Revision 9771
Added by Aaron Marcuse-Kubitza over 11 years ago
| inputs/GBIF/raw_occurrence_record/new_terms.csv | ||
|---|---|---|
| 1 |
row_num,raw_occurrence_record-row_num,, |
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| 2 |
catalogue_number,accessionNumber,, |
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| 3 |
rank,taxonRank,, |
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| 4 |
order_rank,order,, |
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| 5 |
lat_long_precision,coordinatePrecision_deg,,Tentative |
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| 6 |
max_altitude,maximumElevationInMeters,, |
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| 7 |
min_altitude,minimumElevationInMeters,, |
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| 8 |
min_depth,minimumDepthInMeters,, |
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| 9 |
max_depth,maximumDepthInMeters,, |
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| 10 |
collector_name,recordedBy,, |
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| 11 |
identifier_name,identifiedBy,, |
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| 12 |
identification_date,dateIdentified,, |
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| inputs/GBIF/raw_occurrence_record/unmapped_terms.csv | ||
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| 1 |
raw_occurrence_record-row_num |
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| 2 |
*data_provider_id |
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*data_resource_id |
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| 4 |
*resource_access_point_id |
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authors |
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| 6 |
coordinatePrecision_deg |
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*altitude_precision |
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*depth_precision |
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| 9 |
year |
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| 10 |
month |
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| 11 |
day |
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| 12 |
basisOfRecord |
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| 13 |
*unit_qualifier |
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| 14 |
*created |
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| 15 |
modified |
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*deleted |
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| inputs/GBIF/raw_occurrence_record/header.csv | ||
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| 1 |
row_num,id,data_provider_id,data_resource_id,resource_access_point_id,institution_code,collection_code,catalogue_number,scientific_name,author,rank,kingdom,phylum,class,order_rank,family,genus,species,subspecies,latitude,longitude,lat_long_precision,max_altitude,min_altitude,altitude_precision,min_depth,max_depth,depth_precision,continent_ocean,country,state_province,county,collector_name,locality,year,month,day,basis_of_record,identifier_name,identification_date,unit_qualifier,created,modified,deleted |
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| inputs/GBIF/raw_occurrence_record/postprocess.sql | ||
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| 1 |
CREATE INDEX ON :table ("institution_code");
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|
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-- Remove institutions that we have direct data for |
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DELETE FROM :table |
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WHERE institution_code IN ( |
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'ACAD' |
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, 'ARIZ' |
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, 'BRIT' |
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, 'MO' |
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, 'MT' |
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, 'NY' |
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, 'QFA' |
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, 'TEX' |
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, 'TRT' |
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| 15 |
, 'TRTE' |
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, 'U' |
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, 'UBC' |
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, 'WIN' |
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| 19 |
) |
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/* list obtained using the following on r9459: |
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SELECT DISTINCT dataprovider |
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FROM sourcelist |
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JOIN provider_count ON provider_count.dataprovider = sourcelist.name |
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WHERE source_id = source_by_shortname('GBIF')
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ORDER BY dataprovider |
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*/ |
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; |
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| inputs/GBIF/raw_occurrence_record/run | ||
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| 1 |
#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
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if self_not_included; then |
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herbaria_filter.ih.csv_/make() |
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{
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echo_func; set_make_vars; check_target_exists |
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|
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use_local |
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limit= query='SELECT DISTINCT acronym FROM herbaria.ih ORDER BY acronym' \ |
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to_target pg_export |
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} |
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plant_fraction/make() # runtime: 1 hr ("10603 rows affected (53 min 44.68 sec)")
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{
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echo_func; set_make_vars; mk_table_esc |
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|
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use_local_remote |
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if remaking; then table=plant_fraction table_esc= mk_drop|mysql_ANSI; fi |
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(benign_error=1 mysql <<'EOF' |
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CREATE TABLE `plant_fraction` ( |
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`institution_code` varchar(255) NOT NULL PRIMARY KEY, |
