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SimonGoringSimonGoring
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Updating work in progress. A number of SQL query changes.
1 parent 44ad1c7 commit 864a9d3

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-73
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‎function/ap/gettaxaindatasets.sql‎

Lines changed: 17 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -1,15 +1,18 @@
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CREATE OR REPLACE FUNCTION ap.gettaxaindatasets()
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RETURNS TABLE(taxonid integer,
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taxonname character varying,
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taxagroupid character varying,
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datasettypeid integer)
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LANGUAGE sql
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CREATE OR REPLACE FUNCTION ap.gettaxaindatasets()
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RETURNS TABLE(taxonid integer,
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taxonname character varying,
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taxagroupid character varying,
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datasettypeid jsonb)
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LANGUAGE sql
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AS $function$
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SELECT t.taxonid, t.taxonname, t.taxagroupid, dtgt.datasettypeid
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FROM ndb.taxa AS t LEFT JOIN
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ndb.datasettaxagrouptypes AS dtgt ON t.taxagroupid = dtgt.taxagroupid INNER JOIN
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ndb.variables AS v ON t.taxonid = v.taxonid
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WHERE t.valid = True
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GROUP BY t.taxonid, t.taxonname, dtgt.datasettypeid, t.taxagroupid
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ORDER BY t.taxonname, dtgt.datasettypeid
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$function$
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SELECT t.taxonid,
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t.taxonname,
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t.taxagroupid,
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dtgt.datasettypeid
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FROM ndb.taxa AS t
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LEFT JOIN ndb.datasettaxagrouptypes AS dtgt ON t.taxagroupid = dtgt.taxagroupid
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INNER JOIN ndb.variables AS v ON t.taxonid = v.taxonid
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WHERE t.valid = True
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GROUP BY t.taxonid, t.taxonname, dtgt.datasettypeid, t.taxagroupid
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ORDER BY t.taxonname, dtgt.datasettypeid
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$function$

‎function/doi/01_datasetinfo.sql‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ siteobj AS (
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FROM
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ap.siteobject((SELECT array_agg(siteid) FROM siteid))
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)
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SELECT dts.datasetid,
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SELECT DISTINCT dts.datasetid,
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sts.site ||
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jsonb_build_object('collectionunit', json_build_object('collectionunitid', clu.collectionunitid,
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'depositionalenvironment', dvt.depenvt,
@@ -73,7 +73,7 @@ siteobj AS (
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FROM
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ap.siteobject((SELECT siteid FROM siteid))
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)
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SELECT dts.datasetid,
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SELECT DISTINCT dts.datasetid,
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sts.site ||
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jsonb_build_object('collectionunit', json_build_object('collectionunitid', clu.collectionunitid,
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'depositionalenvironment', dvt.depenvt,

‎function/doi/doifreeze.sql‎

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@@ -21,5 +21,4 @@ FROM
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datameta AS dt
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JOIN chronmeta AS chr ON dt.datasetid = chr.datasetid
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JOIN ids AS ids ON ids.dsid = dt.datasetid
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$function$

‎function/geo/sitegeospatial.sql‎

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@@ -0,0 +1,26 @@
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CREATE INDEX gadm_geom_idx
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ON gadm404
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USING GIST (geom);
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CREATE MATERIALIZED VIEW IF NOT EXISTS public.geositename AS
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SELECT st.siteid,
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st.sitename,
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uid,
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name_0,
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name_1,
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name_2,
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name_3,
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name_4,
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concat_ws(' ', name_0, varname_0, name_1, varname_1,
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nl_name_1, name_2, varname_2, nl_name_2, name_3,
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varname_3, nl_name_3, name_4, varname_4, name_5) AS names,
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array_agg(ds.datasetid)
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FROM ndb.sites AS st
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LEFT OUTER JOIN gadm404 ON ST_Intersects(st.geog::geometry, gadm404.geom)
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LEFT JOIN ndb.collectionunits AS cu ON cu.siteid = st.siteid
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LEFT JOIN ndb.datasets AS ds on ds.collectionunitid = cu.collectionunitid
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GROUP BY st.siteid, st.sitename, uid, name_0, name_1, name_2, name_3, name_4, name_5,
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varname_0, varname_1, varname_2, varname_3, varname_4,
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nl_name_1, nl_name_2, nl_name_3;
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CREATE INDEX pglocation_idx ON geositename USING GIN (to_tsvector('english', names));

