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‎sphinx/software_desc/extended_age_query.md

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@@ -49,3 +49,247 @@ The meta age range for each collection object should appear in the age column of
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The "Any" age query bug is being push to a later issue. For now, do a Age Range query from "13800" to "0" to get all COs with age data (query all of time, the age of the universe 😀
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## Example Queries Generated by Extended Age QB
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Here is a compiled SQLAlchemy query that get generated for a simple CollectionObject Age query:
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```sql
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SELECT
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collectionobject.`CollectionObjectID`,
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concat_ws(' - ',
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ifnull(regexp_replace(CAST(agg_subq.max_start_period AS CHAR), '\\.(0+)$', ''), ''),
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ifnull(regexp_replace(CAST(agg_subq.min_end_period AS CHAR), '\\.(0+)$', ''), '')) AS age
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FROM
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collectionobject
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INNER JOIN (
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SELECT
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unioned.coid AS coid,
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min(unioned.endperiod) AS min_end_period,
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max(unioned.startperiod) AS max_start_period
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FROM
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(
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SELECT
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absoluteage.`CollectionObjectID` AS coid,
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CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) - coalesce(absoluteage.`AgeUncertainty`, 0) AS startperiod,
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CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) + coalesce(absoluteage.`AgeUncertainty`, 0) AS endperiod
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FROM
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absoluteage
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WHERE
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CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) - coalesce(absoluteage.`AgeUncertainty`, 0) <= 2000.0
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AND CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) + coalesce(absoluteage.`AgeUncertainty`, 0) >= 2.0
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UNION ALL
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SELECT
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r.`CollectionObjectID` AS coid,
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CASE
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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))
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ELSE CAST(a.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(a.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0)
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END AS startperiod,
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CASE
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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))
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ELSE (CAST(a.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(a.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0)
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END AS endperiod
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FROM
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relativeage AS r
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INNER JOIN geologictimeperiod AS a ON
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r.`AgeNameID` = a.`GeologicTimePeriodID`
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LEFT OUTER JOIN geologictimeperiod AS aend ON
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r.`AgeNameEndID` = aend.`GeologicTimePeriodID`
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WHERE
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a.`StartPeriod` IS NOT NULL
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AND a.`EndPeriod` IS NOT NULL
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AND a.`StartPeriod` >= a.`EndPeriod`
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AND (r.`AgeNameEndID` IS NULL
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OR aend.`StartPeriod` IS NOT NULL
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AND aend.`EndPeriod` IS NOT NULL
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AND aend.`StartPeriod` >= aend.`EndPeriod`)
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AND CASE
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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))
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ELSE CAST(a.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(a.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0)
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END <= 2000.0
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AND CASE
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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))
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ELSE (CAST(a.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(a.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0)
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END >= 2.0
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UNION ALL
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SELECT
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DISTINCT c.`CollectionObjectID` AS coid,
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CASE
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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))
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ELSE CAST(cs.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(cs.`StartUncertainty`, 0)
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END AS startperiod,
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CASE
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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))
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ELSE CAST(cs.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(cs.`EndUncertainty`, 0)
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END AS endperiod
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FROM
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collectionobject AS c
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LEFT OUTER JOIN collectingevent AS ce ON
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c.`CollectingEventID` = ce.`CollectingEventID`
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LEFT OUTER JOIN locality AS l ON
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ce.`LocalityID` = l.`LocalityID`
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LEFT OUTER JOIN paleocontext AS p ON
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c.`PaleoContextID` = p.`PaleoContextID`
