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SimonGoringSimonGoring
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Updating queries to work with downloads.
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‎README.md‎

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@@ -6,12 +6,11 @@ This is a repository to store the functions used within the Neotoma Database for
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All individuals are welcome to contribute to this repository. Contributions are subject to the [Code of Conduct](https://github.com/neotomadb/Neotoma_SQL/blob/master/code_of_conduct.md) for this repository.
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* Steve Crawford - [Penn State](http://www.ems.psu.edu/node/147)
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* Simon Goring - [University of Wisconsin](http://goring.org)
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* Mike Stryker - [Penn State](http://www.ems.psu.edu/node/2892)
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* Jonathan Nelson - Penn State
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* Adrian George - University of Wisconsin
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* Jack Williams - University of Wisconsin
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* Steve Crawford - [Penn State](http://www.ems.psu.edu/node/147)
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* Simon Goring - [University of Wisconsin](http://goring.org)
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* Mike Stryker - [Penn State](http://www.ems.psu.edu/node/2892)
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* Anna George - University of Wisconsin
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* Jack Williams - University of Wisconsin
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## Description
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‎function/ap/collectionunitobject.sql‎

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CREATE OR REPLACE FUNCTION ap.collectionunitobject(_collectionunitid integer)
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RETURNS TABLE(collectionunitid integer, collectionunit jsonb)
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LANGUAGE sql
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AS $function$
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SELECT clu.collectionunitid,
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jsonb_build_object('site', (SELECT site FROM ap.siteobject(clu.siteid)),
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'collectionunit', json_build_array(jsonb_build_object('collectionunitid', clu.collectionunitid,
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'depositionalenvironment', dvt.depenvt,
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'collectionunit', clu.collunitname,
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'handle', clu.handle,
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'collunittype', cts.colltype,
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'colldate', clu.colldate,
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'waterdepth', clu.waterdepth,
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'notes', clu.notes,
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'collectiondevice', clu.colldevice,
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'location', clu.location,
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'gpslocation', json_build_object('latitude', clu.gpslatitude,
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'longitude', clu.gpslongitude,
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'gpsaltitude', clu.gpsaltitude,
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'gpserror', clu.gpserror),
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'collectors', json_agg(DISTINCT jsonb_build_object('contactid', cnt.contactid,
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'contactname', cnt.contactname,
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'familyname', cnt.familyname,
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'firstname', cnt.givennames,
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'initials', cnt.leadinginitials))))) AS collectionunit
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FROM
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ndb.collectionunits AS clu
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LEFT JOIN ndb.depenvttypes AS dvt ON dvt.depenvtid = clu.depenvtid
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LEFT JOIN ndb.collectiontypes AS cts ON cts.colltypeid = clu.colltypeid
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LEFT OUTER JOIN ndb.collectors AS col ON col.collectionunitid = clu.collectionunitid
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LEFT JOIN ndb.contacts AS cnt ON cnt.contactid = col.contactid
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WHERE clu.collectionunitid = _collectionunitid
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GROUP BY clu.collectionunitid, dvt.depenvt, cts.colltype;
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$function$

