Merge pull request #41 from CBroz1/dev

Add project schema to main

Author: kabilar

CHANGELOG.md

@@ -2,29 +2,26 @@
 
 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] - 2022-12-12
++ Add - `project` schema for project/study/experiment related tables
+
 ## [0.1.2] - 2022-10-17
-### Updated
-+ CICD for triggering PyPI release
++ Update - CICD for triggering PyPI release
 
 ## [0.1.1] - 2022-05-10
-### Added
-+ Adopted black formatting into code base
++ Add - Adopted black formatting into code base
 
 ## [0.1.0b1] - 2022-01-28
-### Added
-+ Added functions to generate dictionaries for NWB export.
-
++ Add - Functions to generate dictionaries for NWB export.
 
 ## [0.1.0b0] - 2021-05-07
-### Added
-+ First beta release
-
++ Add - First beta release
 
 ## [0.1.0a1] - 2021-04-30
-### Added 
-+ Added GitHub Action release process
-+ Added `lab` schema
++ Add - GitHub Action release process
++ Add - `lab` schema
 
+[0.2.0]: https://github.com/datajoint/element-lab/releases/tag/0.2.0
 [0.1.2]: https://github.com/datajoint/element-lab/releases/tag/0.1.2
 [0.1.1]: https://github.com/datajoint/element-lab/releases/tag/0.1.1
 [0.1.0b1]: https://github.com/datajoint/element-lab/releases/tag/0.1.0b1

element_lab/export/nwb.py

@@ -1,5 +1,13 @@
+import logging
 from element_lab import lab
 
+logger = logging.getLogger("datajoint")
+
+logger.warning(
+    'Element Lab\'s "project" schema does not yet feature NWB export.'
+    + "Please use lab.Project and lab.Protocol tables"
+)
+
 
 def _lab_to_nwb_dict(lab_key: dict) -> dict:
     """Generate a dictionary containing all relevant lab and institution info.
@@ -61,7 +69,7 @@ def element_lab_to_nwb_dict(
     lab_key: dict = None, project_key: dict = None, protocol_key: dict = None
 ) -> dict:
     """Generate a NWB-compliant dictionary object for lab metadata
-    
+
     Generate a dictionary object containing all relevant lab information used
        when generating an NWB file at the session level.
        All parameters optional, but should only specify one of respective type.

element_lab/lab.py

@@ -1,5 +1,9 @@
+import logging
+
 import datajoint as dj
 
+logger = logging.getLogger("datajoint")
+
 schema = dj.Schema()
 
 
@@ -19,44 +23,68 @@ def activate(schema_name: str, create_schema: bool = True, create_tables: bool =
     )
 
 
+@schema
+class Organization(dj.Manual):
+    """Top-level list of all organizations involved in any of the projects.
+
+    Attributes:
+        organization ( varchar(24) ): Abbreviated organization name.
+        org_name ( varchar(255) ): Full organization name.
+        org_address ( varchar(512), optional ): Address of the organization.
+        org_comment ( varchar(1024), optional ): Additional notes on the organization.
+    """
+
+    definition = """# Top-level list of all organizations involved in any of the projects
+    organization      : varchar(24)   # Abbreviated organization name
+    ---
+    org_name          : varchar(255)  # Full organization name
+    org_address=''    : varchar(512)  # Address of the organization
+    org_comment=''    : varchar(1024) # Additional notes on the organization
+    """
+
+
 @schema
 class Lab(dj.Lookup):
     """Table for storing general lab info.
 
     Attributes:
         lab ( varchar(24) ): Abbreviated lab name.
         lab_name ( varchar(255) ): Full lab name.
-        institution ( varchar(255) ): Name of the affiliation institution.
         address ( varchar(255) ): Physical lab address.
-        time_zone ( varchar(64) ): If using NWB export, use 'UTC±X' format
+        time_zone ( varchar(64) ): 'UTC±X' format or timezone, e.g., America/New_York.
+            If using NWB export, use 'UTC±X' format.
     """
 
-    definition = """
-    lab             : varchar(24)    # abbreviated lab name
+    definition = """# Table for storing general lab info.
+    lab             : varchar(24)    # Abbreviated lab name
     ---
-    lab_name        : varchar(255)   # full lab name
-    institution     : varchar(255)
-    address         : varchar(255)
-    time_zone       : varchar(64)    # 'UTC±X' format for NWB export
+    lab_name        : varchar(255)   # Full lab name
+    address         : varchar(255)    # Physical lab address
+    time_zone       : varchar(64)    # 'UTC±X' format or timezone, e.g., America/New_York
     """
 
+    class Organization(dj.Part):
+        definition = """
+        -> master
+        -> Organization
+        """
+
 
 @schema
 class Location(dj.Lookup):
-    """Location of research (e.g., animal housing or experimental rigs)
+    """Location of research (e.g., animal housing or experimental rigs).
 
