botany measurements

prisma/migrations/20241128000000_botany_measurements_cdc/migration.sql

@@ -1,22 +1,51 @@
+----------------------------------------------------------------------------------------
+-- Adding percent ENUM if not exists
+----------------------------------------------------------------------------------------
+
+DO $$
+BEGIN
+    IF NOT EXISTS (
+        SELECT 1 
+        FROM pg_type t 
+        JOIN pg_enum e ON t.oid = e.enumtypid
+        JOIN pg_catalog.pg_namespace n ON n.oid = t.typnamespace
+        WHERE t.typname = 'measurement_unit' AND e.enumlabel = 'percent' AND n.nspname = 'critterbase'
+    ) THEN
+        ALTER TYPE critterbase.measurement_unit ADD VALUE 'percent';
+    END IF;
+END $$;
+COMMIT;
+
 ----------------------------------------------------------------------------------------
 -- INSERTING QUANTITATIVE BOTANY MEASUREMENTS 
 ----------------------------------------------------------------------------------------
 INSERT INTO xref_taxon_measurement_quantitative (itis_tsn, measurement_name, min_value, max_value, unit, measurement_desc)
 VALUES
-    (202422, 'Circumference at breast height (CBH)', 0, 100000, 'centimeter', 'The circumference of a tree measured at 1.3 meters (4.5 feet) above the ground.'),
-    (202422, 'Height to live crown', 0, 1000, 'meter', 'The height to effective portion of the live crown for growth.'),
-    (202422, 'Height', 0, 1000, 'meter', 'The measured or estimated height.'), 
-    (202422, 'Percent Cover', 0, 100, 'percent', 'The measured or estimated height.');
-
+    (202422, 'circumference at breast height (CBH)', 0, 100000, 'centimeter', 'The circumference of a tree measured at 1.3 meters (4.5 feet) above the ground.'),
+    (202422, 'height to live crown', 0, 1000, 'meter', 'The height to effective portion of the live crown for growth.'),
+    (202422, 'height', 0, 1000, 'meter', 'The measured or estimated height.'), 
+    (202422, 'percent cover', 0, 100, 'percent', 'The percent area covered.');
 
 ----------------------------------------------------------------------------------------
 -- INSERTING QUALITATIVE BOTANY MEASUREMENTS 
 ----------------------------------------------------------------------------------------
 WITH MeasurementIDs AS (
     INSERT INTO xref_taxon_measurement_qualitative (itis_tsn, measurement_name)
     VALUES
-        (161061, 'life stage'),
-        (159785, 'maturity')
+        (202422, 'life stage'),
+        (202422, 'bark retention'),
+        (202422, 'crown classification'),
+        (202422, 'crown condition'),
+        (202422, 'epiphyte extent'),
+        (202422, 'epiphyte thickness'),
+        (202422, 'lichen abundance'),
+        (202422, 'mistletoe infection: lower third'),
+        (202422, 'mistletoe infection: middle third'),
+        (202422, 'mistletoe infection: upper third'),
+        (202422, 'deciduous tree decay'),
+        (202422, 'evergreen tree decay'),
+        (202422, 'count range'), 
+        (202422, 'standing tree')
     RETURNING itis_tsn, taxon_measurement_id, measurement_name
 )
 
@@ -26,10 +55,84 @@ WITH MeasurementIDs AS (
 INSERT INTO xref_taxon_measurement_qualitative_option (taxon_measurement_id, option_label, option_desc, option_value )
 SELECT m.taxon_measurement_id, o.option_label, o.option_desc, o.option_value
 FROM (
-    SELECT * FROM (
         VALUES
-        (161061, 'maturity', 'Immature', 'Young individuals that have not yet reproduced; fish with underdeveloped gonads.', 0),
-        (159785, 'life stage', 'adult', 'An individual able to reproduce.', 2)
-    ) AS option_data (itis_tsn, measurement_name, option_label, option_desc, option_value)
-) AS o
+        (202422, 'life stage', 'Dead', 'Organism is or appears dead.', 0),
+        (202422, 'life stage', 'Juvenile', 'Developing but not reproducing nor fully mature; seedlings and saplings.', 1),
+        (202422, 'life stage', 'Mature: in bud', 'Has flower buds that are recognizable or strongly swollen.', 2),
+        (202422, 'life stage', 'Mature: dispersing fruit', 'Has fruit or seed that is dispersing.', 3),
+        (202422, 'life stage', 'Mature: flowering', 'Has flowers fading or completely faded.', 4),
