Merge pull request #46 from ttngu207/main

added table for Species

Author: kushalbakshi

.gitignore

@@ -1,87 +1,77 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
+# Temporary and binary files
+*~
 *.py[cod]
-*$py.class
+*.so
+*.cfg
+!.isort.cfg
+!setup.cfg
+*.orig
+*.log
+*.pot
+**/__pycache__
+.cache/*
+.*.swp
+*/.ipynb_checkpoints/*
+.DS_Store
+.mypy_cache/*
 
-# Distribution, packaging, PyInstaller
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
+# Project files
+.ropeproject
+.project
+.pydevproject
+.settings
+.idea
+.vscode
+tags
+profile_default/
+ipython_config.py
+
+# Package files
 *.egg
-*.manifest
-*.spec
-pip-log.txt
-pip-delete*.txt
+*.eggs/
+.installed.cfg
+*.egg-info
+environment.lock.yml
 
-# Unit test / coverage reports
-htmlcov/
-.tox/
+# Unittest and coverage
+htmlcov/*
 .coverage
 .coverage.*
-.cache
-nosetests.xml
+.tox/*
+.nox/*
+junit*.xml
 coverage.xml
-*.cover
-.hypothesis/
-.pytest_cache/
+.pytest_cache/*
 
-# C extension, Translations
-*.so
-*.mo
-*.pot
+# Build and docs folder/files
+build/*
+site/*
+dist/*
+sdist/*
+docs/api/*
+docs/_rst/*
+docs/_build/*
+cover/*
+MANIFEST
 
-# editors: vscode, emacs, Mac
-.vscode
-**/*~
-**/#*#
-**/.#*
-.DS_Store
+# Per-project virtualenvs
+.venv*/
+.conda*/
 
-# Django, Flask, Scrapy, Sphinx, mkdocs
-# PyBuilder, Jupyter, SageMath, celery beat
-*.log
-local_settings.py
-instance/
-.webassets-cache
-.scrapy
-scratchpaper.*
-docs/_build/
-/site
-target/
-.ipynb_checkpoints
-celerybeat-schedule
-*.sage.py
+# Configuration files
+*.env
 
-# dotenv, virtualenv, pyenv, mypy
-./.env
-.venv
-venv/
-ENV/
-.python-version
-.mypy_cache/
-
-# Spyder/Rope project settings
-.spyderproject
-.spyproject
-.ropeproject
-
-# datajoint, notes, nwb export
+# DataJoint files
 dj_local_c*.json
-temp*
-*nwb
+dj_remote_c*.json
+.datajoint_config.json
+
+# Misc files/folders
+pyproject.code-workspace
+scratch/*
+src/deangelis_lab/experimental/*
+.junk/*
 
-# mkdocs documentation
-docs/site
+# Secret keys
+*.ssh
+*.pem

CHANGELOG.md

@@ -3,6 +3,9 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.2.1] - 2023-11-28
++ Add - `Species` table in `subject` schema
+
 ## [0.2.0] - 2023-08-23
 
 + Add - `injection` schema
@@ -63,6 +66,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Add - `subject` schema
 + Add - `genotyping` schema
 
+[0.2.1]: https://github.com/datajoint/element-animal/releases/tag/0.2.1
 [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

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.
 

element_animal/version.py

@@ -1,2 +1,2 @@
 """Package metadata."""
-__version__ = "0.2.0"
+__version__ = "0.2.1"