Insert new method lookup values for SPI ETL

api/src/repositories/code-repository.ts

@@ -62,7 +62,7 @@ export class CodeRepository extends BaseRepository {
       SELECT 
         method_lookup_id as id, 
         name, 
-        description 
+        description
       FROM method_lookup
       ORDER BY name ASC;
     `;

app/src/features/surveys/sampling-information/techniques/components/general-information/TechniqueGeneralInformationForm.tsx

@@ -30,11 +30,15 @@
   }, [codesContext.codesDataLoader]);
 
   const methodOptions: ISelectWithSubtextFieldOption[] =
-    codesContext.codesDataLoader.data?.sample_methods.map((option) => ({
-      value: option.id,
-      label: option.name,
-      subText: option.description
-    })) ?? [];
+    codesContext.codesDataLoader.data?.sample_methods
+      .map((option) => ({
+        value: option.id,
+        label: option.name,
+        subText: option.description
+      }))
+      // TODO https://apps.nrs.gov.bc.ca/int/jira/browse/SIMSBIOHUB-615 - Replace filter with more generic solution
+      // Undetermined is a possible option, but filter from the list to discourage its use
+      .filter((option) => option.label.toLowerCase() !== 'undetermined') ?? [];
 
   if (!codesContext.codesDataLoader.data) {
     return <CircularProgress className="pageProgress" size={40} />;