‎function/ap/datasetobject.sql‎

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CREATE OR REPLACE FUNCTION ap.datasetobject(_datasetid integer)
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RETURNS TABLE(datasetid integer, dataset jsonb)
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LANGUAGE sql
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AS $function$
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SELECT dts.datasetid,
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jsonb_build_object('datasetid', dts.datasetid,
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'datasettype', dst.datasettype,
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'datasetnotes', dts.notes,
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'database', cstdb.databasename,
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'doi', json_agg(DISTINCT doi.doi),
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'datasetpublications', json_agg(DISTINCT jsonb_build_object('publicationid', pub.publicationid,
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'citation', pub.citation)),
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'datasetpi', json_agg(DISTINCT jsonb_build_object('contactid', cnt.contactid,
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'contactname', cnt.contactname,
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'familyname', cnt.familyname,
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'firstname', cnt.givennames,
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'initials', cnt.leadinginitials)),
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'datasetprocessors', json_agg(DISTINCT jsonb_build_object('contactid', cntp.contactid,
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'contactname', cntp.contactname,
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'familyname', cntp.familyname,
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'firstname', cntp.givennames,
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'initials', cntp.leadinginitials)),
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'agerange', json_agg(DISTINCT jsonb_build_object('ageyoung', agerange.younger,
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'ageold', agerange.older,
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'units', agetypes.agetype)),
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'repository', json_agg(DISTINCT ri.repository))
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AS dataset
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FROM
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ndb.datasets AS dts
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LEFT OUTER JOIN ndb.datasettypes AS dst ON dst.datasettypeid = dts.datasettypeid
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LEFT OUTER JOIN ndb.datasetdoi AS doi ON dts.datasetid = doi.datasetid
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LEFT OUTER JOIN ndb.datasetdatabases AS dsdb ON dsdb.datasetid = dts.datasetid
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LEFT OUTER JOIN ndb.datasetpublications AS dtpub ON dtpub.datasetid = dts.datasetid
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LEFT OUTER JOIN ndb.publications AS pub ON pub.publicationid = dtpub.publicationid
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LEFT OUTER JOIN ndb.datasetpis AS dspi ON dspi.datasetid = dts.datasetid
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LEFT OUTER JOIN ndb.dataprocessors AS dspr ON dspr.datasetid = dts.datasetid
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LEFT OUTER JOIN ndb.contacts AS cntp ON cntp.contactid = dspi.contactid
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LEFT OUTER JOIN ndb.contacts AS cnt ON cnt.contactid = dspi.contactid
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LEFT OUTER JOIN ndb.dsageranges AS agerange ON dts.datasetid = agerange.datasetid
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LEFT OUTER JOIN ndb.agetypes AS agetypes ON agetypes.agetypeid = agerange.agetypeid
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LEFT OUTER JOIN ndb.constituentdatabases AS cstdb ON dsdb.databaseid = cstdb.databaseid
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LEFT OUTER JOIN ndb.repositoryspecimens AS rpspec ON rpspec.datasetid = dts.datasetid
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LEFT OUTER JOIN ndb.repositoryinstitutions AS ri ON ri.repositoryid = rpspec.repositoryid
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WHERE dts.datasetid = _datasetid
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GROUP BY
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dts.datasetid,
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dst.datasettype,
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dts.notes,
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cstdb.databasename
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$function$

‎function/ap/objectstructures/sitelinkobject.sql‎

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--
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DROP FUNCTION IF EXISTS ap.sitelink(_siteid integer);
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CREATE OR REPLACE FUNCTION ap.sitelink(_siteid integer)
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RETURNS TABLE(siteid integer, sitelink jsonb)
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LANGUAGE sql
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AS $function$
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SELECT sts.siteid,
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json_build_object('collectionunitid', clu.collectionunitid,
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'collectionunit', clu.collunitname,
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'handle', clu.handle,
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'collectionunittype', cts.colltype,
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'datasets', json_agg(json_build_object('datasetid', dts.datasetid,
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'datasettype', dst.datasettype))) AS collectionunit
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FROM
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ndb.datasets AS dts
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LEFT JOIN ndb.collectionunits AS clu ON clu.collectionunitid = dts.collectionunitid
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LEFT JOIN ndb.sites AS sts ON sts.siteid = clu.siteid
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LEFT JOIN ndb.datasettypes AS dst ON dst.datasettypeid = dts.datasettypeid
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LEFT OUTER JOIN ndb.collectiontypes as cts ON clu.colltypeid = cts.colltypeid
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WHERE sts.siteid = _siteid
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GROUP BY sts.siteid, clu.collectionunitid, cts.colltype
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$function$;
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DROP FUNCTION IF EXISTS ap.sitelink(_siteid integer[]);
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CREATE OR REPLACE FUNCTION ap.sitelink(_siteid integer[])
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RETURNS TABLE(siteid integer, sitelink jsonb)
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LANGUAGE sql
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AS $function$
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SELECT sts.siteid,
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json_build_object('collectionunitid', clu.collectionunitid,
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'collectionunit', clu.collunitname,
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'handle', clu.handle,
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'collectionunittype', cts.colltype,
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'datasets', json_agg(json_build_object('datasetid', dts.datasetid,
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'datasettype', dst.datasettype))) AS collectionunit
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FROM
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ndb.datasets AS dts
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LEFT JOIN ndb.collectionunits AS clu ON clu.collectionunitid = dts.collectionunitid
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LEFT JOIN ndb.sites AS sts ON sts.siteid = clu.siteid
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LEFT JOIN ndb.datasettypes AS dst ON dst.datasettypeid = dts.datasettypeid
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LEFT OUTER JOIN ndb.collectiontypes as cts ON clu.colltypeid = cts.colltypeid
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WHERE sts.siteid = ANY(_siteid)
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GROUP BY sts.siteid, clu.collectionunitid, cts.colltype
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$function$;