‎function/ndb/datasetconstitdb.sql‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -9,4 +9,4 @@ AS $function$
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WHERE EXTRACT(year from AGE(NOW(), dss.submissiondate))*12 +
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EXTRACT(month from AGE(NOW(), dss.submissiondate)) BETWEEN startperiod and endperiod
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GROUP BY cdb.databasename
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$function$
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$function$;

‎function/ndb/datasetcontribs.sql‎

Lines changed: 12 additions & 0 deletions
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@@ -0,0 +1,12 @@
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CREATE OR REPLACE FUNCTION ndb.datasetcontribs(startperiod integer DEFAULT 0, endperiod integer DEFAULT 1)
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RETURNS TABLE(databasename character varying, counts bigint)
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LANGUAGE sql
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AS $function$
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SELECT ct.contactname, count(*)
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FROM ndb.datasets AS ds
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JOIN ndb.datasetsubmissions AS dss ON dss.datasetid = ds.datasetid
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JOIN ndb.contacts AS ct ON ct.contactid = dss.contactid
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WHERE EXTRACT(year from AGE(NOW(), dss.submissiondate))*12 +
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EXTRACT(month from AGE(NOW(), dss.submissiondate)) BETWEEN startperiod and endperiod
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GROUP BY ct.contactname
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$function$;

‎function/ndb/datasettypecontrib.sql‎

Lines changed: 1 addition & 1 deletion
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@@ -9,4 +9,4 @@ AS $function$
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WHERE EXTRACT(year from AGE(NOW(), dss.submissiondate))*12 +
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EXTRACT(month from AGE(NOW(), dss.submissiondate)) BETWEEN startperiod and endperiod
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GROUP BY dst.datasettype
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$function$
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$function$;

‎function/ts/insertsteward.sql‎

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@@ -14,3 +14,4 @@ AS $function$
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values ((select stewardid from ti.stewards AS stw where (stw.contactid = _contactid)), _databaseid)
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RETURNING stewardid
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$function$
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‎function/working/dataupload.sql‎

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CREATE OR REPLACE FUNCTION ts.upload(uploadobject jsonb)
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RETURNS INTEGER
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LANGUAGE pgsql
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AS $function$
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/* YAML shows that we often first insert variables */
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siteid := (SELECT ts.insertsite(_sitename := (SELECT uploadobject #>> '{data,0,site,sitename}'),
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_altitude := (SELECT uploadobject #> '{data,0,site,altitude}'),
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_area := (SELECT uploadobject #> '{data,0,site,area}'),
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_descript := (SELECT uploadobject #> '{data,0,site,sitedescription}'),
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_notes := (SELECT uploadobject #> '{data,0,site,notes}')))
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/* SELECT ts.insertcontact() */
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/* YAML shows insert lake parameters */
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/* YAML shows insert sitegeopol */
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collinutid := SELECT ts.insertcollectionunit(_handle := (SELECT uploadobject #>> '{data,0,site,collectionunit, handle}'),
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_siteid := siteid,
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_colltypeid integer DEFAULT NULL::integer,
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_depenvtid integer DEFAULT NULL::integer,
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_collunitname character varying DEFAULT NULL::character varying,
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_colldate date DEFAULT NULL::date,
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_colldevice := (SELECT uploadobject #>> '{data,0,site,collectionunit, collectiondevice}'),
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_gpslatitude double precision DEFAULT NULL::double precision,
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_gpslongitude double precision DEFAULT NULL::double precision,
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_gpsaltitude double precision DEFAULT NULL::double precision,
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_gpserror double precision DEFAULT NULL::double precision,
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_waterdepth := (SELECT uploadobject #>> '{data,0,site,collectionunit, waterdepth}'),
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_watertabledepth double precision DEFAULT NULL::double precision,
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_substrateid integer DEFAULT NULL::integer,
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_slopeaspect integer DEFAULT NULL::integer,
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_slopeangle integer DEFAULT NULL::integer,
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_location := (SELECT uploadobject #>> '{data,0,site,collectionunit, location}'),
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_notes := (SELECT uploadobject #>> '{data,0,site,collectionunit, notes}'))
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/* Have to do this for the set of collectors */
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SELECT ts.insertcollector(_collunitid := collunitid,
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_contactid integer,
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_collectororder integer)
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/* Add the set of analysis units */
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/* Add the set of chronologies */
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/* With the chronology id, add the chron controls */
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/* Add the dataset info */
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/* Link to the dataset database */
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/* Add the dataset PI info */
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/* Add the data processor info */
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/* Add dataset publication information */
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/* Add dataset repository information */
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/* Add any (dataset level) synonymys */
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/* Add samples */
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/* Add sample analyst */
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/* add sample age */
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/* Insert data */
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/* Insert dataset submission */
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$function$

