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prisma/migrations/20240618114300_measurement_values/migration.sql
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| ---------------------------------------------------------------------------------------- | ||
| -- Updates quant measurement table so that tail belongs to vertebrates and has a description (was previously attributed to all animals) | ||
| ---------------------------------------------------------------------------------------- | ||
| UPDATE xref_taxon_measurement_quantitative | ||
| SET itis_tsn = 158852, measurement_desc = 'The distance between the base and tip of the tail.' | ||
| WHERE itis_tsn = 202423 | ||
| AND measurement_name = 'tail length'; | ||
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| ---------------------------------------------------------------------------------------- | ||
| -- New markings type "Sleeve" | ||
| ---------------------------------------------------------------------------------------- | ||
| INSERT into lk_marking_type | ||
| (name, description) | ||
| VALUES | ||
| ('Sleeve', 'A durable, weather-resistant band typically placed on a leg.'); | ||
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| ---------------------------------------------------------------------------------------- | ||
| -- New marking body locations for vertebrates and tetrapods. | ||
| ---------------------------------------------------------------------------------------- | ||
| INSERT into xref_taxon_marking_body_location | ||
| (body_location, description, itis_tsn) | ||
| VALUES | ||
| ('Neck', NULL, 331030), | ||
| ('Left forelimb', 'The front left limb.', 914181), | ||
| ('Right forelimb', 'The front right limb.', 914181), | ||
| ('Left hindlimb', 'The rear left limb.', 914181), | ||
| ('Right hindlimb', 'The rear right limb.', 914181); | ||
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| ---------------------------------------------------------------------------------------- | ||
| -- Edit enum list to include some more units | ||
| -- Wrapping in a transaction block to fix issue where the alter type otherwise fails | ||
| ---------------------------------------------------------------------------------------- | ||
| BEGIN; | ||
| ALTER TYPE critterbase.measurement_unit ADD VALUE 'years'; | ||
| COMMIT; | ||
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| ---------------------------------------------------------------------------------------- | ||
| -- Add descriptions to measurements | ||
| ---------------------------------------------------------------------------------------- | ||
| UPDATE xref_taxon_measurement_quantitative | ||
| SET measurement_desc = CASE | ||
| WHEN itis_tsn = 331030 AND measurement_name = 'skull length' THEN 'The distance between the anterior-most and posterior-most parts of the skull.' | ||
| WHEN itis_tsn = 331030 AND measurement_name = 'skull width' THEN 'The maximum width of the skull, measured at the widest part of the cranium.' | ||
| WHEN itis_tsn = 914181 AND measurement_name = 'neck circumference' THEN 'The circumference of the neck, measured at its thickest point.' | ||
| WHEN itis_tsn = 914181 AND measurement_name = 'neck length' THEN 'The distance from the base of the skull to the base of the neck.' | ||
| WHEN itis_tsn = 180135 AND measurement_name = 'nest height' THEN 'The vertical distance from the ground to the top of the nest.' | ||
| WHEN itis_tsn = 173747 AND measurement_name = 'snout-vent length' THEN 'The distance from the tip of the snout to the opening of the vent or cloaca.' | ||
| WHEN itis_tsn = 173747 AND measurement_name = 'body length' THEN 'The distance between the anterior-most part and posterior-most part of the body, excluding the tail.' | ||
| WHEN itis_tsn = 173747 AND measurement_name = 'body mass' THEN 'The total weight of the animal.' | ||
| WHEN itis_tsn = 202422 AND measurement_name = 'Diameter at breast height (DBH)' THEN 'The diameter of a tree measured at 1.3 meters (4.5 feet) above the ground.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'baculum length' THEN 'The length of the baculum (penis bone).' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'chest circumference' THEN 'The circumference around the chest, measured at its widest point.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'abdomen circumference' THEN 'The circumference around the abdomen at its widest point.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'canine length' THEN 'The length of the canine teeth from the base to the tip.