+        (202422, 'life stage', 'Mature: fading', 'Has flowers within the range of bud-break to mature flowers.', 5),
+        (202422, 'life stage', 'Mature: Immature fruit', 'Has immature (green) fruit.', 6),
+        (202422, 'life stage', 'Mature: Mature Fruit', 'Has mature (ripe) fruit.', 7),
+        (202422, 'life stage', 'Mature: Vegetative Only', 'Lacks flower buds, flowers, and fruit.', 8),
+        (202422, 'life stage', 'Senescent', 'Alive but declining in vigour and/or reproductive capacity.', 9),
+        (202422, 'bark retention', 'All Bark Present', 'All bark is present.', 0),
+        (202422, 'bark retention', 'Bark lost on damaged areas', 'Bark lost only on damaged areas.', 1),
+        (202422, 'bark retention', 'Approximately 5% or less bark loss', 'Approximately 5% or less of the bark is lost.', 2),
+        (202422, 'bark retention', 'Most Bark Present', 'Bare patches, some bark may be loose (5-25% loss).', 3),
+        (202422, 'bark retention', 'Bare Sections', 'Firm and loose bark remains, about 26%-50% bark loss.', 4),
+        (202422, 'bark retention', 'Most Bark Gone', 'Firm and loose bark remains (51-75% loss).', 5),
+        (202422, 'bark retention', 'Trace Bark Remains', '76-99% bark loss.', 6),
+        (202422, 'bark retention', 'No Bark', 'Total (100%) bark loss.', 7),
+        (202422, 'crown classification', 'Codominant', 'Trees with crowns forming the general level of the crown canopy; crown is generally smaller than those of the dominant trees and usually more crowded on the sides.', 0),
+        (202422, 'crown classification', 'Dominant', 'Trees with crown extending above the general level of the layer; somewhat taller than the codominant trees, and have well developed crowns, which may be somewhat crowded on the sides.', 1),
+        (202422, 'crown classification', 'Intermediate', 'Trees with crowns below but extending into the general level of the crown canopy; crowns usually small and quite crowded on the sides.', 2),
+        (202422, 'crown classification', 'Suppressed', 'Trees with crowns entirely below the general level of the crown canopy.', 3),
+        (202422, 'crown condition', 'Pristine', 'All foliage, twigs, and branches present.', 0),
+        (202422, 'crown condition', 'Partial Foliage Loss', 'Some or all foliage lost; possibly some twigs lost; all branches usually present; possible broken top.', 1),
+        (202422, 'crown condition', 'Defoliated', 'No foliage present; up to 50% of twigs lost; most branches present; possible broken top.', 2),
+        (202422, 'crown condition', 'Severely Damaged', 'No foliage or twigs present; up to 50% of branches lost; top usually broken.', 3),
+        (202422, 'crown condition', 'Mostly Denuded', 'Most branches gone; some sound branch stubs remain; top broken.', 4),
+        (202422, 'crown condition', 'Bare', 'No branches present; some sound and rotting branch stubs, top broken.', 5),
+        (202422, 'epiphyte extent', 'None', 'No epiphytes present.', 0),
+        (202422, 'epiphyte extent', 'Trace', 'Trace amounts of epiphytes present.', 1),
+        (202422, 'epiphyte extent', 'Coverage: 1-33%', 'Epiphyte coverage is between 1% and 33%.', 2),
+        (202422, 'epiphyte extent', 'Coverage: 34-66%', 'Epiphyte coverage is between 34% and 66%.', 3),
+        (202422, 'epiphyte extent', 'Coverage: 67-100%', 'Epiphyte coverage is between 67% and 100%.', 4),
+        (202422, 'epiphyte thickness', 'Sparse', 'Epiphytes are present in sparse amounts.', 0),
+        (202422, 'epiphyte thickness', 'Thick mat', 'Epiphytes form a thick mat.', 1),
+        (202422, 'lichen abundance', 'No Lichen', 'Zero grams of lichen within 4.5m of the root collar.', 0),
+        (202422, 'lichen abundance', 'Class 1 Abundance', '0-5 grams of lichen within 4.5m of the root collar.', 1),
+        (202422, 'lichen abundance', 'Class 2 Abundance', '5-50g of lichen within 4.5m of the root collar.', 2),
+        (202422, 'lichen abundance', 'Class 3 Abundance', '50-250g of lichen within 4.5m of the root collar.', 3),