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`plant_fraction` float NOT NULL, |
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KEY `plant_fraction` (`plant_fraction`) |
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) ENGINE=MyISAM DEFAULT CHARSET=utf8 |
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EOF |
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) || table=plant_fraction skip_table || return 0 |
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mysql_ANSI <<EOF |
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INSERT INTO "plant_fraction" |
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SELECT |
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institution_code |
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, COUNT(NULLIF( |
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family LIKE '%aceae%' OR family IN ('Compositae','Gramineae','Palmae','Guttiferae','Cruciferae','Labiatae','Umbelliferae','Leguminosae')
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, false))/COUNT(*) |
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AS plant_fraction |
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FROM ${limit:+(SELECT * FROM }$table_esc ${limit:+$(prefix= limit)) s}
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GROUP BY institution_code |
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ORDER BY institution_code |
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EOF |
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} |
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plant_fraction/seal() |
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{
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echo_func; set_make_vars |
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use_local_remote |
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table=plant_fraction table_esc= mysql_seal_table |
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} |
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plant_fraction_for_herbaria_filter/make() |
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{
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echo_func; set_make_vars; mk_table_esc |
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plant_fraction/make |
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use_local_remote |
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if remaking; then |
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table=plant_fraction_for_herbaria_filter table_esc= mk_drop|mysql_ANSI |
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fi |
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(benign_error=1 mysql <<'EOF' |
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CREATE VIEW `plant_fraction_for_herbaria_filter` AS |
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SELECT * FROM `plant_fraction` |
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WHERE plant_fraction >= 0.8 |
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EOF |
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) || table=plant_fraction_for_herbaria_filter skip_table || return 0 |
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} |
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herbaria_filter/make() # runtime: ~0 ("0m2.235s"): CSV import, index scans only
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{
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echo_func; set_make_vars |
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use_local_remote |
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local table="$target_stem" |
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if remaking; then mk_drop|mysql_ANSI; fi |
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herbaria_filter.ih.csv_/make |
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plant_fraction_for_herbaria_filter/make |
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(benign_error=1 mysql <<'EOF' |
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CREATE TABLE `herbaria_filter` ( |
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`institution_code` varchar(255) NOT NULL PRIMARY KEY |
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) ENGINE=MyISAM DEFAULT CHARSET=utf8 COMMENT='contains all of IH.vegpath.org?&Index+Herbariorum' |
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EOF |
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) || skip_table || return 0 |
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|
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time ( |
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mysql_ANSI <<EOF |
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INSERT INTO "herbaria_filter" |
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SELECT institution_code FROM plant_fraction_for_herbaria_filter |
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| 90 |
EOF |
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append=1 mysql_import <"$top_dir"/herbaria_filter.ih.csv_ |
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) || return |
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} |
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herbaria_filter/seal() |
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{
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echo_func; set_make_vars |
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| 98 |
|
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use_local_remote |
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table=herbaria_filter table_esc= mysql_seal_table |
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} |
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| 102 |
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# table.tsv.gz/make() runtime: 35 min ("34m55.802s")
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func_override table.tsv/make__src_table_run |
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table.tsv/make() # usage: [remake=1] [limit=...] .../run table.tsv/make |
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{
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echo_func; set_make_vars; check_target_exists |
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herbaria_filter/make |
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filter=" |
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deleted IS NULL |
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AND institution_code IN (SELECT * FROM herbaria_filter)" \ |
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self_make table.tsv/make__src_table_run |
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} |
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| 116 |
|
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| 117 |
fi |
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| 118 | 0 | |
| inputs/GBIF/raw_occurrence_record/map.csv | ||