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'canine width' THEN 'The width of the canine teeth at their base.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'ear length' THEN 'The distance from the base to the tip of the ear.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'forearm length' THEN 'The distance from the elbow to the wrist.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'hind leg length' THEN 'The distance from the hip to the ankle.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'foot length' THEN 'The distance from the heel to the tip of the longest toe.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'paw length' THEN 'The length of the paw from the heel pad to the tip of the longest toe.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'paw width' THEN 'The width of the paw at its widest point.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'foot width' THEN 'The width of the foot at its widest point.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'hallux length' THEN 'The length of the first digit (big toe).' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'nipple length' THEN 'The length of the nipple from its base to the tip.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'shoulder height' THEN 'The vertical distance from the ground to the top of the shoulder.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'shoulder width' THEN 'The distance between the outer edges of the shoulders.' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'body length' THEN 'The distance from the tip of the snout (or beak) to the base of the tail (excluding the tail).' | ||
| WHEN itis_tsn = 179913 AND measurement_name = 'body mass' THEN 'The total weight of the animal.' | ||
| WHEN itis_tsn = 174371 AND measurement_name = 'cere depth' THEN 'The depth of the cere (the fleshy, typically colored area at the base of the upper beak).' | ||
| WHEN itis_tsn = 174371 AND measurement_name = 'culmen length' THEN 'The length of the upper beak from the tip to where it meets the forehead.' | ||
| WHEN itis_tsn = 174371 AND measurement_name = 'culmen width' THEN 'The width of the upper beak at its base.' | ||
| WHEN itis_tsn = 174371 AND measurement_name = 'nest diameter (inner)' THEN 'The diameter of the inner part of the nest.' | ||
| WHEN itis_tsn = 174371 AND measurement_name = 'nest diameter (outer)' THEN 'The diameter of the outer part of the nest.' | ||
| WHEN itis_tsn = 174371 AND measurement_name = 'cavity opening diameter' THEN 'The diameter of the entrance to a nest cavity.' | ||
| WHEN itis_tsn = 174371 AND measurement_name = 'nest height' THEN 'The vertical distance from the ground to the top of the nest.' | ||
| WHEN itis_tsn = 174371 AND measurement_name = 'body mass' THEN 'The total weight of the animal.' | ||
| WHEN itis_tsn = 174371 AND measurement_name = 'tarsus length' THEN 'The length of the tarsus (the part of a bird''s leg between the knee and the ankle).' | ||
| WHEN itis_tsn = 174371 AND measurement_name = 'tarsus width' THEN 'The width of the tarsus at its widest point.' | ||
| WHEN itis_tsn = 174371 AND measurement_name = 'wing chord' THEN 'The length of the wing from the shoulder to the tip of the longest primary feather.' | ||
| WHEN itis_tsn = 180692 AND measurement_name = 'antler point count' THEN 'The number of points on an antler.' | ||
| WHEN itis_tsn = 202423 AND measurement_name = 'age' THEN 'The number of years that the animal has been alive for.' | ||
| WHEN itis_tsn = 202423 AND measurement_name = 'offspring count' THEN 'The number of affiliated offspring.' | ||
| WHEN itis_tsn = 202423 AND measurement_name = 'tail length' THEN 'The distance from the base to the tip of the tail.' | ||
| ELSE measurement_desc | ||
| END; | ||
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| ---------------------------------------------------------------------------------------- | ||
| -- Update year unit in age | ||
| ---------------------------------------------------------------------------------------- | ||
| UPDATE xref_taxon_measurement_quantitative | ||
| SET unit = CASE | ||
| WHEN itis_tsn = 202423 AND measurement_name = 'age' THEN 'years' | ||
| ELSE unit | ||
| END; | ||
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| ---------------------------------------------------------------------------------------- | ||
| -- Create fin length, otoliths and operculum quant measurements for all 4 fish taxa | ||
| ---------------------------------------------------------------------------------------- | ||
| INSERT INTO xref_taxon_measurement_quantitative (itis_tsn, measurement_name, min_value, max_value, unit, measurement_desc) | ||
