class="edge"><title>injection.InjectionProtocol-&gt;injection.Injection</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M549.353,-70.9728C525.218,-60.0885 493.741,-45.893 469.613,-35.0118"/>
+</g>
+<!-- surgery.CoordinateReference -->
+<g id="node13" class="node"><title>surgery.CoordinateReference</title>
+<g id="a_node13"><a xlink:title="reference            
">
+<polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="142,-177 0,-177 0,-142 142,-142 142,-177"/>
+<text text-anchor="start" x="8" y="-158" font-family="arial" text-decoration="underline" font-size="10.00">surgery.CoordinateReference</text>
+</a>
+</g>
+</g>
+<!-- surgery.CoordinateReference&#45;&gt;28 -->
+<g id="edge14" class="edge"><title>surgery.CoordinateReference-&gt;28</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M71,-141.797C71,-123.929 71,-97.2901 71,-90.9096"/>
+</g>
+<!-- surgery.CoordinateReference&#45;&gt;29 -->
+<g id="edge15" class="edge"><title>surgery.CoordinateReference-&gt;29</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M79.7146,-141.797C89.0371,-123.929 102.936,-97.2901 106.265,-90.9096"/>
+</g>
+<!-- surgery.CoordinateReference&#45;&gt;27 -->
+<g id="edge13" class="edge"><title>surgery.CoordinateReference-&gt;27</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M88.4292,-141.797C107.074,-123.929 134.871,-97.2901 141.529,-90.9096"/>
+</g>
+<!-- surgery.Implantation&#45;&gt;surgery.Implantation.Coordinate -->
+<g id="edge16" class="edge"><title>surgery.Implantation-&gt;surgery.Implantation.Coordinate</title>
+<path fill="none" stroke="#000000" stroke-width="2" stroke-opacity="0.250980" d="M219.349,-70.797C210.6,-57.0768 198.553,-38.1854 191.589,-27.2652"/>
+</g>
+<!-- surgery.Implantation&#45;&gt;injection.Injection -->
+<g id="edge17" class="edge"><title>surgery.Implantation-&gt;injection.Injection</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M278.624,-70.9728C310.645,-60.0885 352.409,-45.893 384.422,-35.0118"/>
+</g>
+</g>
+</svg>
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index 41a088b..4f7998f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,2 +1,3 @@
 datajoint>=0.13
+element-lab
 pynwb>=1.4.0

From e78dfe461bf82de9bb77df3d9fa8cea50c0deb55 Mon Sep 17 00:00:00 2001
From: kushalbakshi <kushalbakshi@gmail.com>
Date: Wed, 23 Aug 2023 16:32:54 -0500
Subject: [PATCH 04/13] Attempt 1: Modify for formatting

---
 element_animal/injection.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/element_animal/injection.py b/element_animal/injection.py
index 1e57dd2..7299024 100644
--- a/element_animal/injection.py
+++ b/element_animal/injection.py
@@ -145,7 +145,8 @@ class Injection(dj.Manual):
         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.
+        total_volume (float): Total volume injected at the current injection 
+        site.
         injection_comment (str): Comments about the virus injection. 
     """
 

From 6d7b1355c165d420dce5f9998c6a633cfec5e818 Mon Sep 17 00:00:00 2001
From: kushalbakshi <kushalbakshi@gmail.com>
Date: Wed, 23 Aug 2023 16:40:14 -0500
Subject: [PATCH 05/13] Attempt 2: Modify for formatting

---
 element_animal/injection.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/element_animal/injection.py b/element_animal/injection.py
index 7299024..dfabe20 100644
--- a/element_animal/injection.py
+++ b/element_animal/injection.py
@@ -129,7 +129,7 @@ class VirusName(dj.Manual):
     """
 
     definition = """
-    virus_name: varchar(64)  # Full virus name. Ex: AAV1.CAG.Flex.ArchT.GFP. 
+    virus_name: varchar(64)  # Full virus name. Ex: AAV1.CAG.Flex.ArchT.GFP.
     ---
     -> [nullable] VirusSerotype
     """
@@ -145,8 +145,7 @@ class Injection(dj.Manual):
         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.
+        total_volume (float): Total volume injected at the current injection site. 
         injection_comment (str): Comments about the virus injection. 
     """
 

From 7b2dd72bd6d1c59110c95bb5825a4356dadce166 Mon Sep 17 00:00:00 2001
From: kushalbakshi <kushalbakshi@gmail.com>
Date: Wed, 23 Aug 2023 16:56:15 -0500
Subject: [PATCH 06/13] Attempt 3: formatting with local pre-commit

---
 element_animal/injection.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/element_animal/injection.py b/element_animal/injection.py
index dfabe20..c744ab9 100644
--- a/element_animal/injection.py
+++ b/element_animal/injection.py
@@ -7,7 +7,6 @@
 from . import surgery
 
 schema = dj.Schema()
-
 _linking_module = None
 
 
@@ -99,7 +98,7 @@ class VirusSerotype(dj.Lookup):
 @schema
 class InjectionProtocol(dj.Manual):
     """Injection device protocol.
-    
+
     Attributes:
         protocol_id (int): Unique protocol ID.
         lab.Device (foreign key): Primary key from lab.Device.
@@ -145,8 +144,8 @@ class Injection(dj.Manual):
         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. 
+        total_volume (float): Total volume injected at the current injection site.
+        injection_comment (str): Comments about the virus injection.
     """
 
     definition = """