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| 1 |
GBIF,VegCore,Filter,Comments |
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| 2 |
row_num,raw_occurrence_record-row_num,, |
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| 3 |
id,dataProviderRecordID,, |
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| 4 |
data_provider_id,*data_provider_id,, |
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| 5 |
data_resource_id,*data_resource_id,, |
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| 6 |
resource_access_point_id,*resource_access_point_id,, |
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| 7 |
institution_code,specimenHolderInstitutions,, |
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| 8 |
collection_code,collection,, |
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| 9 |
catalogue_number,accessionNumber,, |
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| 10 |
scientific_name,scientificName,, |
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| 11 |
author,authors,, |
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| 12 |
rank,taxonRank,, |
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| 13 |
kingdom,kingdom,, |
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| 14 |
phylum,phylum,, |
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| 15 |
class,class,, |
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| 16 |
order_rank,order,, |
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| 17 |
family,family,, |
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| 18 |
genus,genus,, |
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| 19 |
species,specificEpithet,, |
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| 20 |
subspecies,subspecies,, |
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| 21 |
latitude,decimalLatitude,, |
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| 22 |
longitude,decimalLongitude,, |
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| 23 |
lat_long_precision,coordinatePrecision_deg,,Tentative |
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| 24 |
max_altitude,maximumElevationInMeters,, |
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| 25 |
min_altitude,minimumElevationInMeters,, |
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| 26 |
altitude_precision,*altitude_precision,, |
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| 27 |
min_depth,minimumDepthInMeters,, |
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| 28 |
max_depth,maximumDepthInMeters,, |
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| 29 |
depth_precision,*depth_precision,, |
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| 30 |
continent_ocean,continent,, |
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| 31 |
country,country,, |
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| 32 |
state_province,stateProvince,, |
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| 33 |
county,county,, |
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| 34 |
collector_name,recordedBy,, |
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| 35 |
locality,locality,, |
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| 36 |
year,year,, |
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| 37 |
month,month,, |
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| 38 |
day,day,, |
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| 39 |
basis_of_record,basisOfRecord,, |
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| 40 |
identifier_name,identifiedBy,, |
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| 41 |
identification_date,dateIdentified,, |
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| 42 |
unit_qualifier,*unit_qualifier,, |
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| 43 |
created,*created,, |
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| 44 |
modified,modified,, |
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| 45 |
deleted,*deleted,, |
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| inputs/GBIF/raw_occurrence_record/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
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| 2 |
<VegBIEN> |
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<_setDefault id="-1"> |
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<source_id><source><shortname>GBIF</shortname></source></source_id> |
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<path> |
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<_simplifyPath> |
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<next>parent_id</next> |
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<path> |
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<location> |
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<authorlocationcode> |
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<_alt> |
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<1>$id</1> |
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<2> |
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<_join> |
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<1>$institution_code</1> |
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<2>$collection_code</2> |
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<3>$catalogue_number</3> |
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</_join> |
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</2> |
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</_alt> |
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| 21 |
</authorlocationcode> |
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| 22 |
<elevation_m> |
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| 23 |
<_avg> |
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<1>$min_altitude</1> |
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<2>$max_altitude</2> |
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</_avg> |
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</elevation_m> |
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<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
|
| 29 |
<locationevent> |
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| 30 |
<taxonoccurrence> |
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| 31 |
<aggregateoccurrence> |
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| 32 |
<plantobservation> |
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| 33 |
<specimenreplicate> |
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| 34 |
<catalognumber_dwc>$catalogue_number</catalognumber_dwc> |
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| 35 |
<collectioncode_dwc>$collection_code</collectioncode_dwc> |
|
| 36 |
<institution_id> |
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| 37 |
<sourcelist> |
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<name>$institution_code</name> |
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| 39 |
<sourcename> |
