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

…orepo

bindings/sirius/src/sirius.rs

@@ -94,13 +94,21 @@ impl<V: Version> Sirius<V> {
 
         // We check that the provided sirius username and password are not empty
         if sirius_username.is_empty() {
+<<<<<<< HEAD
+            return Err(format!(concat!(
+=======
             return Err(concat!(
+>>>>>>> 846f0feac57a70f394fa531de8010a2013d16a77
                 "The sirius username provided in the environment variable SIRIUS_USERNAME is empty. ",
                 "We expected there to exist a .env file in the current directory ",
                 "with the SIRIUS_USERNAME variable set to the username of the sirius account. ",
                 "The variable may also be set in the environment directly, for instance ",
                 "in the .bashrc file."
+<<<<<<< HEAD
+            )));
+=======
             ).to_string());
+>>>>>>> 846f0feac57a70f394fa531de8010a2013d16a77
         }
 
         if sirius_password.is_empty() {
@@ -153,6 +161,22 @@ impl<V: Version> Sirius<V> {
             ));
         }
 
+        // We check that the extension of the input file is MGF, in either upper or lower case
+        let input_file_extension = input_file_path
+            .extension()
+            .ok_or_else(|| format!(concat!(
+                "The input file {:?} does not have an extension. ",
+                "We expected the input file to have the extension .mgf"
+            ), input_file_path))?;
+
+        if input_file_extension.to_string_lossy().to_lowercase() != "mgf" {
+            return Err(format!(
+                "The input file {:?} does not have the extension .mgf",
+                input_file_path
+            ));
+        }
+
+
         // Prepare the command
         let mut command = Command::new(sirius_path);
 

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

@@ -6,4 +6,22 @@
 -- items. This table defines the items that are tracked and managed by the system.
 -- An item can be movable or immovable.
 -- An example of an Item may be a measurement device, a tube potentially containing a sample,
--- or a sample itself.
+-- or a sample itself.
+CREATE TABLE items (
+  id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
+  name TEXT NOT NULL,
+  description TEXT,
+  created_at TIMESTAMPTZ NOT NULL DEFAULT now(),
+  updated_at TIMESTAMPTZ NOT NULL DEFAULT now(),
+  created_by UUID NOT NULL,
+  updated_by UUID NOT NULL,
+  project_id UUID NOT NULL,
+  parent_id UUID,
+  location_id UUID,
+  FOREIGN KEY (created_by) REFERENCES users(id),
+  FOREIGN KEY (updated_by) REFERENCES users(id),
+  FOREIGN KEY (project_id) REFERENCES projects(id),
+  FOREIGN KEY (parent_id) REFERENCES items(id),
+  FOREIGN KEY (item_type_id) REFERENCES item_types(id),
+  FOREIGN KEY (location_id) REFERENCES locations(id)
+);

web/backend/migrations/2024-02-09-102550_create_procedure_item_requirements_table/up.sql → web/backend/migrations/2024-02-09-102550_create_procedure_item_discrete_requirements_table/up.sql

@@ -12,4 +12,4 @@ CREATE TABLE procedure_item_requirements (
   updated_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
   PRIMARY KEY (procedure_id, item_category_id),
   FOREIGN KEY (item_category_id, unit_id) REFERENCES item_units(item_id, unit_id)
-);  
+);

web/backend/migrations/2024-02-09-143242_create_item_real_quantities_table/down.sql

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

web/backend/migrations/2024-02-09-143242_create_item_real_quantities_table/up.sql

@@ -0,0 +1,19 @@
+-- SQL defining the item_real_quantities table.
+-- Each item, being a physical object, has a weight. This table defines the weights of items.
+-- The weight of an item may change over time, and be measured using different scales and by
+-- different people.
+CREATE TABLE item_real_quantities (
+    id SERIAL PRIMARY KEY,
+    item_id INTEGER REFERENCES items(id),
+    weight DECIMAL(10, 2) NOT NULL,
+    unit_id INTEGER REFERENCES units(id),
+    sensor_id INTEGER REFERENCES items(id),
+    measured_at TIMESTAMPTZ NOT NULL DEFAULT now(),
+    measured_by INTEGER REFERENCES users(id),
+    created_at TIMESTAMPTZ NOT NULL DEFAULT now(),
+    updated_at TIMESTAMPTZ NOT NULL DEFAULT now(),
+    created_by INTEGER NOT NULL REFERENCES users(id),
+    updated_by INTEGER NOT NULL REFERENCES users(id),
+    FOREIGN KEY (item_id, unit_id) REFERENCES items(item_id, unit_id),
+    FOREIGN KEY (unit_id) REFERENCES real_units(id)
+);

web/backend/migrations/2024-02-09-144314_create_item_discrete_quantities_table/down.sql

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

web/backend/migrations/2024-02-09-144314_create_item_discrete_quantities_table/up.sql

@@ -0,0 +1,22 @@
+-- SQL defining the item_quantities table.
+-- Some items may be counted discretely, as opposed to a weight in grams.
+-- This table defines the discrete quantities of items that we have in stock.
+-- The quantity of an item may change over time, so multiple quantity entries
+-- may be inserted for the same item.
+-- While these quantities are discrete, in order to facilitate the semantics of
+-- the system, we will still allow for the user to specify the counter unit for 
+-- the item. For example, a counter unit may be a box, a tube, or a vial.
+CREATE TABLE item_discrete_quantities (
+    id SERIAL PRIMARY KEY,
+    item_id INTEGER REFERENCES items(id),
+    quantity INTEGER NOT NULL,
+    unit_id INTEGER REFERENCES weight_units(id),
+    measured_at TIMESTAMPTZ NOT NULL DEFAULT now(),
+    measured_by INTEGER REFERENCES users(id),
+    created_at TIMESTAMPTZ NOT NULL DEFAULT now(),
+    updated_at TIMESTAMPTZ NOT NULL DEFAULT now(),
+    created_by INTEGER NOT NULL REFERENCES users(id),
+    updated_by INTEGER NOT NULL REFERENCES users(id),
+    FOREIGN KEY (item_id, unit_id) REFERENCES item_units(item_id, unit_id),
+    FOREIGN KEY (unit_id) REFERENCES discrete_units(id)
+);

web/backend/migrations/2024-02-09-155933_create_discrete_units_table/down.sql

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

web/backend/migrations/2024-02-09-155933_create_discrete_units_table/up.sql

@@ -0,0 +1,7 @@
+-- SQL describing the discrete_units table.
+-- The discrete_units table is used as the finite set of units that can be used to measure
+-- the discrete quantities of items. For example, a box, a tube, or a vial.
+CREATE TABLE discrete_units (
+    id INTEGER PRIMARY KEY,
+    FOREIGN KEY (id) REFERENCES units(id)
+);

web/backend/migrations/2024-02-09-160358_create_real_units_table/down.sql

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

web/backend/migrations/2024-02-09-160358_create_real_units_table/up.sql

@@ -0,0 +1,7 @@
+-- SQL describing the real_units table.
+-- The real_units table is used as the finite set of units that can be used to measure
+-- the real quantities of items. For example, a box, a tube, or a vial.
+CREATE TABLE real_units (
+    id INTEGER PRIMARY KEY,
+    FOREIGN KEY (id) REFERENCES units(id)
+);