Merge branch 'main' of github.com:earth-metabolome-initiative/emi-mon…

…orepo

web/backend/migrations/2024-01-24-233039_create_samples_table/up.sql

@@ -2,11 +2,6 @@
 CREATE TABLE samples (
     id SERIAL PRIMARY KEY,
     taxon_id INTEGER NOT NULL REFERENCES taxons(id) ON DELETE CASCADE,
-    name VARCHAR(255) NOT NULL,
-    description VARCHAR(512) NOT NULL,
-    latitude DOUBLE PRECISION,
-    longitude DOUBLE PRECISION,
-    altitude DOUBLE PRECISION,
     sample_type_id INTEGER NOT NULL REFERENCES sample_types(id) ON DELETE CASCADE,
     derived_from INTEGER REFERENCES samples(id) ON DELETE SET NULL,
     created_at TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,

web/backend/migrations/2024-02-06-144906_create_items_table/up.sql

@@ -3,4 +3,5 @@
 -- Items can be associated with one or more projects, and can be part of other items.
 -- The ownership of an item may change over time, and an item may be associated with
 -- one or more users. An item may have a parent item, and may be a container of other
--- items. This table defines the items that are tracked and managed by the system.
+-- items. This table defines the items that are tracked and managed by the system.
+-- An item can be movable or immovable.

web/backend/migrations/2024-02-08-085202_create_organization_locations_table/up.sql

@@ -0,0 +1,14 @@
+-- SQL defining the organizations locations table.
+-- An organization may be present in one or more locations.
+-- An organization may change locations over time.
+CREATE TABLE organization_locations (
+  id SERIAL PRIMARY KEY,
+  organization_id INTEGER REFERENCES organizations(id),
+  location_id INTEGER REFERENCES locations(id),
+  previous_location_id INTEGER REFERENCES organization_locations(id),
+  state INTEGER NOT NULL,
+  created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
+  updated_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
+  created_by INTEGER REFERENCES users(id),
+  updated_by INTEGER REFERENCES users(id)
+);

web/backend/migrations/2024-02-06-144814_create_laboratories_table/down.sql → web/backend/migrations/2024-02-08-090153_create_container_vertical_rules_table/down.sql

@@ -1,2 +1 @@
 -- This file should undo anything in `up.sql`
-DROP TABLE laboratories;

web/backend/migrations/2024-02-08-090153_create_container_vertical_rules_table/up.sql

@@ -0,0 +1,20 @@
+-- SQL defining the container_vertical_rules table.
+-- The container rules define whether an item type can contain another item type.
+-- For instance a rack can contain tubes, but a tube cannot contain a rack.
+-- We define such rules in an allow-list fashion, meaning that if a rule is not defined,
+-- then the item type cannot contain another item type. The rules are defined by an admin
+-- user, and are used to enforce the containment rules when creating or updating items.
+-- Some containers may only contain items that are within a certain temperature, humidity,
+-- or pressure range. These constraints are also defined in the container rules.
+CREATE TABLE container_vertical_rules (
+  id SERIAL PRIMARY KEY,
+  container_item_type_id INTEGER REFERENCES item_types(id),
+  contained_item_type_id INTEGER REFERENCES item_types(id),
+  temperature INTERVAL DEFAULT NULL,
+  humidity INTERVAL DEFAULT NULL,
+  pressure INTERVAL DEFAULT NULL,
+  created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
+  updated_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
+  created_by INTEGER REFERENCES users(id),
+  updated_by INTEGER REFERENCES users(id)
+);

web/backend/migrations/2024-02-08-090409_create_item_types_table/down.sql

@@ -0,0 +1 @@
+-- This file should undo anything in `up.sql`

web/backend/migrations/2024-02-08-090409_create_item_types_table/up.sql

@@ -0,0 +1,15 @@
+-- SQL defining the item_types table.
+-- An item type is a type of item that can be tracked and managed, may have a cost,
+-- and may be rented. As such it as two different columns one for the cost, its currency,
+-- and a cost per day for renting and the current of the renting cost. An item may have
+-- an expiration date and may be associated with one or more projects (which is tracked
+-- in the item_projects table).
+CREATE TABLE item_types (
+  id SERIAL PRIMARY KEY,
+  name VARCHAR(255) NOT NULL UNIQUE,
+  description TEXT,
+  created_by INTEGER REFERENCES users(id),
+  updated_by INTEGER REFERENCES users(id),
+  created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
+  updated_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP
+);

web/backend/migrations/2024-02-08-091232_create_container_horizontal_rules_table/down.sql