From ba04bae87173f659dd62cd0aed83f89907d045ec Mon Sep 17 00:00:00 2001
From: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
Date: Thu, 24 Aug 2023 12:57:52 -0500
Subject: [PATCH 07/13] Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_animal/surgery.py | 4 ++--
 requirements.txt          | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/element_animal/surgery.py b/element_animal/surgery.py
index 62ca7f3..63ebfd4 100644
--- a/element_animal/surgery.py
+++ b/element_animal/surgery.py
@@ -133,14 +133,14 @@ class Implantation(dj.Manual):
 
     Attributes:
         Subject (foreign key): Subject primary key.
-        implant_date (datetime): ID of brain location.
+        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) ): Comments about the implant.
+        implant_comment ( varchar(1024), optional ): Comments about the implant.
     """
 
     definition = """
diff --git a/requirements.txt b/requirements.txt
index 4f7998f..db7fa11 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,3 @@
 datajoint>=0.13
-element-lab
+element-lab>=0.3.0
 pynwb>=1.4.0

From bf0b25c6fc222f466ffb3f87234c75bd1b3119f7 Mon Sep 17 00:00:00 2001
From: kushalbakshi <kushalbakshi@gmail.com>
Date: Thu, 24 Aug 2023 13:02:03 -0500
Subject: [PATCH 08/13] Add `lab.Device` to schema diagram

---
 images/injection_diagram.svg | 238 +++++++++++++++++------------------
 1 file changed, 119 insertions(+), 119 deletions(-)