‎function/ap/sample.sql‎

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CREATE OR REPLACE FUNCTION ap.sample(_datasetid integer)
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RETURNS TABLE(datasetid integer, sample jsonb)
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LANGUAGE sql
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AS $function$
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SELECT
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ds.datasetid,
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jsonb_build_object('sampleid', dsd.sampleid,
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'keywords', array_agg(DISTINCT ky.keyword),
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'depth', anu.depth,
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'datum', jsonb_agg(DISTINCT jsonb_build_object('value', dt.value,
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'variablename', tx.taxonname,
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'taxonid', tx.taxonid,
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'taxongroup', txg.taxagroup,
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'ecologicalgroup', ecg.ecolgroupid,
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'element', ve.variableelement,
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'elementtype', vt.elementtype,
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'symmetry', vs.symmetry,
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'context', vc.variablecontext,
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'units', vru.variableunits)),
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'sampleanalyst', json_agg(DISTINCT jsonb_build_object('contactid', cnt.contactid,
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'contactname', cnt.contactname,
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'familyname', cnt.familyname,
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'firstname', cnt.givennames,
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'initials', cnt.leadinginitials)),
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'ages', jsonb_agg(
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DISTINCT jsonb_build_object('chronologyid', ch.chronologyid,
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'chronologyname', ch.chronologyname,
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'agetype', cht.agetype,
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'age', sma.age,
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'ageyounger', sma.ageyounger,
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'ageolder', sma.ageolder))) AS sampledata
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FROM
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ndb.datasets AS ds
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LEFT OUTER JOIN ndb.dsdatasample AS dsd ON dsd.datasetid = ds.datasetid
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LEFT OUTER JOIN ndb.data AS dt ON dt.dataid = dsd.dataid
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LEFT OUTER JOIN ndb.variables AS var ON var.variableid = dsd.variableid
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LEFT OUTER JOIN ndb.taxa AS tx ON tx.taxonid = var.taxonid
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LEFT OUTER JOIN ndb.taxagrouptypes AS txg ON txg.taxagroupid = tx.taxagroupid
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LEFT OUTER JOIN ndb.ecolgroups AS ecg ON ecg.taxonid = tx.taxonid
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LEFT OUTER JOIN ndb.variableunits AS vru ON vru.variableunitsid = var.variableunitsid
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LEFT OUTER JOIN ndb.samples AS smp ON smp.sampleid = dsd.sampleid
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LEFT OUTER JOIN ndb.sampleanalysts AS san ON san.sampleid = smp.sampleid
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LEFT JOIN ndb.contacts AS cnt ON cnt.contactid = san.contactid
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LEFT OUTER JOIN ndb.analysisunits AS anu ON anu.analysisunitid = smp.analysisunitid
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LEFT JOIN ndb.variableelements AS ve ON ve.variableelementid = var.variableelementid
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LEFT OUTER JOIN ndb.elementsymmetries AS vs ON vs.symmetryid = ve.symmetryid
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LEFT OUTER JOIN ndb.elementtypes AS vt ON vt.elementtypeid = ve.elementtypeid
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LEFT JOIN ndb.variablecontexts AS vc ON vc.variablecontextid = var.variablecontextid
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LEFT OUTER JOIN ndb.sampleages AS sma ON sma.sampleid = smp.sampleid
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LEFT OUTER JOIN ndb.chronologies AS ch ON sma.chronologyid = ch.chronologyid
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LEFT OUTER JOIN ndb.agetypes AS cht ON cht.agetypeid = ch.agetypeid
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LEFT OUTER JOIN ndb.samplekeywords AS smpky ON smpky.sampleid = smp.sampleid
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LEFT OUTER JOIN ndb.keywords AS ky ON ky.keywordid = smpky.keywordid
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WHERE
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ds.datasetid = _datasetid
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GROUP BY ds.datasetid,
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dsd.sampleid,
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anu.depth,
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anu.thickness
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ORDER BY anu.depth ASC;
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$function$

