Project

General

Profile

« Previous | Next » 

Revision 11475

schemas/vegbien.sql: analytical_stem_view: moved specimen-specific fields to occurrence section

View differences:

vegbien.sql
1740 1740

  
1741 1741
CREATE TABLE analytical_stem (
1742 1742
    datasource text NOT NULL,
1743
    "specimenHolderInstitutions" text,
1744
    collection text,
1745
    "accessionNumber" text,
1746
    "occurrenceID" text,
1747 1743
    country text,
1748 1744
    "stateProvince" text,
1749 1745
    county text,
......
1770 1766
    stratum__name text,
1771 1767
    communities text[],
1772 1768
    plot__collectors text[],
1769
    "specimenHolderInstitutions" text,
1770
    collection text,
1771
    "accessionNumber" text,
1772
    "occurrenceID" text,
1773 1773
    "recordedBy" text,
1774 1774
    "recordNumber" text,
1775 1775
    "dateCollected" date,
......
2731 2731
--
2732 2732

  
2733 2733
CREATE VIEW analytical_stem_view AS
2734
    SELECT source.shortname AS datasource, sourcelist.name AS "specimenHolderInstitutions", specimenreplicate.collectioncode_dwc AS collection, specimenreplicate.catalognumber_dwc AS "accessionNumber", specimenreplicate.sourceaccessioncode AS "occurrenceID", COALESCE(geoscrub_output."acceptedCountry", place.country) AS country, COALESCE(geoscrub_output."acceptedStateProvince", place.stateprovince) AS "stateProvince", COALESCE(geoscrub_output."acceptedCounty", place.county) AS county, location.locationnarrative AS locality, CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.latitude_deg ELSE county_centroids.latitude END AS "decimalLatitude", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.longitude_deg ELSE county_centroids.longitude END AS "decimalLongitude", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.coordsaccuracy_m ELSE _km_to_m(county_centroids.error_km) END AS "coordinateUncertaintyInMeters", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN 'source data'::coordinatesource WHEN (county_centroids.row_num IS NOT NULL) THEN 'georeferencing'::coordinatesource ELSE NULL::coordinatesource END AS "coordinateSource_bien", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN NULL::text WHEN (county_centroids.row_num IS NOT NULL) THEN 'county centroid'::text ELSE NULL::text END AS "georeferenceProtocol_bien", (geoscrub_output.geovalid)::integer AS geovalid_bien, ("newWorldCountries"."isNewWorld")::integer AS "isNewWorld_bien", COALESCE(project.sourceaccessioncode, project.projectname) AS "projectID", COALESCE(location.sourceaccessioncode, NULLIF(pg_catalog.concat_ws('; '::text, COALESCE(parent_location.sourceaccessioncode, parent_location.authorlocationcode), location.authorlocationcode), ''::text)) AS "locationID", COALESCE(parent_location.authorlocationcode, location.authorlocationcode) AS "locationName", CASE WHEN (parent_location.location_id IS NOT NULL) THEN location.authorlocationcode ELSE NULL::text END AS subplot, location.iscultivated AS location__cultivated__bien, locationevent.locationevent_id AS locationevent__pkey, COALESCE(locationevent.obsstartdate, parent_event.obsstartdate) AS "eventDate", COALESCE(location.elevation_m, parent_location.elevation_m) AS "elevationInMeters", _m2_to_ha(COALESCE(location.area_m2, parent_location.area_m2)) AS "plotArea_ha", method.name AS "samplingProtocol", COALESCE(locationevent.temperature_c, parent_event.temperature_c) AS "temperature_C", COALESCE(locationevent.precipitation_m, parent_event.precipitation_m) AS precipitation_m, stratum.stratumname AS stratum__name, COALESCE(locationevent__communities__array(locationevent.locationevent_id), locationevent__communities__array(parent_event.locationevent_id)) AS communities, COALESCE(locationevent__contributors__array(locationevent.locationevent_id), locationevent__contributors__array(parent_event.locationevent_id)) AS plot__collectors, collector.fullname AS "recordedBy", plantobservation.authorplantcode AS "recordNumber", COALESCE(aggregateoccurrence.collectiondate, locationevent.obsstartdate, parent_event.obsstartdate) AS "dateCollected", taxonverbatim.family AS