diff --git a/images/injection_diagram.svg b/images/injection_diagram.svg
index 1e11c50..2ea9c25 100644
--- a/images/injection_diagram.svg
+++ b/images/injection_diagram.svg
@@ -1,187 +1,187 @@
-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="668pt" height="256pt" viewBox="0.00 0.00 668.00 256.00">
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="647pt" height="256pt" viewBox="0.00 0.00 647.00 256.00">
 <g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 252)">
 <title>%3</title>
-<polygon fill="white" stroke="none" points="-4,4 -4,-252 664,-252 664,4 -4,4"/>
-<!-- 28 -->
-<g id="node1" class="node"><title>28</title>
+<polygon fill="white" stroke="none" points="-4,4 -4,-252 643,-252 643,4 -4,4"/>
+<!-- 19 -->
+<g id="node1" class="node"><title>19</title>
+<ellipse fill="#ff8800" fill-opacity="0.501961" stroke="#ff8800" stroke-opacity="0.501961" cx="313" cy="-159.5" rx="2" ry="2"/>
+<text text-anchor="middle" x="313" y="-159.2" font-family="arial" font-size="1.00" fill="#ff8800">19</text>
+</g>
+<!-- surgery.Implantation -->
+<g id="node8" class="node"><title>surgery.Implantation</title>
+<g id="a_node8"><a xlink:title="→ subject.Subject
implant_date         
→ surgery.ImplantationType
→ surgery.BrainRegion.proj(target_region=&quot;region_acronym&quot;)
→ surgery.Hemisphere.proj(target_hemisphere=&quot;hemisphere&quot;)
------------------------------
→ `kushalbakshi_`.`#user`.proj(surgeon=&quot;user&quot;)
implant_comment=&quot;&quot;   
">
+<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="290,-106 170,-106 170,-71 290,-71 290,-106"/>
+<text text-anchor="start" x="178" y="-86.4" font-family="arial" text-decoration="underline" font-size="12.00" fill="darkgreen">surgery.Implantation</text>
+</a>
+</g>
+</g>
+<!-- 19&#45;&gt;surgery.Implantation -->
+<g id="edge1" class="edge"><title>19-&gt;surgery.Implantation</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M311.979,-157.595C309.147,-155.091 300.944,-147.861 294,-142 279.614,-129.857 263.192,-116.394 250.585,-106.142"/>
+</g>
+<!-- 23 -->
+<g id="node2" class="node"><title>23</title>
 <ellipse fill="#ff8800" fill-opacity="0.501961" stroke="#ff8800" stroke-opacity="0.501961" cx="71" cy="-88.5" rx="2" ry="2"/>
-<text text-anchor="middle" x="71" y="-88.2" font-family="arial" font-size="1.00" fill="#ff8800">28</text>
+<text text-anchor="middle" x="71" y="-88.2" font-family="arial" font-size="1.00" fill="#ff8800">23</text>
 </g>
 <!-- surgery.Implantation.Coordinate -->
-<g id="node15" class="node"><title>surgery.Implantation.Coordinate</title>
-<g id="a_node15"><a xlink:title="→ surgery.Implantation
------------------------------
ap=null              
→ [nullable] surgery.CoordinateReference.proj(ap_ref=&quot;reference&quot;)
ml=null              
→ [nullable] surgery.CoordinateReference.proj(ml_ref=&quot;reference&quot;)
dv=null              
→ [nullable] surgery.CoordinateReference.proj(dv_ref=&quot;reference&quot;)
theta=null           
phi=null             
beta=null            
">
+<g id="node9" class="node"><title>surgery.Implantation.Coordinate</title>
+<g id="a_node9"><a xlink:title="→ surgery.Implantation
------------------------------
ap=null              
→ [nullable] surgery.CoordinateReference.proj(ap_ref=&quot;reference&quot;)
ml=null              
→ [nullable] surgery.CoordinateReference.proj(ml_ref=&quot;reference&quot;)
dv=null              
→ [nullable] surgery.CoordinateReference.proj(dv_ref=&quot;reference&quot;)
theta=null           
phi=null             
beta=null            
">
 <polygon fill="none" stroke="none" points="263,-27 109,-27 109,-8 263,-8 263,-27"/>
 <text text-anchor="middle" x="186" y="-15" font-family="arial" font-size="10.00">surgery.Implantation.Coordinate</text>
 </a>
 </g>
 </g>
-<!-- 28&#45;&gt;surgery.Implantation.Coordinate -->
-<g id="edge1" class="edge"><title>28-&gt;surgery.Implantation.Coordinate</title>
+<!-- 23&#45;&gt;surgery.Implantation.Coordinate -->
+<g id="edge2" class="edge"><title>23-&gt;surgery.Implantation.Coordinate</title>
 <path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M71.9037,-86.5169C74.4241,-83.8112 81.8184,-76.1163 89,-71 114.421,-52.8895 146.795,-36.5575 166.961,-27.0814"/>
 </g>
-<!-- 24 -->
-<g id="node2" class="node"><title>24</title>
+<!-- 18 -->
+<g id="node3" class="node"><title>18</title>
 <ellipse fill="#ff8800" fill-opacity="0.501961" stroke="#ff8800" stroke-opacity="0.501961" cx="349" cy="-159.5" rx="2" ry="2"/>
-<text text-anchor="middle" x="349" y="-159.2" font-family="arial" font-size="1.00" fill="#ff8800">24</text>
-</g>
-<!-- surgery.Implantation -->
-<g id="node14" class="node"><title>surgery.Implantation</title>
-<g id="a_node14"><a xlink:title="→ subject.Subject
implant_date         
→ surgery.ImplantationType
→ surgery.BrainRegion.proj(target_region=&quot;region_acronym&quot;)
→ surgery.Hemisphere.proj(target_hemisphere=&quot;hemisphere&quot;)
------------------------------
→ `kushalbakshi_`.`#user`.proj(surgeon=&quot;user&quot;)
implant_comment=&quot;&quot;   
">
-<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="290,-106 170,-106 170,-71 290,-71 290,-106"/>
-<text text-anchor="start" x="178" y="-86.4" font-family="arial" text-decoration="underline" font-size="12.00" fill="darkgreen">surgery.Implantation</text>
-</a>
+<text text-anchor="middle" x="349" y="-159.2" font-family="arial" font-size="1.00" fill="#ff8800">18</text>
 </g>
+<!-- 18&#45;&gt;surgery.Implantation -->
+<g id="edge3" class="edge"><title>18-&gt;surgery.Implantation</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M348.101,-157.511C345.592,-154.789 338.224,-147.056 331,-142 311.086,-128.062 286.992,-115.398 267.332,-106.001"/>
 </g>