‎function/working/tesingapi.sql‎

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1+
SELECT '{"status":"success","data":[{"site":{"area":null,"notes":null,"siteid":970,"altitude":690,"sitename":"Hail Lake","geography":"{\"type\":\"Point\",\"crs\":{\"type\":\"name\",\"properties\":{\"name\":\"EPSG:4326\"}},\"coordinates\":[-129.01667,60.03333]}","geopolitical":["Canada","Yukon Territory"],"collectionunit":{"notes":null,"handle":"HAIL","colldate":null,"location":null,"waterdepth":7.39,"gpslocation":{"gpserror":null,"latitude":null,"longitude":null,"gpsaltitude":null},"collunittype":"Core","collectionunit":null,"collectiondevice":"Wright square-rod piston corer (5cm)","collectionunitid":969,"depositionalenvironment":"Glacial Origin Lake","dataset":{"doi":["10.21233/n31d9w","10.21233/n3f91j"],"agerange":[{"units":null,"ageold":null,"ageyoung":null}],"database":"North American Pollen Database","datasetid":1001,"datasetpi":[{"initials":"L.C.","contactid":129,"firstname":"Les C.","familyname":"Cwynar","contactname":"Cwynar, Les C."}],"datasetname":null,"datasettype":"pollen","datasetnotes":null,"samples":[{"ages":[{"age":null,"agetype":null,"ageolder":null,"ageyounger":null,"chronologyid":null,"chronologyname":null}],"igsn":null,"datum":[{"units":null,"value":null,"context":null,"element":null,"taxonid":null,"symmetry":null,"taxongroup":null,"elementtype":null,"variablename":null,"ecologicalgroup":null}],"depth":null,"sampleid":null,"thickness":null,"samplename":null,"sampleanalyst":[{"initials":null,"contactid":null,"firstname":null,"familyname":null,"contactname":null}],"analysisunitid":null,"analysisunitname":null}]},"chronologies":[{"chronology":{"chronology":{"notes":"Chron excludes three oldest ages and the reversed level at 457 cm","contact":[{"contactid":971,"givenname":"Mathieu L.","familyname":"Duvall","contactname":"Duvall, Mathieu L.","leadinginitial":"M.L."}],"agemodel":"linear interpolation","agerange":{"ageboundolder":9950,"ageboundyounger":60},"isdefault":true,"dateprepared":"1998-03-06","modelagetype":"Radiocarbon years BP","chronologyname":"PALE 1"},"chronologyid":485,"chroncontrols":[{"depth":0,"geochron":{"agetype":null,"delta13c":null,"delta15n":null,"infinite":null,"percentc":null,"percentn":null,"labnumber":null,"reservoir":null,"geochronid":null,"geochronage":null,"geochrontype":null,"geochronnotes":null,"percentcollagen":null,"radiocarbonmethod":null,"geochronerrorolder":null,"geochronerroryounger":null,"geochronmaterialdated":null},"thickness":null,"agelimitolder":0,"chroncontrolid":2818,"agelimityounger":0,"chroncontrolage":0,"chroncontroltype":"Core top"},{"depth":128,"geochron":{"agetype":"Radiocarbon years BP","delta13c":null,"delta15n":null,"infinite":false,"percentc":null,"percentn":null,"labnumber":"TO-1152","reservoir":null,"geochronid":1648,"geochronage":2870,"geochrontype":"Carbon-14","geochronnotes":"asal three dates >30,000 rejected. Probably redeposited wood.","percentcollagen":null,"radiocarbonmethod":"accelerator mass spectrometry","geochronerrorolder":50,"geochronerroryounger":50,"geochronmaterialdated":"Carbonized twigs and wood frag"},"thickness":4,"agelimitolder":2920,"chroncontrolid":2819,"agelimityounger":2820,"chroncontrolage":2870,"chroncontroltype":"Radiocarbon"},{"depth":204,"geochron":{"agetype":"Radiocarbon years BP","delta13c":null,"delta15n":null,"infinite":false,"percentc":null,"percentn":null,"labnumber":"TO-1153","reservoir":null,"geochronid":1649,"geochronage":4840,"geochrontype":"Carbon-14","geochronnotes":null,"percentcollagen":null,"radiocarbonmethod":"accelerator