909 |
909 |
CREATE TABLE analytical_aggregate AS SELECT * FROM analytical_aggregate_view LIMIT 0;
|
910 |
910 |
|
911 |
911 |
ALTER TABLE analytical_aggregate ALTER COLUMN "institutionCode" SET NOT NULL;
|
912 |
|
ALTER TABLE analytical_aggregate ALTER COLUMN "plotName" SET NOT NULL;
|
|
912 |
ALTER TABLE analytical_aggregate ALTER COLUMN "locationName" SET NOT NULL;
|
913 |
913 |
|
914 |
|
CREATE INDEX ON analytical_aggregate ("institutionCode", "plotName", "dateCollected" );
|
|
914 |
CREATE INDEX ON analytical_aggregate ("institutionCode", "locationName", "dateCollected" );
|
915 |
915 |
$$;
|
916 |
916 |
|
917 |
917 |
|
... | ... | |
926 |
926 |
CREATE TABLE analytical_stem AS SELECT * FROM analytical_stem_view LIMIT 0;
|
927 |
927 |
|
928 |
928 |
ALTER TABLE analytical_stem ALTER COLUMN "institutionCode" SET NOT NULL;
|
929 |
|
ALTER TABLE analytical_stem ALTER COLUMN "plotName" SET NOT NULL;
|
|
929 |
ALTER TABLE analytical_stem ALTER COLUMN "locationName" SET NOT NULL;
|
930 |
930 |
|
931 |
931 |
CREATE INDEX ON analytical_stem ("institutionCode", "occurrenceID" );
|
932 |
932 |
CREATE INDEX ON analytical_stem ("institutionCode", "subInstitutionCode", "collectionCode", "catalogNumber" );
|
933 |
|
CREATE INDEX ON analytical_stem ("institutionCode", "projectID", "plotName", "dateCollected" );
|
|
933 |
CREATE INDEX ON analytical_stem ("institutionCode", "projectID", "locationName", "dateCollected" );
|
934 |
934 |
$$;
|
935 |
935 |
|
936 |
936 |
|
... | ... | |
1447 |
1447 |
"coordinateUncertaintyInMeters" double precision,
|
1448 |
1448 |
geovalid boolean,
|
1449 |
1449 |
"isNewWorld" boolean,
|
1450 |
|
"plotName" text NOT NULL,
|
|
1450 |
"locationName" text NOT NULL,
|
1451 |
1451 |
"elevationInMeters" double precision,
|
1452 |
1452 |
"plotArea_ha" double precision,
|
1453 |
1453 |
"samplingProtocol" text,
|
... | ... | |
1491 |
1491 |
geovalid boolean,
|
1492 |
1492 |
"isNewWorld" boolean,
|
1493 |
1493 |
"projectID" text,
|
1494 |
|
"plotName" text NOT NULL,
|
|
1494 |
"locationName" text NOT NULL,
|
1495 |
1495 |
"elevationInMeters" double precision,
|
1496 |
1496 |
"plotArea_ha" double precision,
|
1497 |
1497 |
"samplingProtocol" text,
|
... | ... | |
1529 |
1529 |
--
|
1530 |
1530 |
|
1531 |
1531 |
CREATE VIEW analytical_aggregate_view AS
|
1532 |
|
SELECT analytical_stem."institutionCode", analytical_stem.country, analytical_stem."stateProvince", analytical_stem.county, analytical_stem."decimalLatitude", analytical_stem."decimalLongitude", analytical_stem."coordinateUncertaintyInMeters", analytical_stem.geovalid, analytical_stem."isNewWorld", analytical_stem."plotName", analytical_stem."elevationInMeters", analytical_stem."plotArea_ha", analytical_stem."samplingProtocol", analytical_stem."dateCollected", analytical_stem."higherPlantGroup", analytical_stem.family, analytical_stem.genus, analytical_stem."speciesBinomial", analytical_stem."scientificName", analytical_stem."scientificNameAuthorship", analytical_stem."scientificNameWithMorphospecies", analytical_stem.threatened, analytical_stem."identifiedBy", analytical_stem."growthForm", analytical_stem.cultivated, analytical_stem."cultivatedBasis", sum(analytical_stem."coverPercent") AS "coverPercent", count(analytical_stem."diameterBreastHeight_cm") AS "individualCount", count((analytical_stem."diameterBreastHeight_cm" >= _cm_to_m((1)::double precision))) AS "individualCount_1cm_or_more", count((analytical_stem."diameterBreastHeight_cm" >= _cm_to_m((2.5)::double precision))) AS "individualCount_2_5cm_or_more", count((analytical_stem."diameterBreastHeight_cm" >= _cm_to_m((10)::double precision))) AS "individualCount_10cm_or_more" FROM analytical_stem GROUP BY analytical_stem."institutionCode", analytical_stem.country, analytical_stem."stateProvince", analytical_stem.county, analytical_stem."decimalLatitude", analytical_stem."decimalLongitude", analytical_stem."coordinateUncertaintyInMeters", analytical_stem.geovalid, analytical_stem."isNewWorld", analytical_stem."plotName", analytical_stem."elevationInMeters", analytical_stem."plotArea_ha", analytical_stem."samplingProtocol", analytical_stem."dateCollected", analytical_stem."higherPlantGroup", analytical_stem.family, analytical_stem.genus, analytical_stem."speciesBinomial", analytical_stem."scientificName", analytical_stem."scientificNameAuthorship", analytical_stem."scientificNameWithMorphospecies", analytical_stem.threatened, analytical_stem."identifiedBy", analytical_stem."growthForm", analytical_stem.cultivated, analytical_stem."cultivatedBasis";
|
|
1532 |
SELECT analytical_stem."institutionCode", analytical_stem.country, analytical_stem."stateProvince", analytical_stem.county, analytical_stem."decimalLatitude", analytical_stem."decimalLongitude", analytical_stem."coordinateUncertaintyInMeters", analytical_stem.geovalid, analytical_stem."isNewWorld", analytical_stem."locationName", analytical_stem."elevationInMeters", analytical_stem."plotArea_ha", analytical_stem."samplingProtocol", analytical_stem."dateCollected", analytical_stem."higherPlantGroup", analytical_stem.family, analytical_stem.genus, analytical_stem."speciesBinomial", analytical_stem."scientificName", analytical_stem."scientificNameAuthorship", analytical_stem."scientificNameWithMorphospecies", analytical_stem.threatened, analytical_stem."identifiedBy", analytical_stem."growthForm", analytical_stem.cultivated, analytical_stem."cultivatedBasis", sum(analytical_stem."coverPercent") AS "coverPercent", count(analytical_stem."diameterBreastHeight_cm") AS "individualCount", count((analytical_stem."diameterBreastHeight_cm" >= _cm_to_m((1)::double precision))) AS "individualCount_1cm_or_more", count((analytical_stem."diameterBreastHeight_cm" >= _cm_to_m((2.5)::double precision))) AS "individualCount_2_5cm_or_more", count((analytical_stem."diameterBreastHeight_cm" >= _cm_to_m((10)::double precision))) AS "individualCount_10cm_or_more" FROM analytical_stem GROUP BY analytical_stem."institutionCode", analytical_stem.country, analytical_stem."stateProvince", analytical_stem.county, analytical_stem."decimalLatitude", analytical_stem."decimalLongitude", analytical_stem."coordinateUncertaintyInMeters", analytical_stem.geovalid, analytical_stem."isNewWorld", analytical_stem."locationName", analytical_stem."elevationInMeters", analytical_stem."plotArea_ha", analytical_stem."samplingProtocol", analytical_stem."dateCollected", analytical_stem."higherPlantGroup", analytical_stem.family, analytical_stem.genus, analytical_stem."speciesBinomial", analytical_stem."scientificName", analytical_stem."scientificNameAuthorship", analytical_stem."scientificNameWithMorphospecies", analytical_stem.threatened, analytical_stem."identifiedBy", analytical_stem."growthForm", analytical_stem.cultivated, analytical_stem."cultivatedBasis";
