Revision 11749
Added by Aaron Marcuse-Kubitza about 11 years ago
| inputs/CVS/stemCount_/postprocess.sql | ||
|---|---|---|
| 1 | 1 |
SELECT util.search_path_append('util');
|
| 2 | 2 |
|
| 3 |
SELECT create_if_not_exists($$CREATE INDEX $$||:table_str||%'__parent'||$$ ON $$||:table_str||$$ ("taxonObservation_ID")$$); -- runtime: 3 s ("3003.022 ms") @starscream
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|
| 3 |
SELECT create_if_not_exists($$CREATE INDEX $$||:table_str||%'__parent'||$$ ON $$||:table_str||$$ ("taxonOccurrenceID")$$); -- runtime: 3 s ("3003.022 ms") @starscream
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|
| 4 | 4 |
|
| 5 | 5 |
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| 6 | 6 |
SELECT mk_derived_col((:table_str, 'aggregateOrganismObservationID'), |
| 7 |
$$_join("taxonImportance_ID"::text, "STEMCOUNT_ID"::text)$$)
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|
| 7 |
$$_join("aggregateOrganismObservationID__taxon_presence"::text, "aggregateOrganismObservationID__individual_count"::text)$$)
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|
| 8 | 8 |
; -- runtime: 25 s ("26272.523 ms") @starscream
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| 9 | 9 |
|
| 10 | 10 |
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| inputs/CVS/stemCount_/run | ||
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| 1 |
#!/bin/bash -e |
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| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
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| 0 | 3 | |
| inputs/CVS/stemCount_/map.csv | ||
|---|---|---|
| 32 | 32 |
stemCount_entry_treeLineID,*stemCount_entry_treeLineID,, |
| 33 | 33 |
entry_recordCount,*entry_recordCount,, |
| 34 | 34 |
entry_sortOrder,*entry_sortOrder,, |
| 35 |
aggregateOrganismObservationID,aggregateOrganismObservationID,, |
|
| inputs/CVS/stemCount_/test.xml.ref | ||
|---|---|---|
| 11 | 11 |
<locationevent fkey="parent_id"> |
| 12 | 12 |
<taxonoccurrence> |
| 13 | 13 |
<aggregateoccurrence> |
| 14 |
<count>$stemCount</count>
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|
| 15 |
<cover_fraction><_percent_to_fraction><value>$cover</value></_percent_to_fraction></cover_fraction> |
|
| 14 |
<count>$individualCount</count>
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|
| 15 |
<cover_fraction><_percent_to_fraction><value>$coverPercent</value></_percent_to_fraction></cover_fraction>
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|
| 16 | 16 |
<plantobservation> |
| 17 | 17 |
<stemobservation> |
| 18 |
<diameterbreastheight_m><_cm_to_m><value>$stemDiameter</value></_cm_to_m></diameterbreastheight_m>
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|
| 19 |
<height_m>$stemHeight</height_m>
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|
| 18 |
<diameterbreastheight_m><_cm_to_m><value>$diameterBreastHeight_cm</value></_cm_to_m></diameterbreastheight_m>
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| 19 |
<height_m>$height_m</height_m>
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|
| 20 | 20 |
</stemobservation> |
| 21 | 21 |
</plantobservation> |
| 22 | 22 |
<sourceaccessioncode>$aggregateOrganismObservationID</sourceaccessioncode> |
| 23 | 23 |
</aggregateoccurrence> |
| 24 |
<sourceaccessioncode>$taxonObservation_ID</sourceaccessioncode>
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|
| 24 |
<sourceaccessioncode>$taxonOccurrenceID</sourceaccessioncode>
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|
| 25 | 25 |
</taxonoccurrence> |
| 26 | 26 |
</locationevent> |
| 27 | 27 |
</locationevent> |
| inputs/CVS/stemCount_/VegBIEN.csv | ||
|---|---|---|
| 1 |
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
taxonObservation_ID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 3 |
stemCount,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/count, |
