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SIMSBIOHUB-498: Seed Critterbase Measurements #1228

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SIMSBIOHUB-498: Seed Critterbase Measurements #1228

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c9f41fb
initial table and data inserted
KjartanE Feb 29, 2024
2f77d5b
lookup table, connection table and seed data created
KjartanE Mar 1, 2024
02bf825
Merge remote-tracking branch 'origin/dev' into SIMSBIOHUB-498
KjartanE Mar 1, 2024
80a93b7
Merge branch 'dev' into SIMSBIOHUB-498
KjartanE Mar 1, 2024
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214 changes: 214 additions & 0 deletions database/src/migrations/20240229000000_observation_measurements.ts
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import { Knex } from 'knex';

/**
* Create new tables:

*
* @export
* @param {Knex} knex
* @return {*} {Promise<void>}
*/
export async function up(knex: Knex): Promise<void> {
await knex.raw(`--sql
-------------------------------------------------------------------------
-- Create tables
-------------------------------------------------------------------------
SET search_path = biohub;

CREATE TABLE cb_measurements_lookup(
cb_measurements_lookup_id integer GENERATED ALWAYS AS IDENTITY (START WITH 1 INCREMENT BY 1),
rank varchar(50) NOT NULL,
tsn integer NOT NULL,
measurement varchar(50) NOT NULL,
unit varchar(50),
type varchar(50) NOT NULL,
options varchar(200),
description varchar(250),
create_date timestamptz(6) DEFAULT now() NOT NULL,
create_user integer NOT NULL,
update_date timestamptz(6),
update_user integer,
revision_count integer DEFAULT 0 NOT NULL,
CONSTRAINT cb_measurements_lookup_pk PRIMARY KEY (cb_measurements_lookup_id)
);

COMMENT ON COLUMN cb_measurements_lookup.cb_measurements_lookup_id IS 'System generated surrogate primary key identifier.';
COMMENT ON COLUMN cb_measurements_lookup.rank IS 'The rank of the taxon.';
COMMENT ON COLUMN cb_measurements_lookup.tsn IS 'The taxonomic serial number.';
COMMENT ON COLUMN cb_measurements_lookup.measurement IS 'The measurement value.';
COMMENT ON COLUMN cb_measurements_lookup.unit IS 'The unit of measurement.';
COMMENT ON COLUMN cb_measurements_lookup.type IS 'The type of measurement.';
COMMENT ON COLUMN cb_measurements_lookup.options IS 'The options for the measurement.';
COMMENT ON COLUMN cb_measurements_lookup.description IS 'The description of the measurement.';
COMMENT ON COLUMN cb_measurements_lookup.create_date IS 'The datetime the record was created.';
COMMENT ON COLUMN cb_measurements_lookup.create_user IS 'The id of the user who created the record as identified in the system user table.';
COMMENT ON COLUMN cb_measurements_lookup.update_date IS 'The datetime the record was updated.';
COMMENT ON COLUMN cb_measurements_lookup.update_user IS 'The id of the user who updated the record as identified in the system user table.';
COMMENT ON COLUMN cb_measurements_lookup.revision_count IS 'Revision count used for concurrency control.';
COMMENT ON TABLE cb_measurements_lookup IS 'A measurement lookup table.';

----------------------------------------------------------------------------------------

CREATE TABLE survey_observation_measurement (
survey_observation_measurement_id integer GENERATED ALWAYS AS IDENTITY (START WITH 1 INCREMENT BY 1),
survey_observation_id integer NOT NULL,
cb_measurements_lookup_id integer NOT NULL,
value integer NOT NULL,
create_date timestamptz(6) DEFAULT now() NOT NULL,
create_user integer NOT NULL,
update_date timestamptz(6),
update_user integer,
revision_count integer DEFAULT 0 NOT NULL,
CONSTRAINT survey_observation_measurement_pk PRIMARY KEY (survey_observation_measurement_id)
);

COMMENT ON COLUMN survey_observation_measurement.survey_observation_measurement_id IS 'System generated surrogate primary key identifier.';
COMMENT ON COLUMN survey_observation_measurement.survey_observation_id IS 'The id of the survey observation as identified in the survey observation table.';
COMMENT ON COLUMN survey_observation_measurement.cb_measurements_lookup_id IS 'The id of the measurement as identified in the cb_measurements_lookup table.';
COMMENT ON COLUMN survey_observation_measurement.value IS 'The value of the measurement.';
COMMENT ON COLUMN survey_observation_measurement.create_date IS 'The datetime the record was created.';
COMMENT ON COLUMN survey_observation_measurement.create_user IS 'The id of the user who created the record as identified in the system user table.';
COMMENT ON COLUMN survey_observation_measurement.update_date IS 'The datetime the record was updated.';
COMMENT ON COLUMN survey_observation_measurement.update_user IS 'The id of the user who updated the record as identified in the system user table.';
COMMENT ON COLUMN survey_observation_measurement.revision_count IS 'Revision count used for concurrency control.';
COMMENT ON TABLE survey_observation_measurement IS 'A table to store the measurements for a survey observation.';

----------------------------------------------------------------------------------------
-- Create Indexes and Constraints for table: survey_observation_measurement
----------------------------------------------------------------------------------------

-- Add foreign key constraint
ALTER TABLE survey_observation_measurement ADD CONSTRAINT survey_observation_measurement_fk1
FOREIGN KEY (survey_observation_id)
REFERENCES survey_observation(survey_observation_id);

ALTER TABLE survey_observation_measurement ADD CONSTRAINT survey_observation_measurement_fk2
FOREIGN KEY (cb_measurements_lookup_id)
REFERENCES cb_measurements_lookup(cb_measurements_lookup_id);