database/src/migrations/20240911000011_method_lookup_updates.ts

@@ -0,0 +1,203 @@
+import { Knex } from 'knex';
+
+/**
+ * Update method_lookup values and associated attributes for SPI ETL.
+ *
+ * @export
+ * @param {Knex} knex
+ * @return {*}  {Promise<void>}
+ */
+export async function up(knex: Knex): Promise<void> {
+  await knex.raw(`
+    SET SEARCH_PATH=biohub;
+
+    ----------------------------------------------------------------------------------------
+    -- Allow method lookup options to be soft deleted
+    ----------------------------------------------------------------------------------------
+    ALTER TABLE method_lookup ADD COLUMN record_end_date DATE;
+    ALTER TABLE method_lookup ADD COLUMN record_effective_date DATE DEFAULT now();
+
+    COMMENT ON COLUMN method_lookup.record_end_date IS 'Record level end date.';
+    COMMENT ON COLUMN method_lookup.record_effective_date IS 'Record level effective date.';
+
+    CREATE OR REPLACE VIEW biohub_dapi_v1.method_lookup AS SELECT * FROM biohub.method_lookup;
+
+    ----------------------------------------------------------------------------------------
+    -- Insert new method lookup values
+    ----------------------------------------------------------------------------------------
+    INSERT INTO method_lookup (name, description)
+    VALUES
+        ('Drone', 'Detecting species using cameras or sensors mounted to a drone.'),
+        ('Hair snag', 'Detecting species using barbs or similar devices that collect species hair or fur.'),
+        ('Undetermined', 'Insufficient information to determine the method.'),
+        ('Audio encounter', 'Detecting species by songs, calls, or other noises made by the species.');
+
+    ----------------------------------------------------------------------------------------
+    -- Insert quantitative attributes for the new method lookup values
+    ----------------------------------------------------------------------------------------
+    INSERT INTO technique_attribute_quantitative (name, description)
+    VALUES ('Altitude', 'Elevation above sea level.');
+
+    INSERT INTO method_lookup_attribute_quantitative (technique_attribute_quantitative_id, method_lookup_id, min, max, unit)
+    VALUES
+        (
+            (SELECT technique_attribute_quantitative_id FROM technique_attribute_quantitative WHERE name = 'Altitude'),
+            (SELECT method_lookup_id FROM method_lookup WHERE name = 'Drone'),
+            0,
+            10000, 
+            'meter'
+        ),
+        (
+            (SELECT technique_attribute_quantitative_id FROM technique_attribute_quantitative WHERE name = 'Height above ground'),
+            (SELECT method_lookup_id FROM method_lookup WHERE name = 'Hair snag'),
+            0, 
+            1000, 
+            'centimeter'
+        );
+
+    ----------------------------------------------------------------------------------------
+    -- Insert qualitative attributes for the new method lookup values
+    ----------------------------------------------------------------------------------------
+    INSERT INTO technique_attribute_qualitative (name, description)
+    VALUES
+        ('Camera type', 'The type of camera mounted on the drone, such as RGB, thermal, or multispectral.'),
+        ('Trap type', 'The specific design or material of the hair snagging device.');
+
+    INSERT INTO method_lookup_attribute_qualitative (technique_attribute_qualitative_id, method_lookup_id)
+    VALUES
+        (
+            (SELECT technique_attribute_qualitative_id FROM technique_attribute_qualitative WHERE name = 'Camera type'),
+            (SELECT method_lookup_id FROM method_lookup WHERE name = 'Drone')
+        ),
+        (
+            (SELECT technique_attribute_qualitative_id FROM technique_attribute_qualitative WHERE name = 'Trap type'),
+            (SELECT method_lookup_id FROM method_lookup WHERE name = 'Hair snag')
+        );
+
+    INSERT INTO method_lookup_attribute_qualitative_option (method_lookup_attribute_qualitative_id, name, description)
+    VALUES
+        (
+            (
+                SELECT method_lookup_attribute_qualitative_id 
+                FROM method_lookup_attribute_qualitative mlaq 
+                INNER JOIN technique_attribute_qualitative taq ON taq.technique_attribute_qualitative_id = mlaq.technique_attribute_qualitative_id 
+                INNER JOIN method_lookup ml ON ml.method_lookup_id = mlaq.method_lookup_id
+                WHERE taq.name = 'Camera type' AND ml.name = 'Drone'
+            ),
+            'RGB',
+            'Captures images in the visible light spectrum using three color channels (red, green, blue).'
+        ),
+        (
+            (
+                SELECT method_lookup_attribute_qualitative_id 
+                FROM method_lookup_attribute_qualitative mlaq 
+                INNER JOIN technique_attribute_qualitative taq ON taq.technique_attribute_qualitative_id = mlaq.technique_attribute_qualitative_id 
+                INNER JOIN method_lookup ml ON ml.method_lookup_id = mlaq.method_lookup_id
+                WHERE taq.name = 'Camera type' AND ml.name = 'Drone'
+            ),
+            'Thermal',
+            'Captures infrared radiation emitted by objects.'
+        ),
+        (
+            (
+                SELECT method_lookup_attribute_qualitative_id 
+                FROM method_lookup_attribute_qualitative mlaq 