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OR ce.`PaleoContextID` = p.`PaleoContextID`
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OR l.`PaleoContextID` = p.`PaleoContextID`
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LEFT OUTER JOIN geologictimeperiod AS cs ON
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p.`ChronosStratID` = cs.`GeologicTimePeriodID`
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LEFT OUTER JOIN geologictimeperiod AS csend ON
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p.`ChronosStratEndID` = csend.`GeologicTimePeriodID`
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WHERE
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p.`PaleoContextID` IS NOT NULL
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AND cs.`StartPeriod` IS NOT NULL
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AND cs.`EndPeriod` IS NOT NULL
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AND cs.`StartPeriod` >= cs.`EndPeriod`
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AND (p.`ChronosStratEndID` IS NULL
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OR csend.`StartPeriod` IS NOT NULL
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AND csend.`EndPeriod` IS NOT NULL
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AND csend.`StartPeriod` >= csend.`EndPeriod`)
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AND CASE
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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))
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ELSE CAST(cs.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(cs.`StartUncertainty`, 0)
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END <= 2000.0
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AND CASE
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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))
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ELSE CAST(cs.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(cs.`EndUncertainty`, 0)
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END >= 2.0) AS unioned
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GROUP BY
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unioned.coid) AS agg_subq ON
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collectionobject.`CollectionObjectID` = agg_subq.coid
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WHERE
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collectionobject.`CollectionID` = 98304;
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```
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Here is another example of a compiled SQLAlchemy query that gets generated:
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```sql
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SELECT
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collectionobject.`CollectionObjectID`,
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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,
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absoluteage_1.`AbsoluteAge`,
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geologictimeperiod_1.`Name`,
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geologictimeperiod_2.`Name`,
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geologictimeperiod_3.`Name`,
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geologictimeperiod_4.`Name`,
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geologictimeperiod_5.`Name`,
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geologictimeperiod_6.`Name`
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FROM
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collectionobject
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INNER JOIN (
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SELECT
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unioned.coid AS coid,
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min(unioned.endperiod) AS min_end_period,
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max(unioned.startperiod) AS max_start_period
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FROM
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(
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SELECT
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absoluteage.`CollectionObjectID` AS coid,
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CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) - coalesce(absoluteage.`AgeUncertainty`, 0) AS startperiod,
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CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) + coalesce(absoluteage.`AgeUncertainty`, 0) AS endperiod
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FROM
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absoluteage
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WHERE
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CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) - coalesce(absoluteage.`AgeUncertainty`, 0) <= 2000.0
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AND CAST(absoluteage.`AbsoluteAge` AS DECIMAL(10, 6)) + coalesce(absoluteage.`AgeUncertainty`, 0) >= 2.0
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UNION ALL
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SELECT
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r.`CollectionObjectID` AS coid,
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CASE
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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))
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ELSE CAST(a.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(a.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0)
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END AS startperiod,
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CASE
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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))
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ELSE (CAST(a.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(a.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0)
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END AS endperiod
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FROM
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relativeage AS r
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INNER JOIN geologictimeperiod AS a ON
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r.`AgeNameID` = a.`GeologicTimePeriodID`
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LEFT OUTER JOIN geologictimeperiod AS aend ON
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r.`AgeNameEndID` = aend.`GeologicTimePeriodID`
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WHERE
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a.`StartPeriod` IS NOT NULL
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AND a.`EndPeriod` IS NOT NULL
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AND a.`StartPeriod` >= a.`EndPeriod`
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AND (r.`AgeNameEndID` IS NULL
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OR aend.`StartPeriod` IS NOT NULL
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AND aend.`EndPeriod` IS NOT NULL
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AND aend.`StartPeriod` >= aend.`EndPeriod`)
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AND CASE
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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))