     Attributes:
         Lab (foreign key): Lab key.
         location ( varchar(32) ): Location of a space related to the lab.
         location_description ( varchar(255), optional ): Description of the location.
     """
 
-    definition = """
-    # location of research (e.g., animal housing or experimental rigs)
+    definition = """# location of research (e.g., animal housing or experimental rigs)
     -> Lab
-    location                   : varchar(32)
+    location                   : varchar(32)   # Location of a space related to the lab
     ---
-    location_description=''    : varchar(255)
+    location_description=''    : varchar(255)  # Description of the location
     """
 
 
@@ -65,11 +93,11 @@ class UserRole(dj.Lookup):
     """Roles assigned to a user or a job title.
 
     Attributes:
-        user_role ( varchar(16) ): Role within the lab (e.g., PI, Postdoc, etc.).
+        user_role ( varchar(24) ): Role within the lab (e.g., PI, Postdoc, etc.).
     """
 
-    definition = """
-    user_role           : varchar(16) # Role within the lab (e.g., PI, Postdoc, etc.)
+    definition = """# Roles assigned to a user or a job title.
+    user_role           : varchar(24) # Role within the lab (e.g., PI, Postdoc, etc.)
     """
 
 
@@ -79,15 +107,17 @@ class User(dj.Lookup):
 
     Attributes:
         user ( varchar(32) ): User name.
-        user_email ( varchar(128) ): User email address.
-        user_cellphone ( varchar(32) ): User cellphone number.
+        user_email ( varchar(128), optional ): User email address.
+        user_cellphone ( varchar(32), optional ): User cellphone number.
+        user_fullname ( varchar(64), optional ): User full name
     """
 
-    definition = """
-    user                : varchar(32)
+    definition = """# Table for storing user information.
+    user                : varchar(32)  # username, short identifier
     ---
     user_email=''       : varchar(128)
     user_cellphone=''   : varchar(32)
+    user_fullname=''    : varchar(64)  # Full name used to uniquely identify an individual
     """
 
 
@@ -101,7 +131,7 @@ class LabMembership(dj.Lookup):
         UserRole (foreign key): Optional. UserRole primary key.
     """
 
-    definition = """
+    definition = """# Store lab membership information using three lookup tables.
     -> Lab
     -> User
     ---
@@ -117,26 +147,26 @@ class ProtocolType(dj.Lookup):
         protocol_type ( varchar(32) ): Protocol types (e.g., IACUC, IRB, etc.).
     """
 
-    definition = """
-    protocol_type           : varchar(32)
+    definition = """# Type of protocol or issuing agency
+    protocol_type           : varchar(32)  # Protocol types (e.g., IACUC, IRB, etc.)
     """
 
 
 @schema
 class Protocol(dj.Lookup):
-    """Protocol specifics (e.g., protocol number and title).
+    """Protocol approved by institutions (e.g. IACUC, IRB), or experimental protocol.
 
     Attributes:
-        protocol ( varchar(16) ): Protocol identifier.
+        protocol ( varchar(36) ): Protocol identifier.
         ProtocolType (foreign key): ProtocolType key.
-        protocol_description( varchar(255) ): Optional. Description of the protocol.
+        protocol_description( varchar(255), optional ): Description of the protocol.
     """
 
-    definition = """
-    protocol                : varchar(16)
+    definition = """# Protocol approved by institutions (e.g. IACUC, IRB), or experimental protocol.
+    protocol                : varchar(36)   # Protocol identifier.
     ---
     -> ProtocolType
-    protocol_description='' : varchar(255)
+    protocol_description='' : varchar(255)  # Description of the protocol
     """
 
 
@@ -149,6 +179,11 @@ class Project(dj.Lookup):
         project_description ( varchar(1024) ): Description about the project.
     """
 
+    logger.warning(
+        "lab.Project and related tables will be removed in a future version of"
+        + " Element Lab. Please use the project schema."
+    )
+
     definition = """
     project                 : varchar(32)
     ---