|
| 4 |
cover,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value, |
|
| 5 |
stemDiameter,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value, |
|
| 6 |
stemHeight,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m, |
|
| 7 |
aggregateOrganismObservationID,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/sourceaccessioncode, |
|
| 8 |
taxonObservation_ID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 9 |
taxonObservation_ID,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/sourceaccessioncode/_first/1, |
|
| 10 |
aggregateOrganismObservationID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
|
| 11 |
taxonObservation_ID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/_if[@name=""if has taxondetermination""]/cond/_exists", |
|
| 12 |
STEMCOUNT_ID,,** No join mapping for aggregateOrganismObservationID__individual_count ** |
|
| 13 |
basalArea,,** No join mapping for *basalarea ** |
|
| 14 |
biomass,,** No join mapping for *biomass ** |
|
| 15 |
cust_cvs_StemFrequency,,** No join mapping for *cust_cvs_StemFrequency ** |
|
| 16 |
cust_cvs_corner1Presence,,** No join mapping for *cust_cvs_corner1Presence ** |
|
| 17 |
cust_cvs_corner2Presence,,** No join mapping for *cust_cvs_corner2Presence ** |
|
| 18 |
cust_cvs_corner3Presence,,** No join mapping for *cust_cvs_corner3Presence ** |
|
| 19 |
cust_cvs_corner4Presence,,** No join mapping for *cust_cvs_corner4Presence ** |
|
| 20 |
cust_cvs_corner5Presence,,** No join mapping for *cust_cvs_corner5Presence ** |
|
| 21 |
cust_cvs_ddh,,** No join mapping for *cust_cvs_ddh ** |
|
| 22 |
cust_cvs_ddhAccuracy,,** No join mapping for *cust_cvs_ddhAccuracy ** |
|
| 23 |
cust_cvs_isPlanted,,** No join mapping for *cust_cvs_isPlanted ** |
|
| 24 |
cust_cvs_originalCoverCode,,** No join mapping for *cust_cvs_originalCoverCode ** |
|
| 25 |
cust_cvs_subsamplingFactor,,** No join mapping for *cust_cvs_subsamplingFactor ** |
|
| 26 |
entry_recordCount,,** No join mapping for *entry_recordCount ** |
|
| 27 |
entry_sortOrder,,** No join mapping for *entry_sortOrder ** |
|
| 28 |
inferenceArea,,** No join mapping for *inferencearea ** |
|
| 29 |
stemCount_dba_src_ID,,** No join mapping for *stemCount_dba_src_ID ** |
|
| 30 |
stemCount_entry_herbLineID,,** No join mapping for *stemCount_entry_herbLineID ** |
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| 31 |
stemCount_entry_treeLineID,,** No join mapping for *stemCount_entry_treeLineID ** |
|
| 32 |
stemDiameterAccuracy,,** No join mapping for *stemdiameteraccuracy ** |
|
| 33 |
stemHeightAccuracy,,** No join mapping for *stemheightaccuracy ** |
|
| 34 |
stemTaxonArea,,** No join mapping for *stemtaxonarea ** |
|
| 35 |
stratum_ID,,** No join mapping for *stratum_id ** |
|
| 36 |
taxonImportance_ID,,** No join mapping for aggregateOrganismObservationID__taxon_presence ** |
|
| 37 |
taxonImportance_dba_src_ID,,** No join mapping for *taxonImportance_dba_src_ID ** |
|
| 38 |
taxonImportance_entry_herbLineID,,** No join mapping for *taxonImportance_entry_herbLineID ** |
|
| 39 |
taxonImportance_entry_treeLineID,,** No join mapping for *taxonImportance_entry_treeLineID ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 40 | 2 | |
| inputs/CVS/plantConcept_/postprocess.sql | ||
|---|---|---|
| 1 | 1 |
SELECT util.search_path_append('util');
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| 2 | 2 |
|
| 3 |
SELECT util.rename_cols(:table_str, $$ |
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| 4 |
genus => *genus, |
|
| 5 |
$$::hstore); |
|
| 3 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("*PLANTCONCEPT_ID")$$); -- runtime: ~0 @starscream
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| 6 | 4 |
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| 7 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("PLANTCONCEPT_ID")$$); -- runtime: ~0 @starscream
