Create dictionaries for NWB export

CHANGELOG.md

@@ -2,6 +2,11 @@
 
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.1.0b1] - 2022-01-28
+### Added
++ Added functions to generate dictionaries for NWB export.
+
+
 ## [0.1.0b0] - 2021-05-07
 ### Added
 + First beta release
@@ -12,6 +17,6 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Added GitHub Action release process
 + Added `lab` schema
 
-
+[0.1.0b1]: https://github.com/datajoint/element-lab/compare/0.1.0b0...0.1.0b1
 [0.1.0b0]: https://github.com/datajoint/element-lab/compare/0.1.0a1...0.1.0b0
 [0.1.0a1]: https://github.com/datajoint/element-lab/releases/tag/0.1.0a1

Dockerfile

@@ -5,9 +5,9 @@ ARG PKG_NAME
 ARG PKG_VERSION
 
 FROM datajoint/${IMAGE}:py${PY_VER}-${DISTRO}
-COPY --chown=dja:anaconda ./requirements.txt ./setup.py \
+COPY --chown=anaconda:anaconda ./requirements.txt ./setup.py \
     /main/
-COPY --chown=dja:anaconda ./${PKG_NAME} /main/${PKG_NAME}
+COPY --chown=anaconda:anaconda ./${PKG_NAME} /main/${PKG_NAME}
 RUN \
     cd /main && \
     pip install . && \

element_lab/__init__.py

@@ -1,4 +0,0 @@
-__author__ = "DataJoint NEURO"
-__date__ = "December 15, 2020"
-__version__ = "0.0.1"
-__all__ = ['__author__', '__version__', '__date__']

element_lab/export/__init__.py

@@ -0,0 +1 @@
+from .nwb import elementlab_nwb_dict

element_lab/export/nwb.py

@@ -0,0 +1,84 @@
+from element_lab import lab
+
+
+def lab_to_nwb_dict(lab_key):
+    """
+    Generate a dictionary containing all relevant lab and institution info
+    :param lab_key: Key specifying one entry in element_lab.lab.Lab
+    :return: dictionary with NWB parameters
+    """
+    lab_info = (lab.Lab & lab_key).fetch1()
+    return dict(
+        institution=lab_info.get('institution'),
+        lab=lab_info.get('lab_name'),
+    )
+
+
+def project_to_nwb_dict(project_key):
+    """
+    Generate a dictionary object containing relevant project information
+        (e.g., experimental description, related publications, etc.).
+    :param project_key: Key specifying one entry in element_lab.lab.Project
+    :return: dictionary with NWB parameters
+    """
+    project_info = (lab.Project & project_key).fetch1()
+    return dict(
+        experiment_description=project_info.get('project_description'),
+        keywords=(lab.ProjectKeywords() & project_key
+                  ).fetch('keyword').tolist() or None,
+        related_publications=(lab.ProjectPublication() & project_key
+                              ).fetch('publication').tolist() or None
+    )
+
+
+def protocol_to_nwb_dict(protocol_key):
+    """
+    Generate a dictionary object containing all protocol title and notes.
+    :param protocol_key: Key specifying one entry in element_lab.lab.Protocol
+    :return: dictionary with NWB parameters
+    """
+    protocol_info = (lab.Protocol & protocol_key).fetch1()
+    return dict(
+        protocol=protocol_info.get('protocol'),
+        notes=protocol_info.get('protocol_description')
+    )
+
+
+def element_lab_to_nwb_dict(lab_key=None, project_key=None, protocol_key=None):
+    """
+    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
+    Use: mynwbfile = pynwb.NWBFile(identifier="your identifier",
+                             session_description="your description",
+                             session_start_time=session_datetime,
+                             **element_lab_to_nwb_dict(
+                                lab_key=key1,
+                                project_key=key2,
+                                protocol_key=key3))
+
+    :param lab_key: Key specifying one entry in element_lab.lab.Lab
+    :param project_key: Key specifying one entry in element_lab.lab.Project
+    :param protocol_key: Key specifying one entry in element_lab.lab.Protocol
+    :return: dictionary with NWB parameters
+    """
+    # Validate input
+    assert any([lab_key, project_key, protocol_key]), 'Must specify one key.'
+    assert lab_key is None or len(lab.Lab & lab_key) == 1, \
+        'Multiple labs error! The lab_key should specify only one lab.'
+    assert project_key is None or len(lab.Project & project_key) == 1, \
+        'Multiple projects error! The project_key should specify only one '\
+        'project.'
+    assert protocol_key is None or len(lab.Protocol & protocol_key) == 1, \
+        'Multiple protocols error! The protocol_key should specify only one '\
+        'protocol.'
+
+    element_info = dict()
+    if lab_key:
+        element_info.update(lab_to_nwb_dict(lab_key))
+    if project_key:
+        element_info.update(project_to_nwb_dict(project_key))
+    if protocol_key:
+        element_info.update(protocol_to_nwb_dict(protocol_key))
+
+    return element_info