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| 40 |
<name> |
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<_split> |
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<separator>[,;] *</separator> |
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<value>$institution_code</value> |
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| 44 |
</_split> |
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| 45 |
</name> |
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| 46 |
</sourcename> |
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| 47 |
</sourcelist> |
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| 48 |
</institution_id> |
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| 49 |
<sourceaccessioncode>$id</sourceaccessioncode> |
|
| 50 |
</specimenreplicate> |
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| 51 |
</plantobservation> |
|
| 52 |
</aggregateoccurrence> |
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| 53 |
<collector_id><party><fullname>$collector_name</fullname></party></collector_id> |
|
| 54 |
<sourceaccessioncode>$id</sourceaccessioncode> |
|
| 55 |
<taxondetermination> |
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| 56 |
<party_id><party><fullname>$identifier_name</fullname></party></party_id> |
|
| 57 |
<taxonverbatim_id> |
|
| 58 |
<taxonverbatim> |
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| 59 |
<taxonlabel_id> |
|
| 60 |
<taxonlabel> |
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| 61 |
<parent_id> |
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| 62 |
<taxonlabel> |
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| 63 |
<rank>$rank</rank> |
|
| 64 |
<parent_id> |
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| 65 |
<taxonlabel> |
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| 66 |
<rank>cultivar</rank> |
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| 67 |
<parent_id> |
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| 68 |
<taxonlabel> |
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| 69 |
<rank>forma</rank> |
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| 70 |
<parent_id> |
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| 71 |
<taxonlabel> |
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| 72 |
<rank>variety</rank> |
|
| 73 |
<parent_id> |
|
| 74 |
<taxonlabel> |
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| 75 |
<rank>subspecies</rank> |
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| 76 |
<taxonepithet>$subspecies</taxonepithet> |
|
| 77 |
<parent_id> |
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| 78 |
<taxonlabel> |
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| 79 |
<rank>species</rank> |
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| 80 |
<taxonepithet>$species</taxonepithet> |
|
| 81 |
<parent_id> |
|
| 82 |
<taxonlabel> |
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| 83 |
<rank>genus</rank> |
|
| 84 |
<taxonepithet>$genus</taxonepithet> |
|
| 85 |
<parent_id> |
|
| 86 |
<taxonlabel> |
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| 87 |
<rank>family</rank> |
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| 88 |
<taxonepithet>$family</taxonepithet> |
|
| 89 |
<parent_id> |
|
| 90 |
<taxonlabel> |
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| 91 |
<rank>order</rank> |
|
| 92 |
<taxonepithet>$order_rank</taxonepithet> |
|
| 93 |
<parent_id> |
|
| 94 |
<taxonlabel> |
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| 95 |
<rank>class</rank> |
|
| 96 |
<taxonepithet>$class</taxonepithet> |
|
| 97 |
<parent_id> |
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| 98 |
<taxonlabel> |
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| 99 |
<rank>phylum</rank> |
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| 100 |
<taxonepithet>$phylum</taxonepithet> |
|
| 101 |
<parent_id> |
|
| 102 |
<taxonlabel> |
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| 103 |
<rank>kingdom</rank> |
|
| 104 |
<taxonepithet>$kingdom</taxonepithet> |
|
| 105 |
</taxonlabel> |
|
| 106 |
</parent_id> |
|
| 107 |
</taxonlabel> |
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| 108 |
</parent_id> |
|
| 109 |
</taxonlabel> |
|
| 110 |
</parent_id> |
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| 111 |
</taxonlabel> |
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| 112 |
</parent_id> |
|
| 113 |
</taxonlabel> |
|
| 114 |
</parent_id> |
|
| 115 |
</taxonlabel> |
|
| 116 |
</parent_id> |
|
| 117 |
</taxonlabel> |
|
| 118 |
</parent_id> |
|
| 119 |
</taxonlabel> |
|
| 120 |
</parent_id> |
|
| 121 |
</taxonlabel> |
|
| 122 |
</parent_id> |
|
| 123 |
</taxonlabel> |
|
| 124 |
</parent_id> |
|
| 125 |
</taxonlabel> |
|
| 126 |
</parent_id> |
|
| 127 |
</taxonlabel> |
|
| 128 |
</parent_id> |
|
| 129 |
<rank>$rank</rank> |
|
| 130 |
<taxonomicname> |
|
| 131 |
<_merge_prefix> |
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| 132 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 133 |
<value> |
|
| 134 |
<_alt> |
|
| 135 |
<1>$scientific_name</1> |
|
| 136 |
<2> |
|
| 137 |
<_join_words> |
|
| 138 |
<2>$genus</2> |
|
| 139 |
<3>$species</3> |
|
| 140 |
<4>$subspecies</4> |
|
| 141 |
</_join_words> |
|
| 142 |
</2> |
|
| 143 |
</_alt> |
|
| 144 |
</value> |
|
| 145 |
</_merge_prefix> |
|
| 146 |
</taxonomicname> |
|
| 147 |
</taxonlabel> |
|
| 148 |
</taxonlabel_id> |
|
| 149 |
<family>$family</family> |
|
| 150 |
<genus>$genus</genus> |
|
| 151 |
<specific_epithet>$species</specific_epithet> |
|
| 152 |
<taxonomicname>$scientific_name</taxonomicname> |
|
| 153 |
<verbatimrank>$rank</verbatimrank> |
|
| 154 |
</taxonverbatim> |
|
| 155 |
</taxonverbatim_id> |
|
| 156 |
<determinationdate><_dateRangeStart><value>$identification_date</value></_dateRangeStart></determinationdate> |
|
| 157 |
</taxondetermination> |
|
| 158 |
</taxonoccurrence> |
|
| 159 |
<waterdepth_m> |
|
| 160 |
<_avg> |
|
| 161 |
<1>$min_depth</1> |
|
| 162 |
<2>$max_depth</2> |
|
| 163 |
</_avg> |
|
| 164 |
</waterdepth_m> |
|
| 165 |
</locationevent> |
|
| 166 |
<locationnarrative>$locality</locationnarrative> |
|
| 167 |
<locationplace> |
|
| 168 |
<place_id> |
|
| 169 |
<place> |
|
| 170 |
<coordinates_id> |
|
| 171 |
<coordinates> |
|
| 172 |
<latitude_deg> |
|
| 173 |
<_nullIf> |
|
| 174 |
<null>0</null> |
|
| 175 |
<type>float</type> |
|
| 176 |
<value>$latitude</value> |
|
| 177 |
</_nullIf> |
|
| 178 |
</latitude_deg> |
|
| 179 |
<longitude_deg> |
|
| 180 |
<_nullIf> |
|
| 181 |
<null>0</null> |
|
| 182 |
<type>float</type> |
|
| 183 |
<value>$longitude</value> |
|
| 184 |
</_nullIf> |
|
| 185 |
</longitude_deg> |
|
| 186 |
</coordinates> |
|
| 187 |
</coordinates_id> |
|
| 188 |
<continent>$continent_ocean</continent> |
|
| 189 |
<country>$country</country> |
|
| 190 |
<county>$county</county> |
|
| 191 |
<matched_place_id> |
|
| 192 |
<place> |
|
| 193 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
|
| 194 |