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| 8 | 5 |
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| 9 |
|
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| 10 | 6 |
SELECT mk_derived_col((:table_str, 'division'), |
| 11 |
$$_alt(denorm_division, "Division")$$)
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|
| 7 |
$$_alt(division_main, division_normalized)$$)
|
|
| 12 | 8 |
; -- runtime: 0.2 s ("212.478 ms") @starscream
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| 13 | 9 |
|
| 14 | 10 |
SELECT mk_derived_col((:table_str, 'genus'), |
| 15 |
$$_alt(denorm_genus, "*genus")$$)
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|
| 11 |
$$_alt(genus_main, genus_normalized)$$)
|
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| 16 | 12 |
; -- runtime: 0.1 s ("127.546 ms") @starscream
|
| inputs/CVS/plantConcept_/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CVS/plantConcept_/map.csv | ||
|---|---|---|
| 52 | 52 |
subspecies,EQUIV#to:species#subspecies,,full taxonomic name at that rank |
| 53 | 53 |
composite variety,EQUIV#to:species#composite variety,,full taxonomic name at that rank |
| 54 | 54 |
variety,EQUIV#to:species#variety,,full taxonomic name at that rank |
| 55 |
division,division,, |
|
| 56 |
genus,genus,, |
|
| inputs/CVS/plantConcept_/test.xml.ref | ||
|---|---|---|
| 17 | 17 |
<taxonlabel> |
| 18 | 18 |
<parent_id> |
| 19 | 19 |
<taxonlabel> |
| 20 |
<rank>$taxonLevel</rank>
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|
| 20 |
<rank>$taxonRank</rank>
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|
| 21 | 21 |
<parent_id> |
| 22 | 22 |
<taxonlabel> |
| 23 | 23 |
<rank>cultivar</rank> |
| ... | ... | |
| 33 | 33 |
<parent_id> |
| 34 | 34 |
<taxonlabel> |
| 35 | 35 |
<rank>species</rank> |
| 36 |
<taxonepithet>$denorm_species</taxonepithet>
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|
| 36 |
<taxonepithet>$specificEpithet</taxonepithet>
|
|
| 37 | 37 |
<parent_id> |
| 38 | 38 |
<taxonlabel> |
| 39 | 39 |
<rank>genus</rank> |
| ... | ... | |
| 41 | 41 |
<parent_id> |
| 42 | 42 |
<taxonlabel> |
| 43 | 43 |
<rank>family</rank> |
| 44 |
<taxonepithet>$denorm_family</taxonepithet>
|
|
| 44 |
<taxonepithet>$family</taxonepithet> |
|
| 45 | 45 |
<parent_id> |
| 46 | 46 |
<taxonlabel> |
| 47 | 47 |
<rank>order</rank> |
| 48 |
<taxonepithet>$Order</taxonepithet>
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|
| 48 |
<taxonepithet>$order</taxonepithet>
|
|
| 49 | 49 |
<parent_id> |
| 50 | 50 |
<taxonlabel> |
| 51 | 51 |
<rank>class</rank> |
| 52 |
<taxonepithet>$Class</taxonepithet>
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|
| 52 |
<taxonepithet>$class</taxonepithet>
|
|
| 53 | 53 |
<parent_id> |
| 54 | 54 |
<taxonlabel> |
| 55 | 55 |
<rank>phylum</rank> |
| 56 | 56 |
<parent_id> |
| 57 | 57 |
<taxonlabel> |
| 58 | 58 |
<rank>kingdom</rank> |
| 59 |
<taxonepithet>$denorm_kingdom</taxonepithet>
|
|
| 59 |
<taxonepithet>$kingdom</taxonepithet> |
|
| 60 | 60 |
</taxonlabel> |
| 61 | 61 |
</parent_id> |
| 62 | 62 |
</taxonlabel> |
| ... | ... | |
| 79 | 79 |
</parent_id> |
| 80 | 80 |
</taxonlabel> |
| 81 | 81 |
</parent_id> |
| 82 |
<taxonepithet>$denorm_triName</taxonepithet>
|
|
| 82 |
<taxonepithet>$infraspecificEpithet</taxonepithet>
|
|
| 83 | 83 |
</taxonlabel> |
| 84 | 84 |
</parent_id> |
| 85 |
<rank>$taxonLevel</rank>
|
|
| 85 |
<rank>$taxonRank</rank>
|
|
| 86 | 86 |
<taxonomicname> |
| 87 | 87 |
<_merge_prefix> |
| 88 |
<prefix><_taxon_family_require_std><family>$denorm_family</family></_taxon_family_require_std></prefix>
|
|
| 88 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 89 | 89 |
<value> |
| 90 | 90 |
<_alt> |
| 91 |
<1>$plantNameWithAuthority</1>
|
|
| 91 |
<1>$scientificName</1>
|
|
| 92 | 92 |
<2> |
| 93 | 93 |
<_alt> |
| 94 |
<1>$plantname</1>
|
|
| 94 |
<1>$taxonName</1>
|
|
| 95 | 95 |
<2> |
| 96 | 96 |