-<!-- 24&#45;&gt;surgery.Implantation -->
-<g id="edge2" class="edge"><title>24-&gt;surgery.Implantation</title>
-<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M348.038,-157.518C345.357,-154.815 337.504,-147.126 330,-142 309.923,-128.286 285.833,-115.54 266.329,-106.042"/>
-</g>
-<!-- 29 -->
-<g id="node3" class="node"><title>29</title>
+<!-- 21 -->
+<g id="node4" class="node"><title>21</title>
 <ellipse fill="#ff8800" fill-opacity="0.501961" stroke="#ff8800" stroke-opacity="0.501961" cx="107" cy="-88.5" rx="2" ry="2"/>
-<text text-anchor="middle" x="107" y="-88.2" font-family="arial" font-size="1.00" fill="#ff8800">29</text>
+<text text-anchor="middle" x="107" y="-88.2" font-family="arial" font-size="1.00" fill="#ff8800">21</text>
 </g>
-<!-- 29&#45;&gt;surgery.Implantation.Coordinate -->
-<g id="edge3" class="edge"><title>29-&gt;surgery.Implantation.Coordinate</title>
+<!-- 21&#45;&gt;surgery.Implantation.Coordinate -->
+<g id="edge4" class="edge"><title>21-&gt;surgery.Implantation.Coordinate</title>
 <path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M107.966,-86.5949C110.645,-84.0885 118.408,-76.8559 125,-71 142.55,-55.411 163.336,-37.6727 175.553,-27.3197"/>
 </g>
-<!-- 25 -->
-<g id="node4" class="node"><title>25</title>
-<ellipse fill="#ff8800" fill-opacity="0.501961" stroke="#ff8800" stroke-opacity="0.501961" cx="169" cy="-159.5" rx="2" ry="2"/>
-<text text-anchor="middle" x="169" y="-159.2" font-family="arial" font-size="1.00" fill="#ff8800">25</text>
-</g>
-<!-- 25&#45;&gt;surgery.Implantation -->
-<g id="edge4" class="edge"><title>25-&gt;surgery.Implantation</title>
-<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M169.862,-157.525C174.728,-152.021 199.107,-124.445 215.292,-106.137"/>
-</g>
-<!-- 27 -->
-<g id="node5" class="node"><title>27</title>
+<!-- 22 -->
+<g id="node5" class="node"><title>22</title>
 <ellipse fill="#ff8800" fill-opacity="0.501961" stroke="#ff8800" stroke-opacity="0.501961" cx="143" cy="-88.5" rx="2" ry="2"/>
-<text text-anchor="middle" x="143" y="-88.2" font-family="arial" font-size="1.00" fill="#ff8800">27</text>
+<text text-anchor="middle" x="143" y="-88.2" font-family="arial" font-size="1.00" fill="#ff8800">22</text>
 </g>
-<!-- 27&#45;&gt;surgery.Implantation.Coordinate -->
-<g id="edge5" class="edge"><title>27-&gt;surgery.Implantation.Coordinate</title>
+<!-- 22&#45;&gt;surgery.Implantation.Coordinate -->
+<g id="edge5" class="edge"><title>22-&gt;surgery.Implantation.Coordinate</title>
 <path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M143.608,-86.5246C147.589,-80.1364 170.102,-44.0113 180.604,-27.1581"/>
 </g>
-<!-- injection.VirusSerotype -->
-<g id="node6" class="node"><title>injection.VirusSerotype</title>
-<g id="a_node6"><a xlink:title="virus_serotype       
">
-<polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="493.5,-177 376.5,-177 376.5,-142 493.5,-142 493.5,-177"/>
-<text text-anchor="start" x="384.5" y="-158" font-family="arial" text-decoration="underline" font-size="10.00">injection.VirusSerotype</text>
+<!-- lab.Device -->
+<g id="node6" class="node"><title>lab.Device</title>
+<g id="a_node6"><a xlink:title="device               
------------------------------
modality             
description=null     
">
+<polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="595.5,-177 534.5,-177 534.5,-142 595.5,-142 595.5,-177"/>
+<text text-anchor="start" x="542.5" y="-158" font-family="arial" text-decoration="underline" font-size="10.00">lab.Device</text>
 </a>
 </g>
 </g>
-<!-- injection.VirusName -->
-<g id="node11" class="node"><title>injection.VirusName</title>
-<g id="a_node11"><a xlink:title="virus_name           
------------------------------
→ injection.VirusSerotype
">
-<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="493.5,-106 372.5,-106 372.5,-71 493.5,-71 493.5,-106"/>
-<text text-anchor="start" x="380.5" y="-86.4" font-family="arial" text-decoration="underline" font-size="12.00" fill="darkgreen">injection.VirusName</text>
+<!-- injection.InjectionProtocol -->
+<g id="node13" class="node"><title>injection.InjectionProtocol</title>
+<g id="a_node13"><a xlink:title="protocol_id          
------------------------------
→ lab.Device
volume_per_pulse     
injection_rate       
interpulse_delay     
">
+<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="639,-106 491,-106 491,-71 639,-71 639,-106"/>
+<text text-anchor="start" x="499" y="-86.4" font-family="arial" text-decoration="underline" font-size="12.00" fill="darkgreen">injection.InjectionProtocol</text>
 </a>
 </g>
 </g>
-<!-- injection.VirusSerotype&#45;&gt;injection.VirusName -->
-<g id="edge6" class="edge"><title>injection.VirusSerotype-&gt;injection.VirusName</title>
-<path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M434.516,-141.797C434.201,-130.949 433.793,-116.867 433.48,-106.049"/>
-</g>
-<!-- injection.MicroInjectionDevice -->
-<g id="node7" class="node"><title>injection.MicroInjectionDevice</title>
-<g id="a_node7"><a xlink:title="micro_injection_device 
">
-<polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="658,-177 514,-177 514,-142 658,-142 658,-177"/>
-<text text-anchor="start" x="522" y="-158" font-family="arial" text-decoration="underline" font-size="10.00">injection.MicroInjectionDevice</text>
+<!-- lab.Device&#45;&gt;injection.InjectionProtocol -->
+<g id="edge6" class="edge"><title>lab.Device-&gt;injection.InjectionProtocol</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M565,-141.797C565,-130.949 565,-116.867 565,-106.049"/>
+</g>
+<!-- injection.VirusName -->
+<g id="node7" class="node"><title>injection.VirusName</title>
+<g id="a_node7"><a xlink:title="virus_name           
------------------------------