@@ -0,0 +1 @@
+-- This file should undo anything in `up.sql`

web/backend/migrations/2024-02-08-091232_create_container_horizontal_rules_table/up.sql

@@ -0,0 +1,21 @@
+-- SQL defining the container_horizontal_rules table.
+-- The container horizontal rules define whether an item type can be placed next to another item type.
+-- For instance a acid product cannot be placed next to a base product. Generally speaking, most items
+-- can be placed next to each other, but some items cannot be placed next to each other. These rules
+-- are defined in the form of a deny-list, meaning that if a rule is not defined, then the item type
+-- can be placed next to any other item type. The rules are defined by an admin user, and are used to
+-- enforce the placement rules when creating or updating items. Some items may only be placed next to
+-- items that are within a certain temperature, humidity, or pressure range. These constraints are also
+-- defined in the container rules.
+CREATE TABLE container_horizontal_rules (
+  id SERIAL PRIMARY KEY,
+  item_type_id INTEGER REFERENCES item_types(id),
+  other_item_type_id INTEGER REFERENCES item_types(id),
+  temperature INTERVAL DEFAULT NULL,
+  humidity INTERVAL DEFAULT NULL,
+  pressure INTERVAL DEFAULT NULL,
+  created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
+  updated_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
+  created_by INTEGER REFERENCES users(id),
+  updated_by INTEGER REFERENCES users(id)
+);

web/backend/migrations/2024-02-08-100852_create_manifactured_item_types_table/down.sql

@@ -0,0 +1 @@
+-- This file should undo anything in `up.sql`

web/backend/migrations/2024-02-08-100852_create_manifactured_item_types_table/up.sql

@@ -0,0 +1,17 @@
+-- SQL defining the manufactured_item_types table.
+-- A manufactured type is an item type that can be manufactured, sold, and bought. As such it
+-- has a cost, its currency, and a cost per day for renting and the current of the renting
+-- cost.
+CREATE TABLE manufactured_item_types (
+  id SERIAL PRIMARY KEY,
+  item_type_id INTEGER REFERENCES item_types(id),
+  cost DECIMAL(10, 2) NOT NULL,
+  cost_per_day DECIMAL(10, 2) NOT NULL,
+  currency VARCHAR(3) NOT NULL,
+  manifacturer_id INTEGER REFERENCES organizations(id),
+  barcode VARCHAR(255) NOT NULL UNIQUE,
+  created_by INTEGER REFERENCES users(id),
+  updated_by INTEGER REFERENCES users(id),
+  created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
+  updated_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP
+);

web/backend/migrations/2024-02-08-101004_create_expirable_item_types_table/down.sql

@@ -0,0 +1,2 @@
+-- This file should undo anything in `up.sql`
+DROP TABLE expirable_item_types;

web/backend/migrations/2024-02-08-101004_create_expirable_item_types_table/up.sql

@@ -0,0 +1,13 @@
+-- SQL defining the expirable_item_types table.
+-- Item types appearing in this table have an expiration date, meaning that
+-- they have an interval of time associated to them after which they are no longer
+-- valid. This table is used to enforce the expiration date of items of a certain type.
+CREATE TABLE expirable_item_types (
+  id SERIAL PRIMARY KEY,
+  item_type_id INTEGER REFERENCES item_types(id),
+  expiration_interval INTERVAL NOT NULL,
+  created_by INTEGER REFERENCES users(id),
+  updated_by INTEGER REFERENCES users(id),
+  created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
+  updated_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP
+);