<_join_words> |
| 97 | 97 |
<2><_filter_genus><value>$genus</value></_filter_genus></2> |
| 98 |
<3>$denorm_species</3>
|
|
| 98 |
<3>$specificEpithet</3>
|
|
| 99 | 99 |
<5> |
| 100 | 100 |
<_join_words> |
| 101 | 101 |
<1> |
| 102 | 102 |
<_if name="if has infraspecificEpithet"> |
| 103 |
<cond>$denorm_triName</cond>
|
|
| 104 |
<then>$taxonLevel</then>
|
|
| 103 |
<cond>$infraspecificEpithet</cond>
|
|
| 104 |
<then>$taxonRank</then>
|
|
| 105 | 105 |
</_if> |
| 106 | 106 |
</1> |
| 107 |
<2>$denorm_triName</2>
|
|
| 107 |
<2>$infraspecificEpithet</2>
|
|
| 108 | 108 |
</_join_words> |
| 109 | 109 |
</5> |
| 110 | 110 |
</_join_words> |
| ... | ... | |
| 117 | 117 |
</taxonomicname> |
| 118 | 118 |
</taxonlabel> |
| 119 | 119 |
</taxonlabel_id> |
| 120 |
<family>$denorm_family</family>
|
|
| 120 |
<family>$family</family> |
|
| 121 | 121 |
<genus>$genus</genus> |
| 122 |
<specific_epithet>$denorm_species</specific_epithet>
|
|
| 123 |
<taxonname>$plantname</taxonname>
|
|
| 124 |
<taxonomicname>$plantNameWithAuthority</taxonomicname>
|
|
| 125 |
<verbatimrank>$taxonLevel</verbatimrank>
|
|
| 122 |
<specific_epithet>$specificEpithet</specific_epithet>
|
|
| 123 |
<taxonname>$taxonName</taxonname>
|
|
| 124 |
<taxonomicname>$scientificName</taxonomicname>
|
|
| 125 |
<verbatimrank>$taxonRank</verbatimrank>
|
|
| 126 | 126 |
</taxonverbatim> |
| 127 | 127 |
</taxonverbatim_id> |
| 128 | 128 |
</taxondetermination> |
| inputs/CVS/plantConcept_/VegBIEN.csv | ||
|---|---|---|
| 1 |
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
plantNameWithAuthority,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
|
| 3 |
plantname,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
|
| 4 |
taxonLevel,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 5 |
denorm_species,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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","unlike VegBank, this is in fact the epithet, not the full name" |
|
| 6 |
genus,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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", |
|
| 7 |
denorm_family,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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", |
|
| 8 |
Order,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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", |
|
| 9 |
Class,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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", |
|
| 10 |
denorm_kingdom,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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", |
|
| 11 |
denorm_triName,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet, |
|
| 12 |
taxonLevel,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 13 |
taxonLevel,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank", |
|
| 14 |
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 15 |
plantNameWithAuthority,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 16 |
plantname,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
|
| 17 |
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 18 |
denorm_species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,"unlike VegBank, this is in fact the epithet, not the full name" |
|
| 19 |
denorm_triName,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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""]/cond", |
|
| 20 |
taxonLevel,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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", |
|
| 21 |
denorm_triName,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
|
| 22 |
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/family, |
|
| 23 |
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/genus, |
|
| 24 |
denorm_species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/specific_epithet,"unlike VegBank, this is in fact the epithet, not the full name" |