+        (202422, 'lichen abundance', 'Class 4 Abundance', '250-650g of lichen within 4.5m of the root collar.', 4),
+        (202422, 'lichen abundance', 'Class 5 Abundance', 'Greater than 625g of lichen within 4.5m of the root collar.', 5),
+        (202422, 'mistletoe infection: lower third', 'None', 'No mistletoe infection in the lower third.', 0),
+        (202422, 'mistletoe infection: lower third', 'Light', 'Light mistletoe infection in the lower third.', 1),
+        (202422, 'mistletoe infection: lower third', 'Heavy', 'Heavy mistletoe infection in the lower third.', 2),
+        (202422, 'mistletoe infection: middle third', 'None', 'No mistletoe infection in the middle third.', 0),
+        (202422, 'mistletoe infection: middle third', 'Light', 'Light mistletoe infection in the middle third.', 1),
+        (202422, 'mistletoe infection: middle third', 'Heavy', 'Heavy mistletoe infection in the middle third.', 2),
+        (202422, 'mistletoe infection: upper third', 'None', 'No mistletoe infection in the upper third.', 0),
+        (202422, 'mistletoe infection: upper third', 'Light', 'Light mistletoe infection in the upper third.', 1),
+        (202422, 'mistletoe infection: upper third', 'Heavy', 'Heavy mistletoe infection in the upper third.', 2),
+        (202422, 'deciduous tree decay', 'No decay', 'Tree is live/healthy.', 0),
+        (202422, 'deciduous tree decay', 'Live with defects', 'Most limbs intact, some internal rot, top usually broken.', 1),
+        (202422, 'deciduous tree decay', 'Dead Stage 1 - Limbless', 'Most limbs gone, top broken, extensive heartrot.', 2),
+        (202422, 'deciduous tree decay', 'Dead Stage 2 - Snag', 'Top 1/3 or more broken off, no branches, extensive heartrot.', 3),
+        (202422, 'deciduous tree decay', 'Dead Stage 3 - Fallen', 'Downed trees, coarse woody debris.', 4),
+        (202422, 'evergreen tree decay', 'Healthy', 'Live/healthy.', 0),
+        (202422, 'evergreen tree decay', 'Damaged', 'Live/diseased or damaged.', 1),
+        (202422, 'evergreen tree decay', 'Dead - Intact', 'Dead/very hard wood with little external deterioration.', 2),
+        (202422, 'evergreen tree decay', 'Dead - Slightly Deteriorated', 'Dead/hard wood with some external deterioration.', 3),
+        (202422, 'evergreen tree decay', 'Dead - Moderately Deteriorated', 'Dead/spongy wood with extensive external deterioration.', 4),
+        (202422, 'evergreen tree decay', 'Dead - Broken Trunk', 'Dead/soft wood, trunk broken-off.', 5),
+        (202422, 'evergreen tree decay', 'Dead - Severely Decayed', 'Dead/very soft wood, trunk broken-off.', 6),
+        (202422, 'evergreen tree decay', 'Decayed Stump', 'Decayed stump.', 7),
+        (202422, 'evergreen tree decay', 'Debris', 'Debris.', 8),
+        (202422, 'count range', '1 - 50', 'Count range between 1 and 50.', 0),
+        (202422, 'count range', '51 - 250', 'Count range between 51 and 250.', 1),
+        (202422, 'count range', '251 - 1,000', 'Count range between 251 and 1,000.', 2),
+        (202422, 'count range', '1,001 - 2,500', 'Count range between 1,001 and 2,500.', 3),
+        (202422, 'count range', '2,501 - 10,000', 'Count range between 2,501 and 10,000.', 4),
+        (202422, 'count range', '10,001 - 100,000', 'Count range between 10,001 and 100,000.', 5),
+        (202422, 'count range', '> 100,000', 'Count range greater than 100,000.', 6),
+        (202422, 'count range', '1 - 250', 'Count range between 1 and 250.', 7),
+        (202422, 'count range', '251 - 2,500', 'Count range between 251 and 2,500.', 8),
+        (202422, 'count range', '2,501 - 100,000', 'Count range between 2,501 and 100,000.', 9),
+        (202422, 'count range', '51 - 1,000', 'Count range between 51 and 1,000.', 10),
+        (202422, 'count range', '1,001 - 10,000', 'Count range between 1,001 and 10,000.', 11),
+        (202422, 'standing tree', 'True', 'Tree is standing.', 0),
+        (202422, 'standing tree', 'False', 'Tree is not standing.', 1)
+    ) AS o (itis_tsn, measurement_name, option_label, option_desc, option_value)
 JOIN MeasurementIDs m ON o.itis_tsn = m.itis_tsn AND o.measurement_name = m.measurement_name;