Age Extension Query with Formatted Age Range

[acwhite211]

Fixes #6089
Fixes #6016

Creates a new functions that builds a SQLAlchemy subquery that, in addition to the previous implementation's use case of filter CollectionObjects by all it's paths to chronostrat age, returns a formatted age range for a CollectionObject's maximum start age to its minimum end age. This allows the query QB to display this formatted range in the age column in the query results.

Here is a compiled SQLAlchemy query that get generated for a simple CollectionObject Age query:

SELECT
	collectionobject.`CollectionObjectID`,
	concat_ws(' - ',
			  ifnull(regexp_replace(CAST(agg_subq.max_start_period AS CHAR), '\\.(0+)$', ''), ''),
			  ifnull(regexp_replace(CAST(agg_subq.min_end_period AS CHAR), '\\.(0+)$', ''), '')) AS age
FROM
	collectionobject
INNER JOIN (
	SELECT
		unioned.coid AS coid,
		min(unioned.endperiod) AS min_end_period,
		max(unioned.startperiod) AS max_start_period
	FROM
		(
		SELECT
			absoluteage.`CollectionObjectID` AS coid,
			CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) - coalesce(absoluteage.`AgeUncertainty`, 0) AS startperiod,
			CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) + coalesce(absoluteage.`AgeUncertainty`, 0) AS endperiod
		FROM
			absoluteage
		WHERE
			CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) - coalesce(absoluteage.`AgeUncertainty`, 0) <= 2000.0
			AND CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) + coalesce(absoluteage.`AgeUncertainty`, 0) >= 2.0
	UNION ALL
		SELECT
			r.`CollectionObjectID` AS coid,
			CASE
				WHEN (r.`AgeNameEndID` IS NOT NULL) THEN greatest(CAST(a.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(a.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0), CAST(aend.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(aend.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0))
				ELSE CAST(a.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(a.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0)
			END AS startperiod,
			CASE
				WHEN (r.`AgeNameEndID` IS NOT NULL) THEN least((CAST(a.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(a.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0), (CAST(aend.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(aend.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0))
				ELSE (CAST(a.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(a.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0)
			END AS endperiod
		FROM
			relativeage AS r
		INNER JOIN geologictimeperiod AS a ON
			r.`AgeNameID` = a.`GeologicTimePeriodID`
		LEFT OUTER JOIN geologictimeperiod AS aend ON
			r.`AgeNameEndID` = aend.`GeologicTimePeriodID`
		WHERE
			a.`StartPeriod` IS NOT NULL
			AND a.`EndPeriod` IS NOT NULL
			AND a.`StartPeriod` >= a.`EndPeriod`
			AND (r.`AgeNameEndID` IS NULL
				OR aend.`StartPeriod` IS NOT NULL
				AND aend.`EndPeriod` IS NOT NULL
				AND aend.`StartPeriod` >= aend.`EndPeriod`)
			AND CASE
				WHEN (r.`AgeNameEndID` IS NOT NULL) THEN greatest(CAST(a.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(a.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0), CAST(aend.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(aend.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0))
				ELSE CAST(a.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(a.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0)
			END <= 2000.0
			AND CASE
				WHEN (r.`AgeNameEndID` IS NOT NULL) THEN least((CAST(a.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(a.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0), (CAST(aend.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(aend.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0))
				ELSE (CAST(a.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(a.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0)
			END >= 2.0
	UNION ALL
		SELECT
			DISTINCT c.`CollectionObjectID` AS coid,
			CASE
				WHEN (p.`ChronosStratEndID` IS NOT NULL) THEN least(CAST(cs.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(cs.`StartUncertainty`, 0), CAST(csend.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(csend.`StartUncertainty`, 0))
				ELSE CAST(cs.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(cs.`StartUncertainty`, 0)
			END AS startperiod,
			CASE
				WHEN (p.`ChronosStratEndID` IS NOT NULL) THEN greatest(CAST(cs.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(cs.`EndUncertainty`, 0), CAST(csend.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(csend.`EndUncertainty`, 0))
				ELSE CAST(cs.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(cs.`EndUncertainty`, 0)
			END AS endperiod
		FROM
			collectionobject AS c
		LEFT OUTER JOIN collectingevent AS ce ON
			c.`CollectingEventID` = ce.`CollectingEventID`
		LEFT OUTER JOIN locality AS l ON
			ce.`LocalityID` = l.`LocalityID`
		LEFT OUTER JOIN paleocontext AS p ON
			c.`PaleoContextID` = p.`PaleoContextID`
			OR ce.`PaleoContextID` = p.`PaleoContextID`
			OR l.`PaleoContextID` = p.`PaleoContextID`
		LEFT OUTER JOIN geologictimeperiod AS cs ON
			p.`ChronosStratID` = cs.`GeologicTimePeriodID`
		LEFT OUTER JOIN geologictimeperiod AS csend ON
			p.`ChronosStratEndID` = csend.`GeologicTimePeriodID`
		WHERE
			p.`PaleoContextID` IS NOT NULL
			AND cs.`StartPeriod` IS NOT NULL
			AND cs.`EndPeriod` IS NOT NULL
			AND cs.`StartPeriod` >= cs.`EndPeriod`
			AND (p.`ChronosStratEndID` IS NULL
				OR csend.`StartPeriod` IS NOT NULL
				AND csend.`EndPeriod` IS NOT NULL
				AND csend.`StartPeriod` >= csend.`EndPeriod`)
			AND CASE
				WHEN (p.`ChronosStratEndID` IS NOT NULL) THEN least(CAST(cs.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(cs.`StartUncertainty`, 0), CAST(csend.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(csend.`StartUncertainty`, 0))
				ELSE CAST(cs.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(cs.`StartUncertainty`, 0)
			END <= 2000.0
			AND CASE
				WHEN (p.`ChronosStratEndID` IS NOT NULL) THEN greatest(CAST(cs.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(cs.`EndUncertainty`, 0), CAST(csend.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(csend.`EndUncertainty`, 0))
				ELSE CAST(cs.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(cs.`EndUncertainty`, 0)
			END >= 2.0) AS unioned
	GROUP BY
		unioned.coid) AS agg_subq ON
	collectionobject.`CollectionObjectID` = agg_subq.coid
WHERE
	collectionobject.`CollectionID` = 98304;