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ELSE CAST(a.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(a.`StartUncertainty`, 0) + coalesce(r.`AgeUncertainty`, 0)
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END <= 2000.0
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AND CASE
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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))
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ELSE (CAST(a.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(a.`EndUncertainty`, 0)) - coalesce(r.`AgeUncertainty`, 0)
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END >= 2.0
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UNION ALL
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SELECT
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DISTINCT c.`CollectionObjectID` AS coid,
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CASE
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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))
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ELSE CAST(cs.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(cs.`StartUncertainty`, 0)
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END AS startperiod,
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CASE
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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))
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ELSE CAST(cs.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(cs.`EndUncertainty`, 0)
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END AS endperiod
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FROM
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collectionobject AS c
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LEFT OUTER JOIN collectingevent AS ce ON
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c.`CollectingEventID` = ce.`CollectingEventID`
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LEFT OUTER JOIN locality AS l ON
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ce.`LocalityID` = l.`LocalityID`
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LEFT OUTER JOIN paleocontext AS p ON
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c.`PaleoContextID` = p.`PaleoContextID`
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OR ce.`PaleoContextID` = p.`PaleoContextID`
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OR l.`PaleoContextID` = p.`PaleoContextID`
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LEFT OUTER JOIN geologictimeperiod AS cs ON
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p.`ChronosStratID` = cs.`GeologicTimePeriodID`
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LEFT OUTER JOIN geologictimeperiod AS csend ON
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p.`ChronosStratEndID` = csend.`GeologicTimePeriodID`
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WHERE
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p.`PaleoContextID` IS NOT NULL
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AND cs.`StartPeriod` IS NOT NULL
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AND cs.`EndPeriod` IS NOT NULL
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AND cs.`StartPeriod` >= cs.`EndPeriod`
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AND (p.`ChronosStratEndID` IS NULL
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OR csend.`StartPeriod` IS NOT NULL
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AND csend.`EndPeriod` IS NOT NULL
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AND csend.`StartPeriod` >= csend.`EndPeriod`)
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AND CASE
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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))
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ELSE CAST(cs.`StartPeriod` AS DECIMAL(10, 6)) + coalesce(cs.`StartUncertainty`, 0)
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END <= 2000.0
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AND CASE
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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))
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ELSE CAST(cs.`EndPeriod` AS DECIMAL(10, 6)) - coalesce(cs.`EndUncertainty`, 0)
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END >= 2.0) AS unioned
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GROUP BY
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unioned.coid) AS agg_subq ON
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collectionobject.`CollectionObjectID` = agg_subq.coid
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LEFT OUTER JOIN absoluteage AS absoluteage_1 ON
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collectionobject.`CollectionObjectID` = absoluteage_1.`CollectionObjectID`
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LEFT OUTER JOIN relativeage AS relativeage_1 ON
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collectionobject.`CollectionObjectID` = relativeage_1.`CollectionObjectID`
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LEFT OUTER JOIN geologictimeperiod AS geologictimeperiod_1 ON
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geologictimeperiod_1.`GeologicTimePeriodID` = relativeage_1.`AgeNameID`
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LEFT OUTER JOIN geologictimeperiod AS geologictimeperiod_2 ON
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geologictimeperiod_2.`GeologicTimePeriodID` = relativeage_1.`AgeNameEndID`
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LEFT OUTER JOIN paleocontext AS paleocontext_1 ON
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paleocontext_1.`PaleoContextID` = collectionobject.`PaleoContextID`
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LEFT OUTER JOIN geologictimeperiod AS geologictimeperiod_3 ON
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geologictimeperiod_3.`GeologicTimePeriodID` = paleocontext_1.`ChronosStratID`
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LEFT OUTER JOIN geologictimeperiod AS geologictimeperiod_4 ON
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geologictimeperiod_4.`GeologicTimePeriodID` = paleocontext_1.`ChronosStratEndID`
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LEFT OUTER JOIN collectingevent AS collectingevent_1 ON
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paleocontext_1.`PaleoContextID` = collectingevent_1.`PaleoContextID`
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LEFT OUTER JOIN paleocontext AS paleocontext_2 ON
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paleocontext_2.`PaleoContextID` = collectingevent_1.`PaleoContextID`
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LEFT OUTER JOIN geologictimeperiod AS geologictimeperiod_5 ON
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geologictimeperiod_5.`GeologicTimePeriodID` = paleocontext_2.`ChronosStratID`
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LEFT OUTER JOIN geologictimeperiod AS geologictimeperiod_6 ON
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geologictimeperiod_6.`GeologicTimePeriodID` = paleocontext_2.`ChronosStratEndID`
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WHERE
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collectionobject.`CollectionID` = 98304;
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```

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