[biobank] new module

[HenriRabalais]

Pull Request: Add Biobank Module

Draft Checklist

• make dev works and module loads
• make checkstatic passes
• README written
• Help Text included
• JSDoc written
• Basic Tests written
• Test Plan written
• SQL included (schema, base data, permissions)

Overview

This pull request introduces the Biobank Module to the LORIS platform. The Biobank Module is designed to streamline the management of biological specimens, encompassing their collection, processing, storage, and shipment. It integrates seamlessly with existing workflows, ensuring efficient and standardized biobank operations across various studies and sites.

Purpose

The Biobank Module enables the management of biological specimens by providing functionalities for specimen tracking, container management, pooling, and shipment handling. It ensures standardized operations and maintains data integrity within the LORIS ecosystem.

Intended Users

The primary users of the Biobank Module are:

• Biobank Managers: Oversee the overall biobank operations, including specimen tracking and inventory management.
• Laboratory Technicians: Handle the processing, storage, and preparation of biological specimens.
• Researchers: Access and utilize specimens for various studies and experiments.
• Site Coordinators: Ensure that specimens are correctly collected, processed, and integrated into the LORIS system across multiple sites.

Scope

The Biobank Module facilitates the comprehensive management of biological specimens within the LORIS platform. Its functionalities include:

• Specimen Tracking: Monitor the lifecycle of each specimen from collection to storage and shipment.
• Container Management: Manage storage containers, including their types, capacities, and hierarchical relationships.
• Pooling: Combine multiple specimens into pools for efficient processing and analysis.
• Shipment Handling: Track the shipment of specimens, including logging shipment events and statuses.

NOT in scope:

• Automated quality control of specimens.
• Integration with external laboratory information management systems (LIMS) beyond LORIS.

Permissions

Access to the Biobank Module is controlled through specific permissions to ensure data security and appropriate access levels.

Permission Code	Description	Access Level
biobank_specimen_view	View Specimen Data	View
biobank_specimen_create	Create Specimens	Create
biobank_specimen_edit	Edit/Upload Specimen Data	Edit/Upload
biobank_container_view	View Container Data	View
biobank_container_create	Create Containers	Create
biobank_container_edit	Edit Container Data	Edit
biobank_pool_view	View Pool Data	View
biobank_pool_create	Create Pools	Create
biobank_fullsiteaccess	Full Site Access	View
biobank_fullprojectaccess	Full Project Access	View

Note: Ensure Category and Access Level align with your organization's permission schema.

Configuration

The module's functionality is supported by multiple configuration tables, each serving a specific purpose in managing specimens, containers, pools, and shipments.

Table	Configuration	Description
biobank_specimen_type	Specimen Types	Defines various specimen types (e.g., Blood, RNA) and their relationships with parent specimen types via biobank_specimen_type_parent.
biobank_container_capacity	Container Capacity	Defines the capacity of containers, specifying how many specimens each container can hold.
biobank_container_dimension	Container Dimensions	Stores dimensional data of containers, including size and volume specifications.
biobank_container_status	Container Status	Tracks the status of containers (e.g., Active, Inactive) to monitor their availability and usage.
biobank_container_type	Container Types	Specifies types of containers used for storing specimens, linked to specimen types through biobank_specimen_type_container_type_rel.
biobank_specimen_attribute	Specimen Attributes	Stores attributes related to specimens, such as concentration and quality metrics.
biobank_specimen_attribute_datatype	Specimen Attribute Datatypes	Defines data types for specimen attributes to ensure consistent data entry and validation.
biobank_specimen_protocol	Specimen Protocols	Associates specimens with specific collection and preparation protocols, ensuring standardized handling procedures.
biobank_specimen_protocol_attribute_rel	Specimen Protocol Attribute Relations	Links specimen protocols to their attributes, maintaining data consistency and integrity.
biobank_specimen_type_container_type_rel	Specimen Type Container Type Relations	Links specimen types to container types, ensuring appropriate container usage for each specimen type.
biobank_specimen_type_parent	Specimen Type Parent Relations	Manages parent-child relationships between specimen types, allowing for hierarchical classification and organization.
biobank_specimen_type_unit_rel	Specimen Type Unit Relations	Links specimen types to measurement units, ensuring consistent data entry for specimen measurements.
biobank_unit	Measurement Units	Defines measurement units (e.g., µL, mL) used across the Biobank Module for consistent data entry and reporting.
shipment_status	Shipment Statuses	Tracks the status of shipments (e.g., Pending, Shipped, Delivered) to monitor their progress and completion.
shipment_type	Shipment Types	Defines different types of shipments (e.g., Internal, External) to categorize and manage shipping processes effectively.

Detailed Configuration Settings

• Specimen Types (biobank_specimen_type): Defines various specimen types (e.g., Blood, RNA) and their relationships with parent specimen types via biobank_specimen_type_parent.

• Specimen Attributes (biobank_specimen_attribute & biobank_specimen_attribute_datatype): Stores attributes related to specimens, such as concentration, quantification dates, and quality metrics. Data types are defined in biobank_specimen_attribute_datatype.

• Container Types (biobank_container_type): Specifies types of containers used for storing specimens, linked to specimen types through biobank_specimen_type_container_type_rel.

• Measurement Units (biobank_unit & biobank_specimen_type_unit_rel): Defines measurement units (e.g., µL, mL) and associates them with specimen types to ensure consistent data entry.

• Protocols (biobank_specimen_protocol): Links specimens and pools to specific collection and preparation protocols, ensuring standardized handling procedures.

• Pools (biobank_pool): Manages pools created from multiple specimens, allowing for efficient processing and aliquoting.

• Shipments (shipment, shipment_log, shipment_status, shipment_type): Tracks the shipment of containers, including event logging for comprehensive tracking and accountability.

• Container Hierarchy (biobank_container_parent): Manages parent-child relationships between containers to reflect storage hierarchies.

• Data Integrity (biobank_specimen_protocol_attribute_rel): Ensures that specimen protocols are correctly linked to their attributes, maintaining data consistency.

Interactions with LORIS

The Biobank Module integrates seamlessly with various components of the LORIS platform to enhance functionality and data management:

• Links: Includes links to Session, Sites and Candidate modules.

[HenriRabalais]

@driusan @ridz1208

This is ready for review!

[kongtiaowang]

The permissions ID is not necessary since this will be applied as an update patch.

[ridz1208]

I think the js/biobankIndex.js should be in a gitignore and not committed here

[HenriRabalais]

@ridz1208 I addressed your review!