added table for Species

element_animal/export/nwb.py

@@ -16,6 +16,7 @@ def subject_to_nwb(session_key: dict):
         pynwb.file.Subject: NWB object
     """
     subject_query = subject.Subject & session_key
+    subject_query = subject_query.join(subject.Subject.Species, left=True)
     subject_query = subject_query.join(subject.Subject.Line, left=True)
     subject_query = subject_query.join(subject.Subject.Strain, left=True)
     subject_query = subject_query.join(subject.Subject.Source, left=True)
@@ -29,7 +30,7 @@ def subject_to_nwb(session_key: dict):
             datetime.strptime("00:00:00", "%H:%M:%S").time(),
         ),
         description=json.dumps(subject_info, default=str),
-        species=str((subject.Line & subject_query).fetch("species")),
+        species=str((subject.Species & subject_query).fetch("species")),
         genotype=" x ".join(
             (subject.Line.Allele * subject.Subject.Line & subject_query).fetch("allele")
         ),

element_animal/subject.py

@@ -53,6 +53,19 @@ def activate(
     )
 
 
+@schema
+class Species(dj.Lookup):
+    """Animal species
+
+    Attributes:
+        species ( varchar(64) ): Animal species, Latin name preferred for NWB export
+    """
+
+    definition = """  # Animal species
+    species: varchar(64)  # Animal species, Latin name preferred for NWB export
+    """
+
+
 @schema
 class Strain(dj.Lookup):
     """Genetic strain of an animal. (e.g. C57Bl/6).
@@ -112,7 +125,6 @@ class Line(dj.Lookup):
 
     Attributes:
         line ( varchar(32) ): Abbreviated name for the line.
-        species ( varchar(64) ): Latin name preferred for NWB export.
         line_description ( varchar(2000) ): Optional. Description of the line.
         target_phenotype ( varchar(255) ): Optional. Targeted gene phenotype.
         is_active (boolean) : Whether the line is in active breeding.
@@ -121,7 +133,6 @@ class Line(dj.Lookup):
     definition = """
     line                : varchar(32)  # abbreviated name for the line
     ---
-    species=''          : varchar(64)  # Latin name preferred for NWB export
     line_description='' : varchar(2000)
     target_phenotype='' : varchar(255)
     is_active           : boolean	   # whether the line is in active breeding
@@ -188,6 +199,20 @@ class User(dj.Part):
         -> User
         """
 
+    class Species(dj.Part):
+        """Species of the subject.
+
+        Attributes:
+            Subject (foreign key): Subject key.
+            Species (foreign key): Species key.
+        """
+
+        definition = """
+        -> master
+        ---
+        -> Species
+        """
+
     class Line(dj.Part):
         """Genetic line of the subject.