|
| 25 |
plantname,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/taxonname, |
|
| 26 |
plantNameWithAuthority,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/taxonomicname, |
|
| 27 |
taxonLevel,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/verbatimrank, |
|
| 28 |
Division,,** No join mapping for division_normalized ** |
|
| 29 |
Kingdom,,** No non-empty join mapping for DUPLICATE#of:denorm_kingdom#Kingdom ** |
|
| 30 |
PLANTCONCEPT_ID,,** No join mapping for *PLANTCONCEPT_ID ** |
|
| 31 |
PLANTNAME_ID,,** No join mapping for *PLANTNAME_ID ** |
|
| 32 |
Subclass,,** No join mapping for *Subclass ** |
|
| 33 |
Subkingdom,,** No join mapping for *Subkingdom ** |
|
| 34 |
USDAPlantsCode,,** No join mapping for *USDAPlantsCode ** |
|
| 35 |
VascularPlant,,** No join mapping for *VascularPlant ** |
|
| 36 |
commonName,,** No join mapping for vernacularName ** |
|
| 37 |
composite family,,** No join mapping for *composite family ** |
|
| 38 |
composite genus,,** No join mapping for *composite genus ** |
|
| 39 |
composite species,,** No join mapping for *composite species ** |
|
| 40 |
composite variety,,** No non-empty join mapping for EQUIV#to:species#composite variety ** full taxonomic name at that rank |
|
| 41 |
denorm_category,,** No join mapping for *category ** |
|
| 42 |
denorm_division,,"** No join mapping for division_main ** must be _alt-ed with Division because this is missing in 2 rows that have Division, and different from Division in 1 row" |
|
| 43 |
denorm_genus,,** No join mapping for genus_main ** must be _alt-ed with genus because this is missing in 1 row that has genus |
|
| 44 |
denorm_hybridX,,** No join mapping for *hybridX ** |
|
| 45 |
denorm_quadAbbr,,** No join mapping for infraspecificRank2 ** sometimes misparsed as the last + sign in the plantNameWithAuthority |
|
| 46 |
denorm_quadName,,** No join mapping for infraspecificEpithet2 ** sometimes misparsed as the part after the last + sign in the plantNameWithAuthority |
|
| 47 |
denorm_triAbbr,,** No join mapping for infraspecificRank ** |
|
| 48 |
division,,** No join mapping for division ** |
|
| 49 |
exotic,,** No join mapping for *exotic ** |
|
| 50 |
family,,** No non-empty join mapping for DUPLICATE#of:denorm_family#family ** |
|
| 51 |
genus,,"** No join mapping for genus_normalized ** unlike VegBank, does *not* include genus author" |
|
| 52 |
growthForm_short,,** No join mapping for *growthForm_short ** |
|
| 53 |
lowestChildRank,,** No join mapping for *lowestChildRank ** |
|
| 54 |
lowestParentConcept_ID,,** No join mapping for *lowestParentConcept_ID ** |
|
| 55 |
lowestParentName,,** No join mapping for *lowestParentName ** |
|
| 56 |
plantCode,,** No join mapping for *plantCode ** |
|
| 57 |
plantConcept_accessionCode,,** No join mapping for *plantConcept_accessionCode ** |
|
| 58 |
plantConcept_dba_src_ID,,** No join mapping for *plantConcept_dba_src_ID ** |
|
| 59 |
plantConcept_entry_sppID,,** No join mapping for *plantConcept_entry_sppID ** |
|
| 60 |
plantConcept_reference_ID,,** No join mapping for *plantConcept_reference_ID ** |
|
| 61 |
plantDescription,,** No join mapping for *plantDescription ** |
|
| 62 |
section,,** No join mapping for *section ** |
|
| 63 |
sensitiveSpeciesFuzzPlot,,** No join mapping for *sensitiveSpeciesFuzzPlot ** |
|
| 64 |
species,,** No join mapping for speciesBinomial ** full taxonomic name at that rank |
|
| 65 |
subgenus,,** No join mapping for subgenus ** |
|
| 66 |
subspecies,,** No non-empty join mapping for EQUIV#to:species#subspecies ** full taxonomic name at that rank |
|
| 67 |
taxonRank,,** No non-empty join mapping for OMIT#taxonRank ** Omitted because taxonLevel contains this information in text form |
|
| 68 |
tribe,,** No join mapping for *tribe ** |
|
| 69 |
usda_code,,** No join mapping for *usda_code ** |
|
| 70 |