<coordinates_id> |
|
| 195 |
<coordinates> |
|
| 196 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
|
| 197 |
<latitude_deg> |
|
| 198 |
<_nullIf> |
|
| 199 |
<null>0</null> |
|
| 200 |
<type>float</type> |
|
| 201 |
<value>$latitude</value> |
|
| 202 |
</_nullIf> |
|
| 203 |
</latitude_deg> |
|
| 204 |
<longitude_deg> |
|
| 205 |
<_nullIf> |
|
| 206 |
<null>0</null> |
|
| 207 |
<type>float</type> |
|
| 208 |
<value>$longitude</value> |
|
| 209 |
</_nullIf> |
|
| 210 |
</longitude_deg> |
|
| 211 |
</coordinates> |
|
| 212 |
</coordinates_id> |
|
| 213 |
<country>$country</country> |
|
| 214 |
<county>$county</county> |
|
| 215 |
<stateprovince>$state_province</stateprovince> |
|
| 216 |
</place> |
|
| 217 |
</matched_place_id> |
|
| 218 |
<stateprovince>$state_province</stateprovince> |
|
| 219 |
</place> |
|
| 220 |
</place_id> |
|
| 221 |
</locationplace> |
|
| 222 |
</location> |
|
| 223 |
</path> |
|
| 224 |
</_simplifyPath> |
|
| 225 |
</path> |
|
| 226 |
</_setDefault> |
|
| 227 |
</VegBIEN> |
|
| 228 |
Inserted 0 new rows into database |
|
| inputs/GBIF/raw_occurrence_record/VegBIEN.csv | ||
|---|---|---|
| 1 |
GBIF,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
catalogue_number,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institution_code,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
|
| 6 |
catalogue_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
| 7 |
catalogue_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
|
| 8 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
|
| 9 |
institution_code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then/_first/2", |
|
| 10 |
collection_code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1", |
|
| 11 |
catalogue_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
|
| 12 |
min_altitude,/location/elevation_m/_alt/2/_avg/1, |
|
| 13 |
max_altitude,/location/elevation_m/_alt/2/_avg/2, |
|
| 14 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 15 |
identification_date,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value", |
|
| 16 |
catalogue_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
|
| 17 |
collection_code,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
|
| 18 |
catalogue_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 19 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 20 |
institution_code,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2", |
|
| 21 |
institution_code,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value", |
|
| 22 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 23 |
scientific_name,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
|
| 24 |
collector_name,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
|
| 25 |
id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 26 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 27 |
identifier_name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
|
| 28 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 29 |
subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet", |
|
| 30 |
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
|
| 31 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
|
| 32 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet", |
|
| 33 |
order_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet", |
|
| 34 |
class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet", |
|
| 35 |
phylum,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=phylum]/taxonepithet", |
|
| 36 |
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet", |
|
| 37 |
rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 38 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank", |
|
| 39 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 40 |
scientific_name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 41 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2, |
|
| 42 |
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 43 |
subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4, |
|
| 44 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 45 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 46 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 47 |
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 48 |
scientific_name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
|
| 49 |
rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 50 |
identification_date,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value, |
|
| 51 |
catalogue_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
|
| 52 |
min_depth,/location/locationevent/waterdepth_m/_avg/1, |
|
| 53 |
max_depth,/location/locationevent/waterdepth_m/_avg/2, |
|
| 54 |
locality,/location/locationnarrative/_merge/1, |
|
| 55 |
latitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 56 |
longitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 57 |
continent_ocean,/location/locationplace/*_id/place/continent, |
|
| 58 |
country,/location/locationplace/*_id/place/country, |
|
| 59 |
county,/location/locationplace/*_id/place/county, |
|
| 60 |
latitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings" |
|
| 61 |
longitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings" |
|
| 62 |
country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 63 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 64 |
state_province,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 65 |
state_province,/location/locationplace/*_id/place/stateprovince, |
|
| 66 |
altitude_precision,,** No join mapping for *altitude_precision ** |
|
| 67 |
author,,** No join mapping for authors ** |
|
| 68 |
basis_of_record,,** No join mapping for basisOfRecord ** |
|
| 69 |
created,,** No join mapping for *created ** |
|
| 70 |
data_provider_id,,** No join mapping for *data_provider_id ** |
|
| 71 |
data_resource_id,,** No join mapping for *data_resource_id ** |
|
| 72 |
day,,** No join mapping for day ** |
|
| 73 |
deleted,,** No join mapping for *deleted ** |
|
| 74 |
depth_precision,,** No join mapping for *depth_precision ** |
|
| 75 |
lat_long_precision,,** No join mapping for coordinatePrecision_deg ** Tentative |
|
| 76 |
modified,,** No join mapping for modified ** |
|
| 77 |
month,,** No join mapping for month ** |
|
| 78 |
resource_access_point_id,,** No join mapping for *resource_access_point_id ** |
|
| 79 |
unit_qualifier,,** No join mapping for *unit_qualifier ** |
|
| 80 |
year,,** No join mapping for year ** |
|
| inputs/GBIF/raw_occurrence_record_plants/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 3 |
|
|
| 4 |
if self_not_included; then |
|
| 5 |
|
|
| 6 |
full_table="${table%_plants}"
|
|
| 7 |
|
|
| 8 |
herbaria_filter.ih.csv_/make() |
|
| 9 |
{
|
|
| 10 |
echo_func; set_make_vars; check_target_exists |
|
| 11 |
|
|
| 12 |
use_local |
|
| 13 |
limit= query='SELECT DISTINCT acronym FROM herbaria.ih ORDER BY acronym' \ |
|
| 14 |
to_target pg_export |
|
| 15 |
} |
|
| 16 |
|
|
| 17 |
plant_fraction/make() # runtime: 1 hr ("10603 rows affected (53 min 44.68 sec)")