family_verbatim, COALESCE(taxonverbatim.taxonomicname, NULLIF(pg_catalog.concat_ws(' '::text, taxonverbatim.taxonname, taxonverbatim.author), ''::text), taxonlabel.taxonomicname) AS "scientificName_verbatim", identifiedby.fullname AS "identifiedBy", taxondetermination.determinationdate AS "dateIdentified", taxondetermination.notes AS "identificationRemarks", "ScrubbedTaxon"."matchedFamily" AS family_matched, "ScrubbedTaxon"."matchedTaxonName" AS "taxonName_matched", "ScrubbedTaxon"."matchedScientificNameAuthorship" AS "scientificNameAuthorship_matched", family_higher_plant_group.higher_plant_group AS "higherPlantGroup_bien", "ScrubbedTaxon"."acceptedFamily" AS family, "ScrubbedTaxon"."acceptedGenus" AS genus, COALESCE(COALESCE(NULLIF(pg_catalog.concat_ws(' '::text, COALESCE("ScrubbedTaxon"."acceptedGenus", "ScrubbedTaxon"."acceptedFamily"), "ScrubbedTaxon"."acceptedSpecificEpithet", "ScrubbedTaxon"."morphospeciesSuffix"), ''::text), "ScrubbedTaxon"."acceptedTaxonName"), COALESCE(NULLIF(pg_catalog.concat_ws(' '::text, COALESCE("ScrubbedTaxon"."matchedGenus", "ScrubbedTaxon"."matchedFamily"), "ScrubbedTaxon"."matchedSpecificEpithet", "ScrubbedTaxon"."morphospeciesSuffix"), ''::text), "ScrubbedTaxon"."matchedTaxonName"), "ScrubbedTaxon"."concatenatedScientificName") AS "speciesBinomialWithMorphospecies", "ScrubbedTaxon"."acceptedTaxonName" AS "taxonName", "ScrubbedTaxon"."acceptedScientificNameAuthorship" AS "scientificNameAuthorship", taxonoccurrence.growthform AS "growthForm", plantobservation.reproductivecondition AS "reproductiveCondition", ((threatened_taxonlabel.taxonlabel_id IS NOT NULL))::integer AS threatened_bien, (((cultivated_family_locations.country IS NOT NULL) OR _or(taxonoccurrence.iscultivated, location.iscultivated)))::integer AS cultivated_bien, 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_bien", aggregateoccurrence.notes AS "occurrenceRemarks", _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", aggregateoccurrence.sourceaccessioncode AS "aggregateOrganismObservationID", plantobservation.sourceaccessioncode AS "individualObservationID", plantobservation.authorplantcode AS "individualCode", 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 USING (place_id)) LEFT JOIN coordinates USING (coordinates_id)) LEFT JOIN geoscrub.geoscrub_output ON ((((((ARRAY[geoscrub_output."decimalLatitude"] = ARRAY[coordinates.latitude_deg]) AND (ARRAY[geoscrub_output."decimalLongitude"] = ARRAY[coordinates.longitude_deg])) AND (ARRAY[geoscrub_output.country] = ARRAY[place.country])) AND (ARRAY[geoscrub_output."stateProvince"] = ARRAY[place.stateprovince])) AND (ARRAY[geoscrub_output.county] = ARRAY[place.county])))) LEFT JOIN "newWorld".iso_code_gadm ON ((iso_code_gadm."*GADM country" = COALESCE(geoscrub_output."acceptedCountry", place.country)))) LEFT JOIN "newWorld"."newWorldCountries" ON (("newWorldCountries"."*isoCode" = iso_code_gadm."*2-digit iso code"))) LEFT JOIN geoscrub.county_centroids ON ((((place.country = 'United States'::text) AND (county_centroids.state = COALESCE(geoscrub_output."acceptedStateProvince", place.stateprovince))) AND (county_centroids.county = COALESCE(geoscrub_output."acceptedCounty", place.county))))) 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 stratum ON ((stratum.stratum_id = COALESCE(locationevent.stratum_id, parent_event.stratum_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 aggregateoccurrence USING (taxonoccurrence_id)) LEFT JOIN plantobservation USING (aggregateoccurrence_id)) LEFT JOIN stemobservation USING (plantobservation_id)) LEFT JOIN specimenreplicate USING (plantobservation_id)) LEFT JOIN sourcelist ON ((sourcelist.sourcelist_id = specimenreplicate.institution_id))) LEFT JOIN taxondetermination ON (((taxondetermination.taxonoccurrence_id = taxonoccurrence.taxonoccurrence_id) AND taxondetermination.is_datasource_current))) LEFT JOIN party identifiedby ON ((identifiedby.party_id = taxondetermination.party_id))) LEFT JOIN taxonverbatim USING (taxonverbatim_id)) LEFT JOIN taxonlabel USING (taxonlabel_id)) LEFT JOIN "TNRS"."ScrubbedTaxon" ON (("ScrubbedTaxon"."concatenatedScientificName" = taxonlabel.taxonomicname))) LEFT JOIN family_higher_plant_group ON ((family_higher_plant_group.family = "ScrubbedTaxon"."acceptedFamily"))) LEFT JOIN cultivated_family_locations ON (((cultivated_family_locations.family = "ScrubbedTaxon"."acceptedFamily") AND (cultivated_family_locations.country = COALESCE(geoscrub_output."acceptedCountry", place.country))))) LEFT JOIN threatened_taxonlabel USING (taxonlabel_id)) ORDER BY source.shortname;