+                INNER JOIN technique_attribute_qualitative taq ON taq.technique_attribute_qualitative_id = mlaq.technique_attribute_qualitative_id 
+                INNER JOIN method_lookup ml ON ml.method_lookup_id = mlaq.method_lookup_id
+                WHERE taq.name = 'Camera type' AND ml.name = 'Drone'
+            ),
+            'Multispectral',
+            'Captures data across a limited number of spectral bands (typically between 3 and 15 bands) in the electromagnetic spectrum.'
+        ),
+        (
+            (
+                SELECT method_lookup_attribute_qualitative_id 
+                FROM method_lookup_attribute_qualitative mlaq 
+                INNER JOIN technique_attribute_qualitative taq ON taq.technique_attribute_qualitative_id = mlaq.technique_attribute_qualitative_id 
+                INNER JOIN method_lookup ml ON ml.method_lookup_id = mlaq.method_lookup_id
+                WHERE taq.name = 'Camera type' AND ml.name = 'Drone'
+            ),
+            'Hyperspectral',
+            'Captures data across numerous spectral bands, providing continuous coverage of a broad spectral range.'
+        ),
+        (
+            (
+                SELECT method_lookup_attribute_qualitative_id 
+                FROM method_lookup_attribute_qualitative mlaq 
+                INNER JOIN technique_attribute_qualitative taq ON taq.technique_attribute_qualitative_id = mlaq.technique_attribute_qualitative_id 
+                INNER JOIN method_lookup ml ON ml.method_lookup_id = mlaq.method_lookup_id
+                WHERE taq.name = 'Camera type' AND ml.name = 'Drone'
+            ),
+            'LiDAR',
+            'Uses laser pulses to measure distances to the Earth''s surface and other objects.'
+        ),
+        (
+            (
+                SELECT method_lookup_attribute_qualitative_id 
+                FROM method_lookup_attribute_qualitative mlaq 
+                INNER JOIN technique_attribute_qualitative taq ON taq.technique_attribute_qualitative_id = mlaq.technique_attribute_qualitative_id 
+                INNER JOIN method_lookup ml ON ml.method_lookup_id = mlaq.method_lookup_id
+                WHERE taq.name = 'Trap type' AND ml.name = 'Hair snag'
+            ),
+            'Barbed wire',
+            'A barbed wire used to collect hair from passing species.'
+        ),
+        (
+            (
+                SELECT method_lookup_attribute_qualitative_id 
+                FROM method_lookup_attribute_qualitative mlaq 
+                INNER JOIN technique_attribute_qualitative taq ON taq.technique_attribute_qualitative_id = mlaq.technique_attribute_qualitative_id 
+                INNER JOIN method_lookup ml ON ml.method_lookup_id = mlaq.method_lookup_id
+                WHERE taq.name = 'Trap type' AND ml.name = 'Hair snag'
+            ),
+            'Adhesive strip',
+            'A sticky strip used to collect hair from passing species.'
+        ),
+        (
+            (
+                SELECT method_lookup_attribute_qualitative_id 
+                FROM method_lookup_attribute_qualitative mlaq 
+                INNER JOIN technique_attribute_qualitative taq ON taq.technique_attribute_qualitative_id = mlaq.technique_attribute_qualitative_id 
+                INNER JOIN method_lookup ml ON ml.method_lookup_id = mlaq.method_lookup_id
+                WHERE taq.name = 'Trap type' AND ml.name = 'Hair snag'
+            ),
+            'Brush',
+            'A brush used to collect hair from passing species.'
+        );
+
+    ----------------------------------------------------------------------------------------
+    -- Drop the radio signal tower option and reassign existing data to the radar option
+    ----------------------------------------------------------------------------------------
+
+    -- Reassign existing attributes for radio signal tower to the radar option
+    UPDATE method_technique
+    SET method_lookup_id = (SELECT method_lookup_id FROM method_lookup WHERE name = 'Radar')
+    WHERE method_lookup_id = (SELECT method_lookup_id FROM method_lookup WHERE name = 'Radio signal tower');
+
+    UPDATE method_lookup_attribute_qualitative
+    SET method_lookup_id = (SELECT method_lookup_id FROM method_lookup WHERE name = 'Radar')
+    WHERE method_lookup_id = (SELECT method_lookup_id FROM method_lookup WHERE name = 'Radio signal tower');
+
+    UPDATE method_lookup_attribute_quantitative
+    SET method_lookup_id = (SELECT method_lookup_id FROM method_lookup WHERE name = 'Radar')
+    WHERE method_lookup_id = (SELECT method_lookup_id FROM method_lookup WHERE name = 'Radio signal tower');
+
+    DELETE FROM method_lookup
+    WHERE name = 'Radio signal tower';
+
+    UPDATE technique_attribute_quantitative
+    SET name = 'Frequency', 
+        description = 'The frequency at which a signal is transmitted or received.'
+    WHERE name = 'Radio frequency';
+
+    ----------------------------------------------------------------------------------------
+    -- Insert new subcount sign option
+    ----------------------------------------------------------------------------------------
+    INSERT INTO biohub.observation_subcount_sign (name, description)
+    VALUES ('Rub or scratch mark', 'A rubbing or scratch mark created by a species');
+    `);
+}
+
+export async function down(knex: Knex): Promise<void> {
+  await knex.raw(``);
+}