→ [nullable] injection.VirusSerotype
">
+<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="472.5,-106 351.5,-106 351.5,-71 472.5,-71 472.5,-106"/>
+<text text-anchor="start" x="359.5" y="-86.4" font-family="arial" text-decoration="underline" font-size="12.00" fill="darkgreen">injection.VirusName</text>
 </a>
 </g>
 </g>
-<!-- injection.InjectionProtocol -->
-<g id="node12" class="node"><title>injection.InjectionProtocol</title>
-<g id="a_node12"><a xlink:title="protocol_id          
------------------------------
→ injection.MicroInjectionDevice
volume_per_pulse     
injection_rate       
interpulse_delay     
">
-<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="660,-106 512,-106 512,-71 660,-71 660,-106"/>
-<text text-anchor="start" x="520" y="-86.4" font-family="arial" text-decoration="underline" font-size="12.00" fill="darkgreen">injection.InjectionProtocol</text>
+<!-- injection.Injection -->
+<g id="node14" class="node"><title>injection.Injection</title>
+<g id="a_node14"><a xlink:title="→ surgery.Implantation
→ injection.VirusName
→ injection.InjectionProtocol
------------------------------
titer                
total_volume         
injection_comment=&quot;&quot; 
">
+<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="464,-35 360,-35 360,-0 464,-0 464,-35"/>
+<text text-anchor="middle" x="412" y="-14.4" font-family="arial" font-size="12.00" fill="darkgreen">injection.Injection</text>
 </a>
 </g>
 </g>
-<!-- injection.MicroInjectionDevice&#45;&gt;injection.InjectionProtocol -->
-<g id="edge7" class="edge"><title>injection.MicroInjectionDevice-&gt;injection.InjectionProtocol</title>
-<path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M586,-141.797C586,-130.949 586,-116.867 586,-106.049"/>
+<!-- injection.VirusName&#45;&gt;injection.Injection -->
+<g id="edge7" class="edge"><title>injection.VirusName-&gt;injection.Injection</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M412,-70.797C412,-59.9485 412,-45.8669 412,-35.0492"/>
+</g>
+<!-- surgery.Implantation&#45;&gt;surgery.Implantation.Coordinate -->
+<g id="edge8" class="edge"><title>surgery.Implantation-&gt;surgery.Implantation.Coordinate</title>
+<path fill="none" stroke="#000000" stroke-width="2" stroke-opacity="0.250980" d="M219.349,-70.797C210.6,-57.0768 198.553,-38.1854 191.589,-27.2652"/>
+</g>
+<!-- surgery.Implantation&#45;&gt;injection.Injection -->
+<g id="edge9" class="edge"><title>surgery.Implantation-&gt;injection.Injection</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M273.594,-70.9728C302.303,-60.0885 339.746,-45.893 368.447,-35.0118"/>
 </g>
 <!-- surgery.Hemisphere -->
-<g id="node8" class="node"><title>surgery.Hemisphere</title>
-<g id="a_node8"><a xlink:title="hemisphere           
">
-<polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="221,-248 117,-248 117,-213 221,-213 221,-248"/>
-<text text-anchor="start" x="125" y="-229" font-family="arial" text-decoration="underline" font-size="10.00">surgery.Hemisphere</text>
+<g id="node10" class="node"><title>surgery.Hemisphere</title>
+<g id="a_node10"><a xlink:title="hemisphere           
">
+<polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="317,-248 213,-248 213,-213 317,-213 317,-248"/>
+<text text-anchor="start" x="221" y="-229" font-family="arial" text-decoration="underline" font-size="10.00">surgery.Hemisphere</text>
 </a>
 </g>
 </g>
-<!-- surgery.Hemisphere&#45;&gt;25 -->
-<g id="edge8" class="edge"><title>surgery.Hemisphere-&gt;25</title>
-<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M169,-212.797C169,-194.929 169,-168.29 169,-161.91"/>
+<!-- surgery.Hemisphere&#45;&gt;19 -->
+<g id="edge10" class="edge"><title>surgery.Hemisphere-&gt;19</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M276.619,-212.797C289.049,-194.929 307.581,-168.29 312.019,-161.91"/>
 </g>
 <!-- surgery.BrainRegion -->
-<g id="node9" class="node"><title>surgery.BrainRegion</title>
-<g id="a_node9"><a xlink:title="region_acronym       
------------------------------
region_name          
">
-<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="410.5,-248 287.5,-248 287.5,-213 410.5,-213 410.5,-248"/>
-<text text-anchor="start" x="295.5" y="-228.4" font-family="arial" text-decoration="underline" font-size="12.00" fill="darkgreen">surgery.BrainRegion</text>
+<g id="node11" class="node"><title>surgery.BrainRegion</title>
+<g id="a_node11"><a xlink:title="region_acronym       
------------------------------
region_name          
">
+<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="458.5,-248 335.5,-248 335.5,-213 458.5,-213 458.5,-248"/>
+<text text-anchor="start" x="343.5" y="-228.4" font-family="arial" text-decoration="underline" font-size="12.00" fill="darkgreen">surgery.BrainRegion</text>
 </a>
 </g>
 </g>
-<!-- surgery.BrainRegion&#45;&gt;24 -->
-<g id="edge9" class="edge"><title>surgery.BrainRegion-&gt;24</title>
-<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M349,-212.797C349,-194.929 349,-168.29 349,-161.91"/>
+<!-- surgery.BrainRegion&#45;&gt;18 -->
+<g id="edge11" class="edge"><title>surgery.BrainRegion-&gt;18</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M385.381,-212.797C372.951,-194.929 354.419,-168.29 349.981,-161.91"/>
 </g>
-<!-- surgery.ImplantationType -->
-<g id="node10" class="node"><title>surgery.ImplantationType</title>
-<g id="a_node10"><a xlink:title="implant_type         
------------------------------
implant_description  
">
-<polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="321.5,-177 196.5,-177 196.5,-142 321.5,-142 321.5,-177"/>
-<text text-anchor="start" x="204.5" y="-158" font-family="arial" text-decoration="underline" font-size="10.00">surgery.ImplantationType</text>