|
|
| 18 |
{
|
|
| 19 |
echo_func; set_make_vars; mk_table_esc |
|
| 20 |
|
|
| 21 |
use_local_remote |
|
| 22 |
if remaking; then table=plant_fraction table_esc= mk_drop|mysql_ANSI; fi |
|
| 23 |
(benign_error=1 mysql <<'EOF' |
|
| 24 |
CREATE TABLE `plant_fraction` ( |
|
| 25 |
`institution_code` varchar(255) NOT NULL PRIMARY KEY, |
|
| 26 |
`plant_fraction` float NOT NULL, |
|
| 27 |
KEY `plant_fraction` (`plant_fraction`) |
|
| 28 |
) ENGINE=MyISAM DEFAULT CHARSET=utf8 |
|
| 29 |
EOF |
|
| 30 |
) || table=plant_fraction skip_table || return 0 |
|
| 31 |
mysql_ANSI <<EOF |
|
| 32 |
INSERT INTO "plant_fraction" |
|
| 33 |
SELECT |
|
| 34 |
institution_code |
|
| 35 |
, COUNT(NULLIF( |
|
| 36 |
family LIKE '%aceae%' OR family IN ('Compositae','Gramineae','Palmae','Guttiferae','Cruciferae','Labiatae','Umbelliferae','Leguminosae')
|
|
| 37 |
, false))/COUNT(*) |
|
| 38 |
AS plant_fraction |
|
| 39 |
FROM ${limit:+(SELECT * FROM }$table_esc ${limit:+$(prefix= limit)) s}
|
|
| 40 |
GROUP BY institution_code |
|
| 41 |
ORDER BY institution_code |
|
| 42 |
EOF |
|
| 43 |
} |
|
| 44 |
|
|
| 45 |
plant_fraction/seal() |
|
| 46 |
{
|
|
| 47 |
echo_func; set_make_vars |
|
| 48 |
|
|
| 49 |
use_local_remote |
|
| 50 |
table=plant_fraction table_esc= mysql_seal_table |
|
| 51 |
} |
|
| 52 |
|
|
| 53 |
plant_fraction_for_herbaria_filter/make() |
|
| 54 |
{
|
|
| 55 |
echo_func; set_make_vars; mk_table_esc |
|
| 56 |
|
|
| 57 |
plant_fraction/make |
|
| 58 |
use_local_remote |
|
| 59 |
if remaking; then |
|
| 60 |
table=plant_fraction_for_herbaria_filter table_esc= mk_drop|mysql_ANSI |
|
| 61 |
fi |
|
| 62 |
(benign_error=1 mysql <<'EOF' |
|
| 63 |
CREATE VIEW `plant_fraction_for_herbaria_filter` AS |
|
| 64 |
SELECT * FROM `plant_fraction` |
|
| 65 |
WHERE plant_fraction >= 0.8 |
|
| 66 |
EOF |
|
| 67 |
) || table=plant_fraction_for_herbaria_filter skip_table || return 0 |
|
| 68 |
} |
|
| 69 |
|
|
| 70 |
herbaria_filter/make() # runtime: ~0 ("0m2.235s"): CSV import, index scans only
|
|
| 71 |
{
|
|
| 72 |
echo_func; set_make_vars |
|
| 73 |
|
|
| 74 |
use_local_remote |
|
| 75 |
local table="$target_stem" |
|
| 76 |
if remaking; then mk_drop|mysql_ANSI; fi |
|
| 77 |
|
|
| 78 |
herbaria_filter.ih.csv_/make |
|
| 79 |
plant_fraction_for_herbaria_filter/make |
|
| 80 |
|
|
| 81 |
(benign_error=1 mysql <<'EOF' |
|
| 82 |
CREATE TABLE `herbaria_filter` ( |
|
| 83 |
`institution_code` varchar(255) NOT NULL PRIMARY KEY |
|
| 84 |
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COMMENT='contains all of IH.vegpath.org?&Index+Herbariorum' |
|
| 85 |
EOF |
|
| 86 |
) || skip_table || return 0 |
|
| 87 |
|
|
| 88 |
time ( |
|
| 89 |
mysql_ANSI <<EOF |
|
| 90 |
INSERT INTO "herbaria_filter" |
|
| 91 |
SELECT institution_code FROM plant_fraction_for_herbaria_filter |
|
| 92 |
EOF |
|
| 93 |
append=1 mysql_import <"$top_dir"/herbaria_filter.ih.csv_ |
|
| 94 |
) || return |
|
| 95 |
} |
|
| 96 |
|
|
| 97 |
herbaria_filter/seal() |
|
| 98 |
{
|
|
| 99 |
echo_func; set_make_vars |
|
| 100 |
|
|
| 101 |
use_local_remote |
|
| 102 |
table=herbaria_filter table_esc= mysql_seal_table |
|
| 103 |
} |
|
| 104 |
|
|
| 105 |
# table.tsv.gz/make() runtime: 35 min ("34m55.802s")
|
|
| 106 |
|
|
| 107 |
func_override table.tsv/make__src_table_run |
|
| 108 |
table.tsv/make() # usage: [remake=1] [limit=...] .../run table.tsv/make |
|
| 109 |
{
|
|
| 110 |
echo_func; set_make_vars; check_target_exists |
|
| 111 |
|
|
| 112 |
herbaria_filter/make |
|
| 113 |
table="$full_table" filter=" |
|
| 114 |
deleted IS NULL |
|
| 115 |
AND institution_code IN (SELECT * FROM herbaria_filter)" \ |
|
| 116 |
self_make table.tsv/make__src_table_run |
|
| 117 |
} |
|
| 118 |
|
|
| 119 |
fi |
|
| 0 | 120 | |
| inputs/GBIF/raw_occurrence_record_plants/postprocess.sql | ||
|---|---|---|
| 1 |
CREATE INDEX ON :table ("institution_code");
|
|
| 2 |
|
|
| 3 |
-- Remove institutions that we have direct data for |
|
| 4 |
DELETE FROM :table |
|
| 5 |
WHERE institution_code IN ( |
|
| 6 |
'ACAD' |
|
| 7 |
, 'ARIZ' |
|
| 8 |
, 'BRIT' |
|
| 9 |
, 'MO' |
|
| 10 |
, 'MT' |
|
| 11 |
, 'NY' |
|
| 12 |
, 'QFA' |
|
| 13 |
, 'TEX' |
|
| 14 |
, 'TRT' |
|
| 15 |
, 'TRTE' |
|
| 16 |
, 'U' |
|
| 17 |
, 'UBC' |
|
| 18 |
, 'WIN' |
|
| 19 |
) |
|
| 20 |
/* list obtained using the following on r9459: |
|
| 21 |
SELECT DISTINCT dataprovider |
|
| 22 |
FROM sourcelist |
|
| 23 |
JOIN provider_count ON provider_count.dataprovider = sourcelist.name |
|
| 24 |
WHERE source_id = source_by_shortname('GBIF')
|
|
| 25 |
ORDER BY dataprovider |
|
| 26 |
*/ |
|
| 27 |
; |
|
| inputs/GBIF/raw_occurrence_record_plants/header.csv | ||
|---|---|---|
| 1 |
row_num,id,data_provider_id,data_resource_id,resource_access_point_id,institution_code,collection_code,catalogue_number,scientific_name,author,rank,kingdom,phylum,class,order_rank,family,genus,species,subspecies,latitude,longitude,lat_long_precision,max_altitude,min_altitude,altitude_precision,min_depth,max_depth,depth_precision,continent_ocean,country,state_province,county,collector_name,locality,year,month,day,basis_of_record,identifier_name,identification_date,unit_qualifier,created,modified,deleted |
|
| inputs/GBIF/raw_occurrence_record_plants/map.csv | ||
|---|---|---|
| 1 |
GBIF,VegCore,Filter,Comments |
|
| 2 |
row_num,raw_occurrence_record-row_num,, |
|
| 3 |
id,dataProviderRecordID,, |
|
| 4 |
data_provider_id,*data_provider_id,, |
|
| 5 |
data_resource_id,*data_resource_id,, |
|
| 6 |
resource_access_point_id,*resource_access_point_id,, |
|
| 7 |
institution_code,specimenHolderInstitutions,, |
|
| 8 |
collection_code,collection,, |
|
| 9 |
catalogue_number,accessionNumber,, |
|
| 10 |
scientific_name,scientificName,, |
|
| 11 |
author,authors,, |
|
| 12 |
rank,taxonRank,, |
|
| 13 |
kingdom,kingdom,, |
|
| 14 |
phylum,phylum,, |
|
| 15 |
class,class,, |
|
| 16 |
order_rank,order,, |
|
| 17 |
family,family,, |
|
| 18 |
genus,genus,, |
|
| 19 |
species,specificEpithet,, |
|
| 20 |
subspecies,subspecies,, |
|
| 21 |
latitude,decimalLatitude,, |
|
| 22 |
longitude,decimalLongitude,, |
|
| 23 |
lat_long_precision,coordinatePrecision_deg,,Tentative |
|
| 24 |
max_altitude,maximumElevationInMeters,, |
|
| 25 |
min_altitude,minimumElevationInMeters,, |
|
| 26 |
altitude_precision,*altitude_precision,, |
|
| 27 |
min_depth,minimumDepthInMeters,, |
|
| 28 |
max_depth,maximumDepthInMeters,, |
|
| 29 |
depth_precision,*depth_precision,, |
|
| 30 |
continent_ocean,continent,, |
|
| 31 |
country,country,, |
|
| 32 |
state_province,stateProvince,, |
|
| 33 |
county,county,, |
|
| 34 |
collector_name,recordedBy,, |
|
| 35 |
locality,locality,, |
|
| 36 |
year,year,, |
|
| 37 |
month,month,, |
|
| 38 |
day,day,, |
|
| 39 |
basis_of_record,basisOfRecord,, |
|
| 40 |
identifier_name,identifiedBy,, |
|
| 41 |
identification_date,dateIdentified,, |
|
| 42 |
unit_qualifier,*unit_qualifier,, |
|
| 43 |
created,*created,, |
|
| 44 |
modified,modified,, |
|
| 45 |
deleted,*deleted,, |
|