|
1533 |
1533 |
|
1534 |
1534 |
|
1535 |
1535 |
--
|
... | ... | |
2334 |
2334 |
--
|
2335 |
2335 |
|
2336 |
2336 |
CREATE VIEW analytical_stem_view AS
|
2337 |
|
SELECT source.shortname AS "institutionCode", sourcename.name AS "subInstitutionCode", specimenreplicate.collectioncode_dwc AS "collectionCode", specimenreplicate.catalognumber_dwc AS "catalogNumber", specimenreplicate.sourceaccessioncode AS "occurrenceID", canon_place.country, canon_place.stateprovince AS "stateProvince", datasource_place.county, coordinates.latitude_deg AS "decimalLatitude", coordinates.longitude_deg AS "decimalLongitude", coordinates.coordsaccuracy_m AS "coordinateUncertaintyInMeters", canon_place.geovalid, "newWorldCountries"."isNewWorld", project.sourceaccessioncode AS "projectID", COALESCE(location.sourceaccessioncode, location.authorlocationcode) AS "plotName", location.elevation_m AS "elevationInMeters", _m2_to_ha(location.area_m2) AS "plotArea_ha", method.name AS "samplingProtocol", COALESCE(locationevent.obsstartdate, parent_event.obsstartdate, aggregateoccurrence.collectiondate) AS "dateCollected", family_higher_plant_group.higher_plant_group AS "higherPlantGroup", accepted_taxonverbatim.family, accepted_taxonverbatim.genus, ((accepted_taxonverbatim.genus || ' '::text) || accepted_taxonverbatim.specific_epithet) AS "speciesBinomial", COALESCE(accepted_taxonverbatim.taxonomicname, accepted_taxonverbatim.taxonname) AS "scientificName", accepted_taxonverbatim.author AS "scientificNameAuthorship", NULLIF(array_to_string(ARRAY[COALESCE(accepted_taxonverbatim.genus, accepted_taxonverbatim.family), COALESCE(accepted_taxonverbatim.specific_epithet, parsed_taxonverbatim.morphospecies)], ' '::text), ''::text) AS "speciesBinomialWithMorphospecies", NULLIF(array_to_string(ARRAY[accepted_taxonverbatim.taxonomicname, parsed_taxonverbatim.morphospecies], ' '::text), ''::text) AS "scientificNameWithMorphospecies", (threatened_taxonlabel.taxonlabel_id IS NOT NULL) AS threatened, identifiedby.fullname AS "identifiedBy", taxonoccurrence.growthform AS "growthForm", ((cultivated_family_locations.country IS NOT NULL) OR _or(taxonoccurrence.iscultivated, location.iscultivated)) AS cultivated, CASE WHEN (taxonoccurrence.iscultivated IS NOT NULL) THEN taxonoccurrence.cultivatedbasis WHEN (location.iscultivated IS NOT NULL) THEN NULL::text ELSE NULL::text END AS "cultivatedBasis", collector.fullname AS "recordedBy", plantobservation.collectionnumber AS "recordNumber", _fraction_to_percent(aggregateoccurrence.cover_fraction) AS "coverPercent", _m_to_cm(stemobservation.diameterbreastheight_m) AS "diameterBreastHeight_cm", stemobservation.height_m, stemobservation.tag, stemobservation.xposition_m AS "organismX_m", stemobservation.yposition_m AS "organismY_m", taxonoccurrence.sourceaccessioncode AS "taxonOccurrenceID", taxonoccurrence.authortaxoncode AS "authorTaxonCode", plantobservation.sourceaccessioncode AS "individualID", stemobservation.authorstemcode AS "authorStemCode" FROM ((((((((((((((((((((((((((((((source JOIN location USING (source_id)) LEFT JOIN locationevent USING (location_id)) LEFT JOIN location