-- add indexes for foreign keys
CREATE INDEX survey_observation_measurement_idx1 ON survey_observation(survey_observation_id);
CREATE INDEX survey_observation_measurement_idx2 ON cb_measurements_lookup(cb_measurements_lookup_id);

----------------------------------------------------------------------------------------
-- Create audit and journal triggers
----------------------------------------------------------------------------------------

CREATE TRIGGER audit_cb_measurements_lookup_lookup BEFORE INSERT OR UPDATE OR DELETE ON biohub.cb_measurements_lookup FOR EACH ROW EXECUTE PROCEDURE tr_audit_trigger();
CREATE TRIGGER journal_cb_measurements_lookup_lookup AFTER INSERT OR UPDATE OR DELETE ON biohub.cb_measurements_lookup FOR EACH ROW EXECUTE PROCEDURE tr_journal_trigger();

CREATE TRIGGER audit_survey_observation_measurement BEFORE INSERT OR UPDATE OR DELETE ON biohub.survey_observation_measurement FOR EACH ROW EXECUTE PROCEDURE tr_audit_trigger();
CREATE TRIGGER journal_survey_observation_measurement AFTER INSERT OR UPDATE OR DELETE ON biohub.survey_observation_measurement FOR EACH ROW EXECUTE PROCEDURE tr_journal_trigger();


----------------------------------------------------------------------------------------
-- Create lookup table data
----------------------------------------------------------------------------------------
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('vertebrata', 331030, 'skull length', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('vertebrata', 331030, 'skull width', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('tetrapoda', 914181, 'neck girth', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('tetrapoda', 914181, 'neck length', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('sciuridae', 180135, 'nest height', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('reptilia', 173747, 'snout-vent length', 'mm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('reptilia', 173747, 'body length', 'mm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('reptilia', 173747, 'body mass', 'g', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('plantae', 202422, 'Diameter at breast height (DBH)', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'baculum length', 'cm', 'quant', 'The length of the baculum bone, measured from start to end.', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'chest girth', 'cm', 'quant', 'The circumference of the chest, measured at the largest point.', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'abdomen girth', 'cm', 'quant', 'The circumference of the abdomen, measured at the largest point.', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'canine length', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'canine width', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'ear length', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'forearm length', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'hind leg length', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'foot length', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'paw length', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'paw width', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'foot width', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'hallux length', 'cm', 'quant', 'Length of the hallux toe, measured from base to tip.', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'nipple length', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'shoulder height', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'shoulder width', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'body length', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'body mass', 'kg', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'fur colour (primary)', '', 'qual', 'black, brown, white, grey, orange', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('mammalia', 179913, 'fur colour (secondary)', '', 'qual', 'black, brown, white, grey, orange', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('aves', 174371, 'cere depth', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('aves', 174371, 'culmen length', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('aves', 174371, 'culmen width', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('aves', 174371, 'nest diameter (inner)', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('aves', 174371, 'nest diameter (outer)', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('aves', 174371, 'cavity opening diameter', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('aves', 174371, 'life stage', '', 'qual', 'nestling, fledgling, hatch year (HY), after hatch year (AHY)', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('aves', 174371, 'nest height', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('aves', 174371, 'body mass', 'g', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('aves', 174371, 'tarsus length', 'mm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('aves', 174371, 'tarsus width', 'mm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('aves', 174371, 'wing chord', 'mm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('artiodactyla', 180692, 'antler point count', '', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('artiodactyla', 180692, 'antler configuration', '', 'qual', 'less than 3 points; more than 3 points', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('animalia', 202423, 'age', 'years', 'quant', 'The number of years that the animal has been alive for', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('animalia', 202423, 'offspring count', '', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('animalia', 202423, 'tail length', 'cm', 'quant', '', '', 1);
INSERT INTO cb_measurements_lookup(rank, tsn, measurement, unit, type, options, description, create_user)
VALUES ('animalia', 202423, 'sex', '', 'qual', 'male, female', '', 1);

----------------------------------------------------------------------------------------
-- Create new views
----------------------------------------------------------------------------------------
SET search_path=biohub_dapi_v1;

CREATE OR REPLACE VIEW cb_measurements_lookup AS SELECT * FROM biohub.cb_measurements_lookup;
CREATE OR REPLACE VIEW survey_observation_measurement AS SELECT * FROM biohub.survey_observation_measurement;
`);
}

export async function down(knex: Knex): Promise<void> {
await knex.raw(``);
}
21 changes: 20 additions & 1 deletion database/src/seeds/03_basic_project_survey_setup.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -93,11 +93,14 @@ export async function seed(knex: Knex): Promise<void> {

const response3 = await knex.raw(insertSurveyObservationData(surveyId));
await knex.raw(insertObservationSubCount(response3.rows[0].survey_observation_id));

await knex.raw(`
${insertSurveyObservationMeasurementData(surveyId)}
`);
}
}
}
}

const checkAnyFundingSourceExists = () => `
SELECT
funding_source_id
Expand Down Expand Up @@ -639,6 +642,22 @@ const insertSurveyObservationData = (surveyId: number) => `
RETURNING survey_observation_id;
`;

const insertSurveyObservationMeasurementData = (surveyId: number) =>
`
INSERT INTO survey_observation_measurement
(
survey_observation_id,
cb_measurements_lookup_id,
value
)
VALUES
(
(SELECT survey_observation_id FROM survey_observation WHERE survey_id = ${surveyId} LIMIT 1),
(SELECT cb_measurements_lookup_id FROM cb_measurements_lookup ORDER BY random() LIMIT 1),
$$${faker.number.int({ min: 1, max: 200 })}$$
);
`;

/**
* SQL to insert Project data
*
Expand Down
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