| inputs/GBIF/raw_occurrence_record_plants/new_terms.csv | ||
|---|---|---|
| 1 |
row_num,raw_occurrence_record-row_num,, |
|
| 2 |
catalogue_number,accessionNumber,, |
|
| 3 |
rank,taxonRank,, |
|
| 4 |
order_rank,order,, |
|
| 5 |
lat_long_precision,coordinatePrecision_deg,,Tentative |
|
| 6 |
max_altitude,maximumElevationInMeters,, |
|
| 7 |
min_altitude,minimumElevationInMeters,, |
|
| 8 |
min_depth,minimumDepthInMeters,, |
|
| 9 |
max_depth,maximumDepthInMeters,, |
|
| 10 |
collector_name,recordedBy,, |
|
| 11 |
identifier_name,identifiedBy,, |
|
| 12 |
identification_date,dateIdentified,, |
|
| inputs/GBIF/raw_occurrence_record_plants/unmapped_terms.csv | ||
|---|---|---|
| 1 |
raw_occurrence_record-row_num |
|
| 2 |
*data_provider_id |
|
| 3 |
*data_resource_id |
|
| 4 |
*resource_access_point_id |
|
| 5 |
authors |
|
| 6 |
coordinatePrecision_deg |
|
| 7 |
*altitude_precision |
|
| 8 |
*depth_precision |
|
| 9 |
year |
|
| 10 |
month |
|
| 11 |
day |
|
| 12 |
basisOfRecord |
|
| 13 |
*unit_qualifier |
|
| 14 |
*created |
|
| 15 |
modified |
|
| 16 |
*deleted |
|
| inputs/GBIF/raw_occurrence_record_plants/VegBIEN.csv | ||
|---|---|---|
| 1 |
GBIF,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
catalogue_number,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institution_code,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
|
| 6 |
catalogue_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
| 7 |
catalogue_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
|
| 8 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
|
| 9 |
institution_code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then/_first/2", |
|
| 10 |
collection_code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1", |
|
| 11 |
catalogue_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
|
| 12 |
min_altitude,/location/elevation_m/_alt/2/_avg/1, |
|
| 13 |
max_altitude,/location/elevation_m/_alt/2/_avg/2, |
|
| 14 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 15 |
identification_date,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value", |
|
| 16 |
catalogue_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
|
| 17 |
collection_code,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
|
| 18 |
catalogue_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 19 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 20 |
institution_code,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2", |
|
| 21 |
institution_code,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value", |
|
| 22 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 23 |
scientific_name,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
|
| 24 |
collector_name,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
|
| 25 |
id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 26 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 27 |
identifier_name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
|
| 28 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 29 |
subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet", |
|
| 30 |
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
|
| 31 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
|
| 32 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet", |
|
| 33 |
order_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet", |
|
| 34 |
class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet", |
|
| 35 |
phylum,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=phylum]/taxonepithet", |
|
| 36 |
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet", |
|
| 37 |
rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 38 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank", |
|
| 39 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 40 |
scientific_name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 41 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2, |
|
| 42 |
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 43 |
subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4, |
|
| 44 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 45 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 46 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 47 |
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 48 |
scientific_name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
|
| 49 |
rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 50 |
identification_date,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value, |
|
| 51 |
catalogue_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
|
| 52 |
min_depth,/location/locationevent/waterdepth_m/_avg/1, |
|
| 53 |
max_depth,/location/locationevent/waterdepth_m/_avg/2, |
|
| 54 |
locality,/location/locationnarrative/_merge/1, |
|
| 55 |
latitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 56 |
longitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 57 |
continent_ocean,/location/locationplace/*_id/place/continent, |
|
| 58 |
country,/location/locationplace/*_id/place/country, |
|
| 59 |
county,/location/locationplace/*_id/place/county, |
|
| 60 |
latitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings" |
|
| 61 |
longitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings" |
|
| 62 |
country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 63 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 64 |
state_province,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 65 |
state_province,/location/locationplace/*_id/place/stateprovince, |
|
| 66 |
altitude_precision,,** No join mapping for *altitude_precision ** |
|
| 67 |
author,,** No join mapping for authors ** |
|
| 68 |
basis_of_record,,** No join mapping for basisOfRecord ** |
|
| 69 |
created,,** No join mapping for *created ** |
|
| 70 |
data_provider_id,,** No join mapping for *data_provider_id ** |
|
| 71 |
data_resource_id,,** No join mapping for *data_resource_id ** |
|
| 72 |
day,,** No join mapping for day ** |
|
| 73 |
deleted,,** No join mapping for *deleted ** |
|
| 74 |
depth_precision,,** No join mapping for *depth_precision ** |
|
| 75 |
lat_long_precision,,** No join mapping for coordinatePrecision_deg ** Tentative |
|
| 76 |
modified,,** No join mapping for modified ** |
|
| 77 |
month,,** No join mapping for month ** |
|
| 78 |
resource_access_point_id,,** No join mapping for *resource_access_point_id ** |
|
| 79 |
unit_qualifier,,** No join mapping for *unit_qualifier ** |
|
| 80 |
year,,** No join mapping for year ** |
|
| inputs/GBIF/raw_occurrence_record_plants/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
|
| 2 |
<VegBIEN> |
|
| 3 |
<_setDefault id="-1"> |
|
| 4 |
<source_id><source><shortname>GBIF</shortname></source></source_id> |
|
| 5 |
<path> |
|
| 6 |
<_simplifyPath> |
|
| 7 |
<next>parent_id</next> |
|
| 8 |
<path> |
|
| 9 |
<location> |
|
| 10 |
<authorlocationcode> |
|
| 11 |
<_alt> |
|
| 12 |
<1>$id</1> |
|
| 13 |
<2> |
|
| 14 |
<_join> |
|
| 15 |
<1>$institution_code</1> |
|
| 16 |
<2>$collection_code</2> |
|