2734
    SELECT source.shortname AS datasource, COALESCE(geoscrub_output."acceptedCountry", place.country) AS country, COALESCE(geoscrub_output."acceptedStateProvince", place.stateprovince) AS "stateProvince", COALESCE(geoscrub_output."acceptedCounty", place.county) AS county, location.locationnarrative AS locality, CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.latitude_deg ELSE county_centroids.latitude END AS "decimalLatitude", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.longitude_deg ELSE county_centroids.longitude END AS "decimalLongitude", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.coordsaccuracy_m ELSE _km_to_m(county_centroids.error_km) END AS "coordinateUncertaintyInMeters", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN 'source data'::coordinatesource WHEN (county_centroids.row_num IS NOT NULL) THEN 'georeferencing'::coordinatesource ELSE NULL::coordinatesource END AS "coordinateSource_bien", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN NULL::text WHEN (county_centroids.row_num IS NOT NULL) THEN 'county centroid'::text ELSE NULL::text END AS "georeferenceProtocol_bien", (geoscrub_output.geovalid)::integer AS geovalid_bien, ("newWorldCountries"."isNewWorld")::integer AS "isNewWorld_bien", COALESCE(project.sourceaccessioncode, project.projectname) AS "projectID", COALESCE(location.sourceaccessioncode, NULLIF(pg_catalog.concat_ws('; '::text, COALESCE(parent_location.sourceaccessioncode, parent_location.authorlocationcode), location.authorlocationcode), ''::text)) AS "locationID", COALESCE(parent_location.authorlocationcode, location.authorlocationcode) AS "locationName", CASE WHEN (parent_location.location_id IS NOT NULL) THEN location.authorlocationcode ELSE NULL::text END AS subplot, location.iscultivated AS location__cultivated__bien, locationevent.locationevent_id AS locationevent__pkey, COALESCE(locationevent.obsstartdate, parent_event.obsstartdate) AS "eventDate", COALESCE(location.elevation_m, parent_location.elevation_m) AS "elevationInMeters", _m2_to_ha(COALESCE(location.area_m2, parent_location.area_m2)) AS "plotArea_ha", method.name AS "samplingProtocol", COALESCE(locationevent.temperature_c, parent_event.temperature_c) AS "temperature_C", COALESCE(locationevent.precipitation_m, parent_event.precipitation_m) AS precipitation_m, stratum.stratumname AS stratum__name, COALESCE(locationevent__communities__array(locationevent.locationevent_id), locationevent__communities__array(parent_event.locationevent_id)) AS communities, COALESCE(locationevent__contributors__array(locationevent.locationevent_id), locationevent__contributors__array(parent_event.locationevent_id)) AS plot__collectors, sourcelist.name AS "specimenHolderInstitutions", specimenreplicate.collectioncode_dwc AS collection, specimenreplicate.catalognumber_dwc AS "accessionNumber", specimenreplicate.sourceaccessioncode AS "occurrenceID", collector.fullname AS "recordedBy", plantobservation.authorplantcode AS "recordNumber", COALESCE(aggregateoccurrence.collectiondate, locationevent.obsstartdate, parent_event.obsstartdate) AS "dateCollected", taxonverbatim.family AS family_verbatim, COALESCE(taxonverbatim.taxonomicname, NULLIF(pg_catalog.concat_ws(' '::text, taxonverbatim.taxonname, taxonverbatim.author), ''::text), taxonlabel.taxonomicname) AS "scientificName_verbatim", identifiedby.fullname AS "identifiedBy", taxondetermination.determinationdate AS "dateIdentified", taxondetermination.notes AS "identificationRemarks", "ScrubbedTaxon"."matchedFamily" AS family_matched, "ScrubbedTaxon"."matchedTaxonName" AS "taxonName_matched", "ScrubbedTaxon"."matchedScientificNameAuthorship" AS "scientificNameAuthorship_matched", family_higher_plant_group.higher_plant_group AS "higherPlantGroup_bien", "ScrubbedTaxon"."acceptedFamily" AS family, "ScrubbedTaxon"."acceptedGenus" AS genus, COALESCE(COALESCE(NULLIF(pg_catalog.concat_ws(' '::text, COALESCE("ScrubbedTaxon"."acceptedGenus", "ScrubbedTaxon"."acceptedFamily"), "ScrubbedTaxon"."acceptedSpecificEpithet", "ScrubbedTaxon"."morphospeciesSuffix"), ''::text), "ScrubbedTaxon"."acceptedTaxonName"), COALESCE(NULLIF(pg_catalog.concat_ws(' '::text, COALESCE("ScrubbedTaxon"."matchedGenus", "ScrubbedTaxon"."matchedFamily"), "ScrubbedTaxon"."matchedSpecificEpithet", "ScrubbedTaxon"."morphospeciesSuffix"), ''::text), "ScrubbedTaxon"."matchedTaxonName"), "ScrubbedTaxon"."concatenatedScientificName") AS "speciesBinomialWithMorphospecies", "ScrubbedTaxon"."acceptedTaxonName" AS "taxonName", "ScrubbedTaxon"."acceptedScientificNameAuthorship" AS "scientificNameAuthorship", taxonoccurrence.growthform AS "growthForm", plantobservation.reproductivecondition AS "reproductiveCondition", ((threatened_taxonlabel.taxonlabel_id IS NOT NULL))::integer AS threatened_bien, (((cultivated_family_locations.country IS NOT NULL) OR _or(taxonoccurrence.iscultivated, location.iscultivated)))::integer AS cultivated_bien, 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_bien", aggregateoccurrence.notes AS "occurrenceRemarks", _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", aggregateoccurrence.sourceaccessioncode AS "aggregateOrganismObservationID", plantobservation.sourceaccessioncode AS "individualObservationID", plantobservation.authorplantcode AS "individualCode", 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 USING (place_id)) LEFT JOIN coordinates USING (coordinates_id)) LEFT JOIN geoscrub.geoscrub_output ON ((((((ARRAY[geoscrub_output."decimalLatitude"] = ARRAY[coordinates.latitude_deg]) AND (ARRAY[geoscrub_output."decimalLongitude"] = ARRAY[coordinates.longitude_deg])) AND (ARRAY[geoscrub_output.country] = ARRAY[place.country])) AND (ARRAY[geoscrub_output."stateProvince"] = ARRAY[place.stateprovince])) AND (ARRAY[geoscrub_output.county] = ARRAY[place.county])))) LEFT JOIN "newWorld".iso_code_gadm ON ((iso_code_gadm."*GADM country" = COALESCE(geoscrub_output."acceptedCountry", place.country)))) LEFT JOIN "newWorld"."newWorldCountries" ON (("newWorldCountries"."*isoCode" = iso_code_gadm."*2-digit iso code"))) LEFT JOIN geoscrub.county_centroids ON ((((place.country = 'United States'::text) AND (county_centroids.state = COALESCE(geoscrub_output."acceptedStateProvince", place.stateprovince))) AND (county_centroids.county = COALESCE(geoscrub_output."acceptedCounty", place.county))))) 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 stratum ON ((stratum.stratum_id = COALESCE(locationevent.stratum_id, parent_event.stratum_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 aggregateoccurrence USING (taxonoccurrence_id)) LEFT JOIN plantobservation USING (aggregateoccurrence_id)) LEFT JOIN stemobservation USING (plantobservation_id)) LEFT JOIN specimenreplicate USING (plantobservation_id)) LEFT JOIN sourcelist ON ((sourcelist.sourcelist_id = specimenreplicate.institution_id))) LEFT JOIN taxondetermination ON (((taxondetermination.taxonoccurrence_id = taxonoccurrence.taxonoccurrence_id) AND taxondetermination.is_datasource_current))) LEFT JOIN party identifiedby ON ((identifiedby.party_id = taxondetermination.party_id))) LEFT JOIN taxonverbatim USING (taxonverbatim_id)) LEFT JOIN taxonlabel USING (taxonlabel_id)) LEFT JOIN "TNRS"."ScrubbedTaxon" ON (("ScrubbedTaxon"."concatenatedScientificName" = taxonlabel.taxonomicname))) LEFT JOIN family_higher_plant_group ON ((family_higher_plant_group.family = "ScrubbedTaxon"."acceptedFamily"))) LEFT JOIN cultivated_family_locations ON (((cultivated_family_locations.family = "ScrubbedTaxon"."acceptedFamily") AND (cultivated_family_locations.country = COALESCE(geoscrub_output."acceptedCountry", place.country))))) LEFT JOIN threatened_taxonlabel USING (taxonlabel_id)) ORDER BY source.shortname;
2735 2735

  
2736 2736

  
2737 2737
--

Also available in: Unified diff