+<!-- injection.VirusSerotype -->
+<g id="node12" class="node"><title>injection.VirusSerotype</title>
+<g id="a_node12"><a xlink:title="virus_serotype       
">
+<polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="493.5,-177 376.5,-177 376.5,-142 493.5,-142 493.5,-177"/>
+<text text-anchor="start" x="384.5" y="-158" font-family="arial" text-decoration="underline" font-size="10.00">injection.VirusSerotype</text>
 </a>
 </g>
 </g>
-<!-- surgery.ImplantationType&#45;&gt;surgery.Implantation -->
-<g id="edge10" class="edge"><title>surgery.ImplantationType-&gt;surgery.Implantation</title>
-<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M251.98,-141.797C247.42,-130.949 241.502,-116.867 236.955,-106.049"/>
+<!-- injection.VirusSerotype&#45;&gt;injection.VirusName -->
+<g id="edge12" class="edge"><title>injection.VirusSerotype-&gt;injection.VirusName</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M429.432,-141.797C425.816,-130.949 421.122,-116.867 417.516,-106.049"/>
 </g>
-<!-- injection.Injection -->
-<g id="node16" class="node"><title>injection.Injection</title>
-<g id="a_node16"><a xlink:title="→ surgery.Implantation
→ injection.VirusName
→ injection.InjectionProtocol
------------------------------
titer                
total_volume         
injection_comment=&quot;&quot; 
">
-<polygon fill="#00ff00" fill-opacity="0.188235" stroke="#00ff00" stroke-opacity="0.188235" points="485,-35 381,-35 381,-0 485,-0 485,-35"/>
-<text text-anchor="middle" x="433" y="-14.4" font-family="arial" font-size="12.00" fill="darkgreen">injection.Injection</text>
-</a>
+<!-- injection.InjectionProtocol&#45;&gt;injection.Injection -->
+<g id="edge13" class="edge"><title>injection.InjectionProtocol-&gt;injection.Injection</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M528.353,-70.9728C504.218,-60.0885 472.741,-45.893 448.613,-35.0118"/>
 </g>
+<!-- surgery.ImplantationType -->
+<g id="node15" class="node"><title>surgery.ImplantationType</title>
+<g id="a_node15"><a xlink:title="implant_type         
------------------------------
implant_description  
">
+<polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="285.5,-177 160.5,-177 160.5,-142 285.5,-142 285.5,-177"/>
+<text text-anchor="start" x="168.5" y="-158" font-family="arial" text-decoration="underline" font-size="10.00">surgery.ImplantationType</text>
+</a>
 </g>
-<!-- injection.VirusName&#45;&gt;injection.Injection -->
-<g id="edge11" class="edge"><title>injection.VirusName-&gt;injection.Injection</title>
-<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M433,-70.797C433,-59.9485 433,-45.8669 433,-35.0492"/>
 </g>
-<!-- injection.InjectionProtocol&#45;&gt;injection.Injection -->
-<g id="edge12" class="edge"><title>injection.InjectionProtocol-&gt;injection.Injection</title>
-<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M549.353,-70.9728C525.218,-60.0885 493.741,-45.893 469.613,-35.0118"/>
+<!-- surgery.ImplantationType&#45;&gt;surgery.Implantation -->
+<g id="edge14" class="edge"><title>surgery.ImplantationType-&gt;surgery.Implantation</title>
+<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M224.695,-141.797C225.795,-130.949 227.224,-116.867 228.321,-106.049"/>
 </g>
 <!-- surgery.CoordinateReference -->
-<g id="node13" class="node"><title>surgery.CoordinateReference</title>
-<g id="a_node13"><a xlink:title="reference            
">
+<g id="node16" class="node"><title>surgery.CoordinateReference</title>
+<g id="a_node16"><a xlink:title="reference            
">
 <polygon fill="#000000" fill-opacity="0.125490" stroke="none" points="142,-177 0,-177 0,-142 142,-142 142,-177"/>
 <text text-anchor="start" x="8" y="-158" font-family="arial" text-decoration="underline" font-size="10.00">surgery.CoordinateReference</text>
 </a>
 </g>
 </g>
-<!-- surgery.CoordinateReference&#45;&gt;28 -->
-<g id="edge14" class="edge"><title>surgery.CoordinateReference-&gt;28</title>
+<!-- surgery.CoordinateReference&#45;&gt;23 -->
+<g id="edge17" class="edge"><title>surgery.CoordinateReference-&gt;23</title>
 <path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M71,-141.797C71,-123.929 71,-97.2901 71,-90.9096"/>
 </g>
-<!-- surgery.CoordinateReference&#45;&gt;29 -->
-<g id="edge15" class="edge"><title>surgery.CoordinateReference-&gt;29</title>
+<!-- surgery.CoordinateReference&#45;&gt;21 -->
+<g id="edge15" class="edge"><title>surgery.CoordinateReference-&gt;21</title>
 <path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M79.7146,-141.797C89.0371,-123.929 102.936,-97.2901 106.265,-90.9096"/>
 </g>
-<!-- surgery.CoordinateReference&#45;&gt;27 -->
-<g id="edge13" class="edge"><title>surgery.CoordinateReference-&gt;27</title>
+<!-- surgery.CoordinateReference&#45;&gt;22 -->
+<g id="edge16" class="edge"><title>surgery.CoordinateReference-&gt;22</title>
 <path fill="none" stroke="#000000" stroke-width="0.75" stroke-dasharray="5,2" stroke-opacity="0.250980" d="M88.4292,-141.797C107.074,-123.929 134.871,-97.2901 141.529,-90.9096"/>
 </g>
-<!-- surgery.Implantation&#45;&gt;surgery.Implantation.Coordinate -->
-<g id="edge16" class="edge"><title>surgery.Implantation-&gt;surgery.Implantation.Coordinate</title>
-<path fill="none" stroke="#000000" stroke-width="2" stroke-opacity="0.250980" d="M219.349,-70.797C210.6,-57.0768 198.553,-38.1854 191.589,-27.2652"/>
-</g>
-<!-- surgery.Implantation&#45;&gt;injection.Injection -->
-<g id="edge17" class="edge"><title>surgery.Implantation-&gt;injection.Injection</title>
-<path fill="none" stroke="#000000" stroke-width="0.75" stroke-opacity="0.250980" d="M278.624,-70.9728C310.645,-60.0885 352.409,-45.893 384.422,-35.0118"/>
-</g>
 </g>
 </svg>
\ No newline at end of file