element_lab/lab.py

@@ -6,22 +6,26 @@
 def activate(schema_name, create_schema=True, create_tables=True):
     """
     activate(schema_name, create_schema=True, create_tables=True)
-        :param schema_name: schema name on the database server to activate the `lab` element
-        :param create_schema: when True (default), create schema in the database if it does not yet exist.
-        :param create_tables: when True (default), create tables in the database if they do not yet exist.
+        :param schema_name: schema name on the database server to activate the
+                            `lab` element
+        :param create_schema: when True (default), create schema in the
+                              database if it does not yet exist.
+        :param create_tables: when True (default), create tables in the
+                              database if they do not yet exist.
     """
-    schema.activate(schema_name, create_schema=create_schema, create_tables=create_tables)
+    schema.activate(schema_name, create_schema=create_schema,
+                    create_tables=create_tables)
 
 
 @schema
 class Lab(dj.Lookup):
     definition = """
-    lab             : varchar(24)  #  Abbreviated lab name 
+    lab             : varchar(24)    #  Abbreviated lab name
     ---
     lab_name        : varchar(255)   # full lab name
     institution     : varchar(255)
     address         : varchar(255)
-    time_zone       : varchar(64)
+    time_zone       : varchar(64)    # 'UTC±X' format for NWB export
     """
 
 
@@ -77,7 +81,7 @@ class Protocol(dj.Lookup):
     protocol                : varchar(16)
     ---
     -> ProtocolType
-    protocol_description=''        : varchar(255)
+    protocol_description='' : varchar(255)
     """
 
 
@@ -86,7 +90,33 @@ class Project(dj.Lookup):
     definition = """
     project                 : varchar(32)
     ---
-    project_description=''         : varchar(1024)
+    project_description=''  : varchar(1024)
+    """
+
+
+class ProjectKeywords(dj.Manual):
+    definition = """
+    # Project keywords, exported dataset meta info
+    -> Project
+    keyword: varchar(32)
+    """
+
+
+class ProjectPublication(dj.Manual):
+    definition = """
+    # Project's resulting publications
+    -> Project
+    publication: varchar(256)
+    """
+
+
+class ProjectSourceCode(dj.Manual):
+    definition = """
+    # URL to source code for replication
+    -> Project
+    repository_url     : varchar(256)
+    ---
+    repository_name='' : varchar(32)
     """
 
 
@@ -102,9 +132,9 @@ class ProjectUser(dj.Manual):
 class Source(dj.Lookup):
     definition = """
     # source or supplier of animals
-    source             : varchar(32)    # abbreviated source name
+    source                : varchar(32)  # abbreviated source name
     ---
-    source_name        : varchar(255)
-    contact_details='' : varchar(255)
-    source_description=''     : varchar(255)
+    source_name           : varchar(255)
+    contact_details=''    : varchar(255)
+    source_description='' : varchar(255)
     """

element_lab/version.py

@@ -1,2 +1,2 @@
 """Package metadata."""
-__version__ = '0.1.0b0'
+__version__ = '0.1.0b1'

requirements.txt

@@ -1 +1,2 @@
 datajoint>=0.13.0
+pynwb==1.4.0