Checklist

• Self-review the PR after opening it to make sure the changes look good and
  self-explanatory (or properly documented)
• Add relevant issue to release milestone
• Add relevant documentation (Tester - Dev)

Testing instructions

TBD

[acwhite211]

Have some code cleanup to do before merging.

Here is another example of a compiled SQLAlchemy query that gets generated:

SELECT
	collectionobject.`CollectionObjectID`,
	concat_ws(' - ', ifnull(regexp_replace(CAST(agg_subq.max_start_period AS CHAR), '\\.(0+)$', ''), ''), ifnull(regexp_replace(CAST(agg_subq.min_end_period AS CHAR), '\\.(0+)$', ''), '')) AS age,
	absoluteage_1.`AbsoluteAge`,
	geologictimeperiod_1.`Name`,
	geologictimeperiod_2.`Name`,
	geologictimeperiod_3.`Name`,
	geologictimeperiod_4.`Name`,
	geologictimeperiod_5.`Name`,
	geologictimeperiod_6.`Name`
FROM
	collectionobject
INNER JOIN (
	SELECT
		unioned.coid AS coid,
		min(unioned.endperiod) AS min_end_period,
		max(unioned.startperiod) AS max_start_period
	FROM
		(
		SELECT
			absoluteage.`CollectionObjectID` AS coid,
			CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) - coalesce(absoluteage.`AgeUncertainty`, 0) AS startperiod,
			CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) + coalesce(absoluteage.`AgeUncertainty`, 0) AS endperiod
		FROM
			absoluteage
		WHERE
			CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) - coalesce(absoluteage.`AgeUncertainty`, 0) <= 2000.0
			AND CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) + coalesce(absoluteage.`AgeUncertainty`, 0) >= 2.0
	UNION ALL
		SELECT
			r.`CollectionObjectID` AS coid,
			CASE
				WHEN (r.`AgeNameEndID` IS NOT NULL) THEN greatest(CAST(a.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(a.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0), CAST(aend.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(aend.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0))
				ELSE CAST(a.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(a.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0)
			END AS startperiod,
			CASE
				WHEN (r.`AgeNameEndID` IS NOT NULL) THEN least((CAST(a.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(a.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0), (CAST(aend.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(aend.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0))
				ELSE (CAST(a.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(a.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0)
			END AS endperiod
		FROM
			relativeage AS r
		INNER JOIN geologictimeperiod AS a ON
			r.`AgeNameID` = a.`GeologicTimePeriodID`
		LEFT OUTER JOIN geologictimeperiod AS aend ON
			r.`AgeNameEndID` = aend.`GeologicTimePeriodID`
		WHERE
			a.`StartPeriod` IS NOT NULL
			AND a.`EndPeriod` IS NOT NULL
			AND a.`StartPeriod` >= a.`EndPeriod`
			AND (r.`AgeNameEndID` IS NULL
				OR aend.`StartPeriod` IS NOT NULL
				AND aend.`EndPeriod` IS NOT NULL
				AND aend.`StartPeriod` >= aend.`EndPeriod`)
			AND CASE
				WHEN (r.`AgeNameEndID` IS NOT NULL) THEN greatest(CAST(a.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(a.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0), CAST(aend.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(aend.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0))
				ELSE CAST(a.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(a.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0)
			END <= 2000.0
			AND CASE
				WHEN (r.`AgeNameEndID` IS NOT NULL) THEN least((CAST(a.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(a.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0), (CAST(aend.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(aend.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0))
				ELSE (CAST(a.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(a.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0)
			END >= 2.0
	UNION ALL
		SELECT
			DISTINCT c.`CollectionObjectID` AS coid,
			CASE