parent_location ON ((parent_location.location_id = location.parent_id))) LEFT JOIN locationplace ON ((locationplace.location_id = COALESCE(parent_location.location_id, location.location_id)))) LEFT JOIN place datasource_place USING (place_id)) LEFT JOIN place canon_place ON ((canon_place.place_id = datasource_place.canon_place_id))) LEFT JOIN coordinates ON ((coordinates.coordinates_id = canon_place.coordinates_id))) LEFT JOIN "newWorld".iso_code_gadm ON ((iso_code_gadm."GADM country" = canon_place.country))) LEFT JOIN "newWorld"."newWorldCountries" ON (("newWorldCountries"."isoCode" = iso_code_gadm."2-digit iso code"))) LEFT JOIN taxonoccurrence USING (locationevent_id)) LEFT JOIN locationevent parent_event ON ((parent_event.locationevent_id = locationevent.parent_id))) LEFT JOIN project ON ((project.project_id = COALESCE(locationevent.project_id, parent_event.project_id)))) LEFT JOIN method ON ((method.method_id = COALESCE(locationevent.method_id, parent_event.method_id)))) LEFT JOIN party collector ON ((collector.party_id = taxonoccurrence.collector_id))) LEFT JOIN taxondetermination USING (taxonoccurrence_id)) LEFT JOIN party identifiedby ON ((identifiedby.party_id = taxondetermination.party_id))) LEFT JOIN taxonverbatim datasource_taxonverbatim USING (taxonverbatim_id)) LEFT JOIN taxonlabel datasource_taxonlabel USING (taxonlabel_id)) LEFT JOIN taxonlabel parsed_taxonlabel ON ((parsed_taxonlabel.taxonlabel_id = datasource_taxonlabel.matched_label_id))) LEFT JOIN taxonverbatim parsed_taxonverbatim ON ((parsed_taxonverbatim.taxonlabel_id = parsed_taxonlabel.taxonlabel_id))) LEFT JOIN taxonlabel accepted_taxonlabel ON ((accepted_taxonlabel.taxonlabel_id = datasource_taxonlabel.canon_label_id))) LEFT JOIN taxonverbatim accepted_taxonverbatim ON ((accepted_taxonverbatim.taxonlabel_id = accepted_taxonlabel.taxonlabel_id))) LEFT JOIN threatened_taxonlabel ON ((threatened_taxonlabel.taxonlabel_id = accepted_taxonlabel.taxonlabel_id))) LEFT JOIN aggregateoccurrence USING (taxonoccurrence_id)) LEFT JOIN family_higher_plant_group ON ((family_higher_plant_group.family = accepted_taxonverbatim.family))) LEFT JOIN cultivated_family_locations ON (((cultivated_family_locations.family = accepted_taxonverbatim.family) AND (cultivated_family_locations.country = canon_place.country)))) LEFT JOIN plantobservation USING (aggregateoccurrence_id)) LEFT JOIN stemobservation USING (plantobservation_id)) LEFT JOIN specimenreplicate USING (plantobservation_id)) LEFT JOIN sourcename ON ((sourcename.sourcename_id = specimenreplicate.institution_id))) WHERE COALESCE(taxondetermination.iscurrent, true);
|
|
2337 |
SELECT source.shortname AS "institutionCode", sourcename.name AS "subInstitutionCode", specimenreplicate.collectioncode_dwc AS "collectionCode", specimenreplicate.catalognumber_dwc AS "catalogNumber", specimenreplicate.sourceaccessioncode AS "occurrenceID", canon_place.country, canon_place.stateprovince AS "stateProvince", datasource_place.county, coordinates.latitude_deg AS "decimalLatitude", coordinates.longitude_deg AS "decimalLongitude", coordinates.coordsaccuracy_m AS "coordinateUncertaintyInMeters", canon_place.geovalid, "newWorldCountries"."isNewWorld", project.sourceaccessioncode AS "projectID", COALESCE(location.sourceaccessioncode, location.authorlocationcode) AS "locationName", location.elevation_m AS "elevationInMeters", _m2_to_ha(location.area_m2) AS "plotArea_ha", method.name AS "samplingProtocol", COALESCE(locationevent.obsstartdate, parent_event.obsstartdate, aggregateoccurrence.collectiondate) AS "dateCollected", family_higher_plant_group.higher_plant_group AS "higherPlantGroup", accepted_taxonverbatim.family, accepted_taxonverbatim.genus, ((accepted_taxonverbatim.genus || ' '::text) || accepted_taxonverbatim.specific_epithet) AS "speciesBinomial", COALESCE(accepted_taxonverbatim.taxonomicname, accepted_taxonverbatim.taxonname) AS "scientificName", accepted_taxonverbatim.author AS "scientificNameAuthorship", NULLIF(array_to_string(ARRAY[COALESCE(accepted_taxonverbatim.genus, accepted_taxonverbatim.family), COALESCE(accepted_taxonverbatim.specific_epithet, parsed_taxonverbatim.morphospecies)], ' '::text), ''::text) AS "speciesBinomialWithMorphospecies", NULLIF(array_to_string(ARRAY[accepted_taxonverbatim.taxonomicname, parsed_taxonverbatim.morphospecies], ' '::text), ''::text) AS "scientificNameWithMorphospecies", (threatened_taxonlabel.taxonlabel_id IS NOT NULL) AS threatened, identifiedby.fullname AS "identifiedBy", taxonoccurrence.growthform AS "growthForm", ((cultivated_family_locations.country IS NOT NULL) OR _or(taxonoccurrence.iscultivated, location.iscultivated)) AS cultivated, CASE WHEN (taxonoccurrence.iscultivated IS NOT NULL) THEN taxonoccurrence.cultivatedbasis WHEN (location.iscultivated IS NOT NULL) THEN NULL::text ELSE NULL::text END AS "cultivatedBasis", collector.fullname AS "recordedBy", plantobservation.collectionnumber AS "recordNumber", _fraction_to_percent(aggregateoccurrence.cover_fraction) AS "coverPercent", _m_to_cm(stemobservation.diameterbreastheight_m) AS "diameterBreastHeight_cm", stemobservation.height_m, stemobservation.tag, stemobservation.xposition_m AS "organismX_m", stemobservation.yposition_m AS "organismY_m", taxonoccurrence.sourceaccessioncode AS "taxonOccurrenceID", taxonoccurrence.authortaxoncode AS "authorTaxonCode", plantobservation.sourceaccessioncode AS "individualID", stemobservation.authorstemcode AS "authorStemCode" FROM ((((((((((((((((((((((((((((((source JOIN location USING (source_id)) LEFT JOIN locationevent USING (location_id)) LEFT JOIN location parent_location ON ((parent_location.location_id = location.parent_id))) LEFT JOIN locationplace ON ((locationplace.location_id = COALESCE(parent_location.location_id, location.location_id)))) LEFT JOIN place datasource_place USING (place_id)) LEFT JOIN place canon_place ON ((canon_place.place_id = datasource_place.canon_place_id))) LEFT JOIN coordinates ON ((coordinates.coordinates_id = canon_place.coordinates_id))) LEFT JOIN "newWorld".iso_code_gadm ON ((iso_code_gadm."GADM country" = canon_place.country))) LEFT JOIN "newWorld"."newWorldCountries" ON (("newWorldCountries"."isoCode" = iso_code_gadm."2-digit iso code"))) LEFT JOIN taxonoccurrence USING (locationevent_id)) LEFT JOIN locationevent parent_event ON ((parent_event.locationevent_id = locationevent.parent_id))) LEFT JOIN project ON ((project.project_id = COALESCE(locationevent.project_id, parent_event.project_id)))) LEFT JOIN method ON ((method.method_id = COALESCE(locationevent.method_id, parent_event.method_id)))) LEFT JOIN party collector ON ((collector.party_id = taxonoccurrence.collector_id))) LEFT JOIN taxondetermination USING (taxonoccurrence_id)) LEFT JOIN party identifiedby ON ((identifiedby.party_id = taxondetermination.party_id))) LEFT JOIN taxonverbatim datasource_taxonverbatim USING (taxonverbatim_id)) LEFT JOIN taxonlabel datasource_taxonlabel USING (taxonlabel_id)) LEFT JOIN taxonlabel parsed_taxonlabel ON ((parsed_taxonlabel.taxonlabel_id = datasource_taxonlabel.matched_label_id))) LEFT JOIN taxonverbatim parsed_taxonverbatim ON ((parsed_taxonverbatim.taxonlabel_id = parsed_taxonlabel.taxonlabel_id))) LEFT JOIN taxonlabel accepted_taxonlabel ON ((accepted_taxonlabel.taxonlabel_id = datasource_taxonlabel.canon_label_id))) LEFT JOIN taxonverbatim accepted_taxonverbatim ON ((accepted_taxonverbatim.taxonlabel_id = accepted_taxonlabel.taxonlabel_id))) LEFT JOIN threatened_taxonlabel ON ((threatened_taxonlabel.taxonlabel_id = accepted_taxonlabel.taxonlabel_id))) LEFT JOIN aggregateoccurrence USING (taxonoccurrence_id)) LEFT JOIN family_higher_plant_group ON ((family_higher_plant_group.family = accepted_taxonverbatim.family))) LEFT JOIN cultivated_family_locations ON (((cultivated_family_locations.family = accepted_taxonverbatim.family) AND (cultivated_family_locations.country = canon_place.country)))) LEFT JOIN plantobservation USING (aggregateoccurrence_id)) LEFT JOIN stemobservation USING (plantobservation_id)) LEFT JOIN specimenreplicate USING (plantobservation_id)) LEFT JOIN sourcename ON ((sourcename.sourcename_id = specimenreplicate.institution_id))) WHERE COALESCE(taxondetermination.iscurrent, true);
|
2338 |
2338 |
|
2339 |
2339 |
|
2340 |
2340 |
--
|
... | ... | |
5956 |
5956 |
|
5957 |
5957 |
|
5958 |
5958 |
--
|
5959 |
|
-- Name: analytical_aggregate_institutionCode_plotName_dateCollected_idx; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
5959 |
-- Name: analytical_aggregate_institutionCode_locationName_dateColle_idx; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
5960 |
5960 |
--
|
5961 |
5961 |
|
5962 |
|
CREATE INDEX "analytical_aggregate_institutionCode_plotName_dateCollected_idx" ON analytical_aggregate USING btree ("institutionCode", "plotName", "dateCollected");
|
|
5962 |
CREATE INDEX "analytical_aggregate_institutionCode_locationName_dateColle_idx" ON analytical_aggregate USING btree ("institutionCode", "locationName", "dateCollected");
|
5963 |
5963 |
|
5964 |
5964 |
|
5965 |
5965 |
--
|
... | ... | |
5970 |
5970 |
|
5971 |
5971 |
|
5972 |
5972 |
--
|
5973 |
|
-- Name: analytical_stem_institutionCode_projectID_plotName_dateColl_idx; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
5973 |
-- Name: analytical_stem_institutionCode_projectID_locationName_date_idx; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
5974 |
5974 |
--
|
5975 |
5975 |
|
5976 |
|
CREATE INDEX "analytical_stem_institutionCode_projectID_plotName_dateColl_idx" ON analytical_stem USING btree ("institutionCode", "projectID", "plotName", "dateCollected");
|
|
5976 |
CREATE INDEX "analytical_stem_institutionCode_projectID_locationName_date_idx" ON analytical_stem USING btree ("institutionCode", "projectID", "locationName", "dateCollected");
|
5977 |
5977 |
|
5978 |
5978 |
|
5979 |
5979 |
--
|
schemas/vegbien.sql: analytical_*: Renamed plotName to locationName to match the new VegCore term name