From f771cfebdfe3fbab8bda946c4bbfa21d01fd402a Mon Sep 17 00:00:00 2001
From: kushalbakshi <kushalbakshi@gmail.com>
Date: Mon, 11 Sep 2023 17:30:51 -0500
Subject: [PATCH 09/13] Update `Device` as a `linking_module` into the element

---
 CHANGELOG.md                 |  1 +
 element_animal/genotyping.py | 17 +++++++++--------
 element_animal/injection.py  | 15 +++++++--------
 element_animal/subject.py    |  8 ++++----
 element_animal/surgery.py    |  8 ++++----
 5 files changed, 25 insertions(+), 24 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a2abfe8..9a2e994 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 ## [0.2.0] - 2023-08-23
 
 + Add - `injection` schema
++ Update - docstrings, `linking_module` within each `activate` function
 
 ## [0.1.8] - 2023-06-20
 
diff --git a/element_animal/genotyping.py b/element_animal/genotyping.py
index 1bb0820..8bb07bf 100644
--- a/element_animal/genotyping.py
+++ b/element_animal/genotyping.py
@@ -6,14 +6,15 @@
 from . import subject
 
 schema = dj.schema()
+_linking_module = None
 
 
 def activate(
-    genotyping_schema_name,
-    subject_schema_name=None,
-    create_schema=True,
-    create_tables=True,
-    linking_module=None,
+    genotyping_schema_name: str,
+    subject_schema_name: str = None,
+    create_schema: bool = True,
+    create_tables: bool = True,
+    linking_module: str = 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__,
     )
 
 
diff --git a/element_animal/injection.py b/element_animal/injection.py
index c744ab9..9ebeeca 100644
--- a/element_animal/injection.py
+++ b/element_animal/injection.py
@@ -3,7 +3,6 @@
 
 import datajoint as dj
 
-from element_lab import lab
 from . import surgery
 
 schema = dj.Schema()
@@ -17,7 +16,7 @@ def activate(
     *,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module: bool = True,
+    linking_module: str = None,
 ):
     """Activate this schema.
 
@@ -28,12 +27,12 @@ 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 `injection` module.
 
     Dependencies:
     Upstream tables:
-        User: the who conducted a particular surgery/implantation
+        Device: table from `element-lab`.
     """
 
     if isinstance(linking_module, str):
@@ -54,13 +53,13 @@ def activate(
         surgery_schema_name,
         create_schema=create_schema,
         create_tables=create_tables,
-        linking_module=linking_module,
+        linking_module=_linking_module,
     )
     schema.activate(
         injection_schema_name,
         create_schema=create_schema,
         create_tables=create_tables,
-        add_objects=linking_module.__dict__,
+        add_objects=_linking_module.__dict__,
     )
 
 
@@ -111,7 +110,7 @@ class InjectionProtocol(dj.Manual):
     definition = """
     protocol_id         : int
     ---
-    -> lab.Device
+    -> Device
     volume_per_pulse    : float
     injection_rate      : float
     interpulse_delay    : float
diff --git a/element_animal/subject.py b/element_animal/subject.py
index d258df3..7eca71b 100644
--- a/element_animal/subject.py
+++ b/element_animal/subject.py
@@ -11,7 +11,7 @@ def activate(
     *,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module: bool = True,
+    linking_module: str = 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__,
     )
 
 
diff --git a/element_animal/surgery.py b/element_animal/surgery.py
index 63ebfd4..48b0644 100644
--- a/element_animal/surgery.py
+++ b/element_animal/surgery.py
@@ -16,7 +16,7 @@ def activate(
     *,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module: bool = True,
+    linking_module: str = 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__,
     )
 