				WHEN (p.`ChronosStratEndID` IS NOT NULL) THEN least(CAST(cs.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(cs.`StartUncertainty`, 0), CAST(csend.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(csend.`StartUncertainty`, 0))
				ELSE CAST(cs.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(cs.`StartUncertainty`, 0)
			END AS startperiod,
			CASE
				WHEN (p.`ChronosStratEndID` IS NOT NULL) THEN greatest(CAST(cs.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(cs.`EndUncertainty`, 0), CAST(csend.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(csend.`EndUncertainty`, 0))
				ELSE CAST(cs.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(cs.`EndUncertainty`, 0)
			END AS endperiod
		FROM
			collectionobject AS c
		LEFT OUTER JOIN collectingevent AS ce ON
			c.`CollectingEventID` = ce.`CollectingEventID`
		LEFT OUTER JOIN locality AS l ON
			ce.`LocalityID` = l.`LocalityID`
		LEFT OUTER JOIN paleocontext AS p ON
			c.`PaleoContextID` = p.`PaleoContextID`
			OR ce.`PaleoContextID` = p.`PaleoContextID`
			OR l.`PaleoContextID` = p.`PaleoContextID`
		LEFT OUTER JOIN geologictimeperiod AS cs ON
			p.`ChronosStratID` = cs.`GeologicTimePeriodID`
		LEFT OUTER JOIN geologictimeperiod AS csend ON
			p.`ChronosStratEndID` = csend.`GeologicTimePeriodID`
		WHERE
			p.`PaleoContextID` IS NOT NULL
			AND cs.`StartPeriod` IS NOT NULL
			AND cs.`EndPeriod` IS NOT NULL
			AND cs.`StartPeriod` >= cs.`EndPeriod`
			AND (p.`ChronosStratEndID` IS NULL
				OR csend.`StartPeriod` IS NOT NULL
				AND csend.`EndPeriod` IS NOT NULL
				AND csend.`StartPeriod` >= csend.`EndPeriod`)
			AND CASE
				WHEN (p.`ChronosStratEndID` IS NOT NULL) THEN least(CAST(cs.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(cs.`StartUncertainty`, 0), CAST(csend.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(csend.`StartUncertainty`, 0))
				ELSE CAST(cs.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(cs.`StartUncertainty`, 0)
			END <= 2000.0
			AND CASE
				WHEN (p.`ChronosStratEndID` IS NOT NULL) THEN greatest(CAST(cs.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(cs.`EndUncertainty`, 0), CAST(csend.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(csend.`EndUncertainty`, 0))
				ELSE CAST(cs.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(cs.`EndUncertainty`, 0)
			END >= 2.0) AS unioned
	GROUP BY
		unioned.coid) AS agg_subq ON
	collectionobject.`CollectionObjectID` = agg_subq.coid
LEFT OUTER JOIN absoluteage AS absoluteage_1 ON
	collectionobject.`CollectionObjectID` = absoluteage_1.`CollectionObjectID`
LEFT OUTER JOIN relativeage AS relativeage_1 ON
	collectionobject.`CollectionObjectID` = relativeage_1.`CollectionObjectID`
LEFT OUTER JOIN geologictimeperiod AS geologictimeperiod_1 ON
	geologictimeperiod_1.`GeologicTimePeriodID` = relativeage_1.`AgeNameID`
LEFT OUTER JOIN geologictimeperiod AS geologictimeperiod_2 ON
	geologictimeperiod_2.`GeologicTimePeriodID` = relativeage_1.`AgeNameEndID`
LEFT OUTER JOIN paleocontext AS paleocontext_1 ON
	paleocontext_1.`PaleoContextID` = collectionobject.`PaleoContextID`
LEFT OUTER JOIN geologictimeperiod AS geologictimeperiod_3 ON
	geologictimeperiod_3.`GeologicTimePeriodID` = paleocontext_1.`ChronosStratID`
LEFT OUTER JOIN geologictimeperiod AS geologictimeperiod_4 ON
	geologictimeperiod_4.`GeologicTimePeriodID` = paleocontext_1.`ChronosStratEndID`
LEFT OUTER JOIN collectingevent AS collectingevent_1 ON
	paleocontext_1.`PaleoContextID` = collectingevent_1.`PaleoContextID`
LEFT OUTER JOIN paleocontext AS paleocontext_2 ON
	paleocontext_2.`PaleoContextID` = collectingevent_1.`PaleoContextID`
LEFT OUTER JOIN geologictimeperiod AS geologictimeperiod_5 ON
	geologictimeperiod_5.`GeologicTimePeriodID` = paleocontext_2.`ChronosStratID`
LEFT OUTER JOIN geologictimeperiod AS geologictimeperiod_6 ON
	geologictimeperiod_6.`GeologicTimePeriodID` = paleocontext_2.`ChronosStratEndID`
WHERE
	collectionobject.`CollectionID` = 98304;

[acwhite211]

It seems that the behavior for querying by the time period name isn't working as expected now. Investigating...