| VALUES | ||
| -- Length | ||
| (161061, 'caudal fin–snout length', 0, 10000, 'centimeter', 'The distance between the tip of the snout and the base of the caudal fin.'), | ||
| (161051, 'caudal fin–snout length', 0, 10000, 'centimeter', 'The distance between the tip of the snout and the base of the caudal fin.'), | ||
| (161039, 'caudal fin–snout length', 0, 10000, 'centimeter', 'The distance between the tip of the snout and the base of the caudal fin.'), | ||
| (159785, 'caudal fin–snout length', 0, 10000, 'centimeter', 'The distance between the tip of the snout and the base of the caudal fin.'), | ||
| (161061, 'otolith growth rings count', 0, 1000, NULL, 'The number of growth rings in the otolith.'), | ||
| (161051, 'otolith growth rings count', 0, 1000, NULL, 'The number of growth rings in the otolith.'), | ||
| (161039, 'otolith growth rings count', 0, 1000, NULL, 'The number of growth rings in the otolith.'), | ||
| (161061, 'cleithrum growth rings count', 0, 1000, NULL, 'The number of growth rings in the cleithrum.'), | ||
| (161051, 'cleithrum growth rings count', 0, 1000, NULL, 'The number of growth rings in the cleithrum.'), | ||
| (161039, 'cleithrum growth rings count', 0, 1000, NULL, 'The number of growth rings in the cleithrum.'), | ||
| (161061, 'operculum growth rings count', 0, 1000, NULL, 'The number of growth rings in the operculum.'), | ||
| (161051, 'operculum growth rings count', 0, 1000, NULL, 'The number of growth rings in the operculum.'), | ||
| (161039, 'operculum growth rings count', 0, 1000, NULL, 'The number of growth rings in the operculum.'); | ||
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| ---------------------------------------------------------------------------------------- | ||
| -- Add new qualitative measurements lifestage and maturity to the 4 fish taxa | ||
| ---------------------------------------------------------------------------------------- | ||
| WITH MeasurementIDs AS ( | ||
| INSERT INTO xref_taxon_measurement_qualitative (itis_tsn, measurement_name) | ||
| VALUES | ||
| (161061, 'life stage'), | ||
| (161061, 'maturity'), | ||
| (161051, 'life stage'), | ||
| (161051, 'maturity'), | ||
| (161039, 'life stage'), | ||
| (161039, 'maturity'), | ||
| (159785, 'life stage'), | ||
| (159785, 'maturity') | ||
| RETURNING itis_tsn, taxon_measurement_id, measurement_name | ||
| ) | ||
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| ---------------------------------------------------------------------------------------- | ||
| -- Insert measurement options for maturiy for all fish taxa | ||
| -- Update measurement options for fish life stage | ||
| ---------------------------------------------------------------------------------------- | ||
| 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), | ||
| (161061, 'maturity', 'Maturing', 'Ovaries and testes begin to fill out and take up a large part of the body cavity; eggs distinguishable to the naked eye.', 1), | ||
| (161061, 'maturity', 'Mature', 'Fish in full spawning colours; gonads at maximum size; body cavity feels full, especially | ||
| females; roe or milt is not produced if the body cavity is lightly squeezed.', 2), | ||
| (161061, 'maturity', 'Spawning', 'Fish in full spawning colours; eggs and milt are expelled when body cavity is lightly squeezed.', 3), | ||
| (161061, 'maturity', 'Spent', 'Still have spawning colours; eggs and sperm totally discharged; body cavity feels empty | ||
| and genital opening is inflamed; gonads empty except for a few remaining eggs or residual sperm.', 4), | ||
| (161051, 'maturity', 'Immature', 'Young individuals that have not yet reproduced; fish with underdeveloped gonads.', 0), | ||
| (161051, 'maturity', 'Maturing', 'Ovaries and testes begin to fill out and take up a large part of the body cavity; eggs distinguishable to the naked eye.', 1), | ||
| (161051, 'maturity', 'Mature', 'Fish in full spawning colours; gonads at maximum size; body cavity feels full, especially | ||
| females; roe or milt is not produced if the body cavity is lightly squeezed.', 2), | ||
| (161051, 'maturity', 'Spawning', 'Fish in full spawning colours; eggs and milt are expelled when body cavity is lightly squeezed.', 3), | ||
| (161051, 'maturity', 'Spent', 'Still have spawning colours; eggs and sperm totally discharged; body cavity feels empty | ||
| and genital opening is inflamed; gonads empty except for a few remaining eggs or residual sperm.', 4), | ||
| (161039, 'maturity', 'Immature', 'Young individuals that have not yet reproduced; fish with underdeveloped gonads.', 0), | ||