‎function/ap/sitelink.sql‎

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CREATE OR REPLACE FUNCTION ap.sitelink(_siteid integer)
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RETURNS TABLE(siteid integer, sitelink jsonb)
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LANGUAGE sql
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AS $function$
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SELECT sts.siteid,
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jsonb_build_object('collectionunitid', clu.collectionunitid,
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'collectionunit', clu.collunitname,
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'handle', clu.handle,
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'collectionunittype', cts.colltype,
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'datasets', json_agg(json_build_object('datasetid', dts.datasetid,
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'datasettype', dst.datasettype))) AS collectionunit
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FROM
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ndb.datasets AS dts
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LEFT JOIN ndb.collectionunits AS clu ON clu.collectionunitid = dts.collectionunitid
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LEFT JOIN ndb.sites AS sts ON sts.siteid = clu.siteid
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LEFT JOIN ndb.datasettypes AS dst ON dst.datasettypeid = dts.datasettypeid
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LEFT OUTER JOIN ndb.collectiontypes as cts ON clu.colltypeid = cts.colltypeid
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WHERE sts.siteid = _siteid
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GROUP BY sts.siteid, clu.collectionunitid, cts.colltype
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$function$

‎function/ap/siteobject.sql‎

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CREATE OR REPLACE FUNCTION ap.siteobject(_siteid integer)
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RETURNS TABLE(siteid integer, site jsonb)
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LANGUAGE sql
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AS $function$
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SELECT sts.siteid,
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jsonb_build_object( 'siteid', sts.siteid,
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'sitename', sts.sitename,
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'sitedescription', sts.sitedescription,
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'geography', ST_AsGeoJSON(sts.geog,5,2),
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'area', sts.area,
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'altitude', sts.altitude,
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'notes', sts.notes,
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'geopolitical', gpn.names) AS site
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FROM
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ndb.sites AS sts
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LEFT JOIN ap.geopolnames AS gpn ON gpn.siteid = sts.siteid
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WHERE sts.siteid = _siteid
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GROUP BY sts.siteid, sts.sitename, sts.sitedescription, ST_AsGeoJSON(sts.geog,5,2),
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sts.area, sts.altitude, sts.notes, gpn.names;
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$function$;

‎function/ap/updatequery.sql‎

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CREATE OR REPLACE FUNCTION ap.updatequery()
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RETURNS trigger
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LANGUAGE plpgsql
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AS $function$
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BEGIN
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REFRESH MATERIALIZED VIEW CONCURRENTLY ap.querytable;
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RETURN NULL;
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END $function$

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