| 17 |
<3>$catalogue_number</3> |
|
| 18 |
</_join> |
|
| 19 |
</2> |
|
| 20 |
</_alt> |
|
| 21 |
</authorlocationcode> |
|
| 22 |
<elevation_m> |
|
| 23 |
<_avg> |
|
| 24 |
<1>$min_altitude</1> |
|
| 25 |
<2>$max_altitude</2> |
|
| 26 |
</_avg> |
|
| 27 |
</elevation_m> |
|
| 28 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
|
| 29 |
<locationevent> |
|
| 30 |
<taxonoccurrence> |
|
| 31 |
<aggregateoccurrence> |
|
| 32 |
<plantobservation> |
|
| 33 |
<specimenreplicate> |
|
| 34 |
<catalognumber_dwc>$catalogue_number</catalognumber_dwc> |
|
| 35 |
<collectioncode_dwc>$collection_code</collectioncode_dwc> |
|
| 36 |
<institution_id> |
|
| 37 |
<sourcelist> |
|
| 38 |
<name>$institution_code</name> |
|
| 39 |
<sourcename> |
|
| 40 |
<name> |
|
| 41 |
<_split> |
|
| 42 |
<separator>[,;] *</separator> |
|
| 43 |
<value>$institution_code</value> |
|
| 44 |
</_split> |
|
| 45 |
</name> |
|
| 46 |
</sourcename> |
|
| 47 |
</sourcelist> |
|
| 48 |
</institution_id> |
|
| 49 |
<sourceaccessioncode>$id</sourceaccessioncode> |
|
| 50 |
</specimenreplicate> |
|
| 51 |
</plantobservation> |
|
| 52 |
</aggregateoccurrence> |
|
| 53 |
<collector_id><party><fullname>$collector_name</fullname></party></collector_id> |
|
| 54 |
<sourceaccessioncode>$id</sourceaccessioncode> |
|
| 55 |
<taxondetermination> |
|
| 56 |
<party_id><party><fullname>$identifier_name</fullname></party></party_id> |
|
| 57 |
<taxonverbatim_id> |
|
| 58 |
<taxonverbatim> |
|
| 59 |
<taxonlabel_id> |
|
| 60 |
<taxonlabel> |
|
| 61 |
<parent_id> |
|
| 62 |
<taxonlabel> |
|
| 63 |
<rank>$rank</rank> |
|
| 64 |
<parent_id> |
|
| 65 |
<taxonlabel> |
|
| 66 |
<rank>cultivar</rank> |
|
| 67 |
<parent_id> |
|
| 68 |
<taxonlabel> |
|
| 69 |
<rank>forma</rank> |
|
| 70 |
<parent_id> |
|
| 71 |
<taxonlabel> |
|
| 72 |
<rank>variety</rank> |
|
| 73 |
<parent_id> |
|
| 74 |
<taxonlabel> |
|
| 75 |
<rank>subspecies</rank> |
|
| 76 |
<taxonepithet>$subspecies</taxonepithet> |
|
| 77 |
<parent_id> |
|
| 78 |
<taxonlabel> |
|
| 79 |
<rank>species</rank> |
|
| 80 |
<taxonepithet>$species</taxonepithet> |
|
| 81 |
<parent_id> |
|
| 82 |
<taxonlabel> |
|
| 83 |
<rank>genus</rank> |
|
| 84 |
<taxonepithet>$genus</taxonepithet> |
|
| 85 |
<parent_id> |
|
| 86 |
<taxonlabel> |
|
| 87 |
<rank>family</rank> |
|
| 88 |
<taxonepithet>$family</taxonepithet> |
|
| 89 |
<parent_id> |
|
| 90 |
<taxonlabel> |
|
| 91 |
<rank>order</rank> |
|
| 92 |
<taxonepithet>$order_rank</taxonepithet> |
|
| 93 |
<parent_id> |
|
| 94 |
<taxonlabel> |
|
| 95 |
<rank>class</rank> |
|
| 96 |
<taxonepithet>$class</taxonepithet> |
|
| 97 |
<parent_id> |
|
| 98 |
<taxonlabel> |
|
| 99 |
<rank>phylum</rank> |
|
| 100 |
<taxonepithet>$phylum</taxonepithet> |
|
| 101 |
<parent_id> |
|
| 102 |
<taxonlabel> |
|
| 103 |
<rank>kingdom</rank> |
|
| 104 |
<taxonepithet>$kingdom</taxonepithet> |
|
| 105 |
</taxonlabel> |
|
| 106 |
</parent_id> |
|
| 107 |
</taxonlabel> |
|
| 108 |
</parent_id> |
|
| 109 |
</taxonlabel> |
|
| 110 |
</parent_id> |
|
| 111 |
</taxonlabel> |
|
| 112 |
</parent_id> |
|
| 113 |
</taxonlabel> |
|
| 114 |
</parent_id> |
|
| 115 |
</taxonlabel> |
|
| 116 |
</parent_id> |
|
| 117 |
</taxonlabel> |
|
| 118 |
</parent_id> |
|
| 119 |
</taxonlabel> |
|
| 120 |
</parent_id> |
|
| 121 |
</taxonlabel> |
|
| 122 |
</parent_id> |
|
| 123 |
</taxonlabel> |
|
| 124 |
</parent_id> |
|
| 125 |
</taxonlabel> |
|
| 126 |
</parent_id> |
|
| 127 |
</taxonlabel> |
|
| 128 |
</parent_id> |
|
| 129 |
<rank>$rank</rank> |
|
| 130 |
<taxonomicname> |
|
| 131 |
<_merge_prefix> |
|
| 132 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 133 |
<value> |
|
| 134 |
<_alt> |
|
| 135 |
<1>$scientific_name</1> |
|
| 136 |
<2> |
|
| 137 |
<_join_words> |
|
| 138 |
<2>$genus</2> |
|
| 139 |
<3>$species</3> |
|
| 140 |
<4>$subspecies</4> |
|
| 141 |
</_join_words> |
|
| 142 |
</2> |
|
| 143 |
</_alt> |
|
| 144 |
</value> |
|
| 145 |
</_merge_prefix> |
|
| 146 |
</taxonomicname> |
|
| 147 |
</taxonlabel> |
|
| 148 |
</taxonlabel_id> |
|
| 149 |
<family>$family</family> |
|
| 150 |
<genus>$genus</genus> |
|
| 151 |
<specific_epithet>$species</specific_epithet> |
|
| 152 |
<taxonomicname>$scientific_name</taxonomicname> |
|
| 153 |
<verbatimrank>$rank</verbatimrank> |
|
| 154 |
</taxonverbatim> |
|
| 155 |
</taxonverbatim_id> |
|
| 156 |
<determinationdate><_dateRangeStart><value>$identification_date</value></_dateRangeStart></determinationdate> |
|
| 157 |
</taxondetermination> |
|
| 158 |
</taxonoccurrence> |
|
| 159 |
<waterdepth_m> |
|
| 160 |
<_avg> |
|
| 161 |
<1>$min_depth</1> |
|
| 162 |
<2>$max_depth</2> |
|
| 163 |
</_avg> |
|
| 164 |
</waterdepth_m> |
|
| 165 |
</locationevent> |
|
| 166 |
<locationnarrative>$locality</locationnarrative> |
|
| 167 |
<locationplace> |
|
| 168 |
<place_id> |
|
| 169 |
<place> |
|
| 170 |
<coordinates_id> |
|
| 171 |
<coordinates> |
|
| 172 |
<latitude_deg> |
|
| 173 |
<_nullIf> |
|
| 174 |
<null>0</null> |
|
| 175 |
<type>float</type> |
|
| 176 |
<value>$latitude</value> |
|
| 177 |
</_nullIf> |
|
| 178 |
</latitude_deg> |
|
| 179 |
<longitude_deg> |
|
| 180 |
<_nullIf> |
|
| 181 |
<null>0</null> |
|
| 182 |
<type>float</type> |
|
| 183 |
<value>$longitude</value> |
|
| 184 |
</_nullIf> |
|
| 185 |
</longitude_deg> |
|
| 186 |
</coordinates> |
|
| 187 |
</coordinates_id> |
|
| 188 |
<continent>$continent_ocean</continent> |
|
| 189 |
<country>$country</country> |
|
| 190 |
<county>$county</county> |
|
| 191 |
<matched_place_id> |
|
| 192 |
<place> |
|
| 193 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
|
| 194 |
<coordinates_id> |
|
| 195 |
<coordinates> |
|
| 196 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
|
| 197 |
<latitude_deg> |
|
| 198 |
<_nullIf> |
|
| 199 |
<null>0</null> |
|
| 200 |
<type>float</type> |
|
| 201 |
<value>$latitude</value> |
|
| 202 |
</_nullIf> |
|
| 203 |
</latitude_deg> |
|
| 204 |
<longitude_deg> |
|
| 205 |
<_nullIf> |
|
| 206 |
<null>0</null> |
|
| 207 |
<type>float</type> |
|
| 208 |
<value>$longitude</value> |
|
| 209 |
</_nullIf> |
|
| 210 |
</longitude_deg> |
|
| 211 |
</coordinates> |
|
| 212 |
</coordinates_id> |
|
| 213 |
<country>$country</country> |
|
| 214 |
<county>$county</county> |
|
| 215 |
<stateprovince>$state_province</stateprovince> |
|
| 216 |
</place> |
|
| 217 |
</matched_place_id> |
|
| 218 |
<stateprovince>$state_province</stateprovince> |
|
| 219 |
</place> |
|
| 220 |
</place_id> |
|
| 221 |
</locationplace> |
|
| 222 |
</location> |
|
| 223 |
</path> |
|
| 224 |
</_simplifyPath> |
|
| 225 |
</path> |
|
| 226 |
</_setDefault> |
|
| 227 |
</VegBIEN> |
|
| 228 |
Inserted 0 new rows into database |
|
Also available in: Unified diff
inputs/GBIF/raw_occurrence_record/: renamed to raw_occurrence_record_plants because it's actually only the plants in raw_occurrence_record, not all of raw_occurrence_record. also, this will allow us to create a separate raw_occurrence_record_plants view whose name matches the folder and does not collide with the raw_occurrence_record table.