 

From 9eec2c01cf0d6f1450a5cb94311fc7a0a51f599c Mon Sep 17 00:00:00 2001
From: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
Date: Fri, 22 Sep 2023 11:01:18 -0500
Subject: [PATCH 10/13] Update requirements.txt

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 requirements.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index db7fa11..41a088b 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,2 @@
 datajoint>=0.13
-element-lab>=0.3.0
 pynwb>=1.4.0

From 5ef30a1bf708afaede433188a8d696efafe054e1 Mon Sep 17 00:00:00 2001
From: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
Date: Fri, 22 Sep 2023 11:01:35 -0500
Subject: [PATCH 11/13] Update element_animal/injection.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_animal/injection.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/element_animal/injection.py b/element_animal/injection.py
index 9ebeeca..ee73184 100644
--- a/element_animal/injection.py
+++ b/element_animal/injection.py
@@ -44,11 +44,6 @@ def activate(
     global _linking_module
     _linking_module = linking_module
 
-    lab.activate(
-        lab_schema_name,
-        create_schema=create_schema,
-        create_tables=create_tables,
-    )
     surgery.activate(
         surgery_schema_name,
         create_schema=create_schema,

From d8d05577f040f966fd1f58cca37a5240db70caad Mon Sep 17 00:00:00 2001
From: kushalbakshi <kushalbakshi@gmail.com>
Date: Tue, 3 Oct 2023 10:02:03 -0500
Subject: [PATCH 12/13] Remove incorrect `linking_module` type

---
 element_animal/genotyping.py | 2 +-
 element_animal/injection.py  | 2 +-
 element_animal/subject.py    | 2 +-
 element_animal/surgery.py    | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/element_animal/genotyping.py b/element_animal/genotyping.py
index 8bb07bf..cd42346 100644
--- a/element_animal/genotyping.py
+++ b/element_animal/genotyping.py
@@ -14,7 +14,7 @@ def activate(
     subject_schema_name: str = None,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module: str = None,
+    linking_module = None,
 ):
     """Activate this schema.
 
diff --git a/element_animal/injection.py b/element_animal/injection.py
index ee73184..2e12bd4 100644
--- a/element_animal/injection.py
+++ b/element_animal/injection.py
@@ -16,7 +16,7 @@ def activate(
     *,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module: str = None,
+    linking_module = None,
 ):
     """Activate this schema.
 
diff --git a/element_animal/subject.py b/element_animal/subject.py
index 7eca71b..61c3da3 100644
--- a/element_animal/subject.py
+++ b/element_animal/subject.py
@@ -11,7 +11,7 @@ def activate(
     *,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module: str = None,
+    linking_module = None,
 ):
     """Activate this schema.
 
diff --git a/element_animal/surgery.py b/element_animal/surgery.py
index 48b0644..a08b7d5 100644
--- a/element_animal/surgery.py
+++ b/element_animal/surgery.py
@@ -16,7 +16,7 @@ def activate(
     *,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module: str = None,
+    linking_module = None,
 ):
     """Activate this schema.
 

From 400c93a398c77c7eb6cc38ddf6ee44df131f6613 Mon Sep 17 00:00:00 2001
From: kushalbakshi <kushalbakshi@gmail.com>
Date: Tue, 3 Oct 2023 10:07:56 -0500
Subject: [PATCH 13/13] Black formatting

---
 element_animal/genotyping.py | 2 +-
 element_animal/injection.py  | 2 +-
 element_animal/subject.py    | 2 +-
 element_animal/surgery.py    | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/element_animal/genotyping.py b/element_animal/genotyping.py
index cd42346..45fabce 100644
--- a/element_animal/genotyping.py
+++ b/element_animal/genotyping.py
@@ -14,7 +14,7 @@ def activate(
     subject_schema_name: str = None,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module = None,
+    linking_module=None,
 ):
     """Activate this schema.
 
diff --git a/element_animal/injection.py b/element_animal/injection.py
index 2e12bd4..af9ab0f 100644
--- a/element_animal/injection.py
+++ b/element_animal/injection.py
@@ -16,7 +16,7 @@ def activate(
     *,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module = None,
+    linking_module=None,
 ):
     """Activate this schema.
 
diff --git a/element_animal/subject.py b/element_animal/subject.py
index 61c3da3..35034ee 100644
--- a/element_animal/subject.py
+++ b/element_animal/subject.py
@@ -11,7 +11,7 @@ def activate(
     *,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module = None,
+    linking_module=None,
 ):
     """Activate this schema.
 
diff --git a/element_animal/surgery.py b/element_animal/surgery.py
index a08b7d5..27ad3d3 100644
--- a/element_animal/surgery.py
+++ b/element_animal/surgery.py
@@ -16,7 +16,7 @@ def activate(
     *,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module = None,
+    linking_module=None,
 ):
     """Activate this schema.