| (161039, 'maturity', 'Maturing', 'Ovaries and testes begin to fill out and take up a large part of the body cavity; eggs distinguishable to the naked eye.', 1), | ||
| (161039, 'maturity', 'Mature', 'Fish in full spawning colours; gonads at maximum size; body cavity feels full, especially | ||
| females; roe or milt is not produced if the body cavity is lightly squeezed.', 2), | ||
| (161039, 'maturity', 'Spawning', 'Fish in full spawning colours; eggs and milt are expelled when body cavity is lightly squeezed.', 3), | ||
| (161039, 'maturity', 'Spent', 'Still have spawning colours; eggs and sperm totally discharged; body cavity feels empty | ||
| and genital opening is inflamed; gonads empty except for a few remaining eggs or residual sperm.', 4), | ||
| (161061, 'maturity', 'Immature', 'Young individuals that have not yet reproduced; fish with underdeveloped gonads.', 0), | ||
| (161061, 'maturity', 'Maturing', 'Ovaries and testes begin to fill out and take up a large part of the body cavity; eggs distinguishable to the naked eye.', 1), | ||
| (161061, 'maturity', 'Mature', 'Fish in full spawning colours; gonads at maximum size; body cavity feels full, especially | ||
| females; roe or milt is not produced if the body cavity is lightly squeezed.', 2), | ||
| (161061, 'maturity', 'Spawning', 'Fish in full spawning colours; eggs and milt are expelled when body cavity is lightly squeezed.', 3), | ||
| (161061, 'maturity', 'Spent', 'Still have spawning colours; eggs and sperm totally discharged; body cavity feels empty | ||
| and genital opening is inflamed; gonads empty except for a few remaining eggs or residual sperm.', 4), | ||
| (159785, 'maturity', 'Immature', 'Young individuals that have not yet reproduced; fish with underdeveloped gonads.', 0), | ||
| (159785, 'maturity', 'Maturing', 'Ovaries and testes begin to fill out and take up a large part of the body cavity; eggs distinguishable to the naked eye.', 1), | ||
| (159785, 'maturity', 'Mature', 'Fish in full spawning colours; gonads at maximum size; body cavity feels full, especially | ||
| females; roe or milt is not produced if the body cavity is lightly squeezed.', 2), | ||
| (159785, 'maturity', 'Spawning', 'Fish in full spawning colours; eggs and milt are expelled when body cavity is lightly squeezed.', 3), | ||
| (159785, 'maturity', 'Spent', 'Still have spawning colours; eggs and sperm totally discharged; body cavity feels empty | ||
| and genital opening is inflamed; gonads empty except for a few remaining eggs or residual sperm.', 4), | ||
| (161061, 'life stage', 'fry', 'Recently hatched fish.', 0), | ||
| (161061, 'life stage', 'juvenile', 'An individual resembling an adult that is not yet able to reproduce.', 1), | ||
| (161061, 'life stage', 'adult', 'An individual able to reproduce.', 2), | ||
| (161051, 'life stage', 'fry', 'Recently hatched fish.', 0), | ||
| (161051, 'life stage', 'juvenile', 'An individual resembling an adult that is not yet able to reproduce.', 1), | ||
| (161051, 'life stage', 'adult', 'An individual able to reproduce.', 2), | ||
| (161039, 'life stage', 'fry', 'Recently hatched fish.', 0), | ||
| (161039, 'life stage', 'juvenile', 'An individual resembling an adult that is not yet able to reproduce.', 1), | ||
| (161039, 'life stage', 'adult', 'An individual able to reproduce.', 2), | ||
| (159785, 'life stage', 'fry', 'Recently hatched fish.', 0), | ||
| (159785, 'life stage', 'juvenile', 'An individual resembling an adult that is not yet able to reproduce.', 1), | ||
| (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 | ||
| JOIN MeasurementIDs m ON o.itis_tsn = m.itis_tsn AND o.measurement_name = m.measurement_name; | ||
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| ---------------------------------------------------------------------------------------- | ||
| -- Update measurement desc for lifestage and maturity. | ||
| ---------------------------------------------------------------------------------------- | ||
| UPDATE xref_taxon_measurement_qualitative | ||
| SET measurement_desc = 'An individual''s reproductive state.' | ||
| WHERE itis_tsn IN (161061, 161051, 161039, 159785) | ||
| AND measurement_name = 'maturity'; |
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| Original file line number | Diff line number | Diff line change |
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@@ -587,6 +587,7 @@ enum measurement_unit { | |
| milligram | ||
| gram | ||
| kilogram | ||
| years | ||
| } | ||
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| enum sex { | ||
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