mass spectrometry","geochronerrorolder":50,"geochronerroryounger":50,"geochronmaterialdated":"Carbonized spruce needle, inse"},"thickness":4,"agelimitolder":4930,"chroncontrolid":2820,"agelimityounger":4830,"chroncontrolage":4840,"chroncontroltype":"Radiocarbon"},{"depth":236,"geochron":{"agetype":"Radiocarbon years BP","delta13c":null,"delta15n":null,"infinite":false,"percentc":null,"percentn":null,"labnumber":"TO-1154","reservoir":null,"geochronid":1650,"geochronage":5860,"geochrontype":"Carbon-14","geochronnotes":null,"percentcollagen":null,"radiocarbonmethod":"accelerator mass spectrometry","geochronerrorolder":410,"geochronerroryounger":410,"geochronmaterialdated":"Carbonized spruce needle, inse"},"thickness":4,"agelimitolder":6270,"chroncontrolid":2821,"agelimityounger":5450,"chroncontrolage":5860,"chroncontroltype":"Radiocarbon"},{"depth":358,"geochron":{"agetype":"Radiocarbon years BP","delta13c":null,"delta15n":null,"infinite":false,"percentc":null,"percentn":null,"labnumber":"TO-1155","reservoir":null,"geochronid":1651,"geochronage":8440,"geochrontype":"Carbon-14","geochronnotes":null,"percentcollagen":null,"radiocarbonmethod":"accelerator mass spectrometry","geochronerrorolder":70,"geochronerroryounger":70,"geochronmaterialdated":"Spruce needles and wood frags"},"thickness":5,"agelimitolder":8510,"chroncontrolid":2822,"agelimityounger":8370,"chroncontrolage":8440,"chroncontroltype":"Radiocarbon"},{"depth":398,"geochron":{"agetype":"Radiocarbon years BP","delta13c":null,"delta15n":null,"infinite":false,"percentc":null,"percentn":null,"labnumber":"TO-1156","reservoir":null,"geochronid":1652,"geochronage":8820,"geochrontype":"Carbon-14","geochronnotes":null,"percentcollagen":null,"radiocarbonmethod":"accelerator mass spectrometry","geochronerrorolder":70,"geochronerroryounger":70,"geochronmaterialdated":"Spruce needles and wood frags"},"thickness":4,"agelimitolder":8890,"chroncontrolid":2823,"agelimityounger":8750,"chroncontrolage":8820,"chroncontroltype":"Radiocarbon"},{"depth":423,"geochron":{"agetype":"Radiocarbon years BP","delta13c":null,"delta15n":null,"infinite":false,"percentc":null,"percentn":null,"labnumber":"TO-1157","reservoir":null,"geochronid":1653,"geochronage":8930,"geochrontype":"Carbon-14","geochronnotes":null,"percentcollagen":null,"radiocarbonmethod":"accelerator mass spectrometry","geochronerrorolder":70,"geochronerroryounger":70,"geochronmaterialdated":"Spruce needles and wood frags"},"thickness":10,"agelimitolder":9000,"chroncontrolid":2824,"agelimityounger":8860,"chroncontrolage":8930,"chroncontroltype":"Radiocarbon"},{"depth":482,"geochron":{"agetype":"Radiocarbon years BP","delta13c":null,"delta15n":null,"infinite":false,"percentc":null,"percentn":null,"labnumber":"TO-1159","reservoir":null,"geochronid":1655,"geochronage":9500,"geochrontype":"Carbon-14","geochronnotes":null,"percentcollagen":null,"radiocarbonmethod":"accelerator mass spectrometry","geochronerrorolder":80,"geochronerroryounger":80,"geochronmaterialdated":"Monocot frags"},"thickness":4,"agelimitolder":9580,"chroncontrolid":2825,"agelimityounger":9420,"chroncontrolage":9500,"chroncontroltype":"Radiocarbon"}]}}],"defaultchronology":485},"sitedescription":"Small lake. Surrounding vegetation: Picea mariana, P. glauca, Pinus contorta."}}],"message":"Retrieved all tables" }'::jsonb #>> '{data,0,site,sitename}';

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