usda_growthForm,,** No join mapping for *usda_growthForm ** |
|
| 71 |
variety,,** No non-empty join mapping for EQUIV#to:species#variety ** full taxonomic name at that rank |
|
| 72 |
woody,,** No join mapping for *woody ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 73 | 2 | |
| inputs/CVS/plantConcept_/new_terms.csv | ||
|---|---|---|
| 12 | 12 |
denorm_quadName,infraspecificEpithet2,,sometimes misparsed as the part after the last + sign in the plantNameWithAuthority |
| 13 | 13 |
denorm_hybridX,*hybridX,, |
| 14 | 14 |
taxonLevel,taxonRank,, |
| 15 |
Division,division_normalized,, |
|
| 15 | 16 |
composite variety,EQUIV#to:species#composite variety,,full taxonomic name at that rank |
| inputs/CVS/plantConcept_/unmapped_terms.csv | ||
|---|---|---|
| 36 | 36 |
*section |
| 37 | 37 |
*composite species |
| 38 | 38 |
speciesBinomial |
| 39 |
division |
|
| inputs/CVS/observation_/postprocess.sql | ||
|---|---|---|
| 1 | 1 |
SELECT util.search_path_append('util');
|
| 2 | 2 |
|
| 3 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("OBSERVATION_ID")$$); -- runtime: ~0 @starscream
|
|
| 3 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("eventID")$$); -- runtime: ~0 @starscream
|
|
| 4 | 4 |
|
| 5 |
SELECT create_if_not_exists($$CREATE INDEX $$||:table_str||%'_parent'||$$ ON $$||:table_str||$$ ("PLOT_ID")$$); -- runtime: ~0 @starscream
|
|
| 5 |
SELECT create_if_not_exists($$CREATE INDEX $$||:table_str||%'_parent'||$$ ON $$||:table_str||$$ ("locationID")$$); -- runtime: ~0 @starscream
|
|
| inputs/CVS/observation_/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CVS/observation_/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<sourceaccessioncode>$PLOT_ID</sourceaccessioncode>
|
|
| 10 |
<sourceaccessioncode>$locationID</sourceaccessioncode>
|
|
| 11 | 11 |
<locationevent> |
| 12 |
<method_id><method><name>$methodNarrative</name></method></method_id>
|
|
| 13 |
<project_id><project><sourceaccessioncode>$PROJECT_ID</sourceaccessioncode></project></project_id>
|
|
| 14 |
<authoreventcode>$authorObsCode</authoreventcode>
|
|
| 15 |
<sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode>
|
|
| 16 |
<locationevent fkey="parent_id"><sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode></locationevent>
|
|
| 17 |
<obsenddate>$obsEndDate</obsenddate>
|
|
| 18 |
<obsstartdate>$obsStartDate</obsstartdate>
|
|
| 12 |
<method_id><method><name>$samplingProtocol</name></method></method_id>
|
|
| 13 |
<project_id><project><sourceaccessioncode>$projectID</sourceaccessioncode></project></project_id>
|
|
| 14 |
<authoreventcode>$authorEventCode</authoreventcode>
|
|
| 15 |
<sourceaccessioncode>$eventID</sourceaccessioncode>
|
|
| 16 |
<locationevent fkey="parent_id"><sourceaccessioncode>$eventID</sourceaccessioncode></locationevent>
|
|
| 17 |
<obsenddate>$endDate</obsenddate>
|
|
| 18 |
<obsstartdate>$startDate</obsstartdate>
|
|
| 19 | 19 |
<soilsample> |
| 20 |
<basesaturation_fraction><_percent_to_fraction><value>$baseSaturation</value></_percent_to_fraction></basesaturation_fraction> |
|
| 21 |
<cationexchangecapacity_cmol_kg>$exchangeCapacity</cationexchangecapacity_cmol_kg>
|
|
| 22 |
<clay_fraction><_percent_to_fraction><value>$soilClay</value></_percent_to_fraction></clay_fraction>
|
|
| 23 |
<organic_fraction><_percent_to_fraction><value>$soilOrganic</value></_percent_to_fraction></organic_fraction>
|
|
| 24 |
<ph>$soilPH</ph>
|
|
| 25 |
<sand_fraction><_percent_to_fraction><value>$soilSand</value></_percent_to_fraction></sand_fraction>
|
|
| 26 |
<silt_fraction><_percent_to_fraction><value>$soilSilt</value></_percent_to_fraction></silt_fraction>
|
|
| 27 |
<texture>$soilTexture</texture>
|
|
| 20 |
<basesaturation_fraction><_percent_to_fraction><value>$baseSaturation_percent</value></_percent_to_fraction></basesaturation_fraction>
|
|
| 21 |
<cationexchangecapacity_cmol_kg>$cationExchangeCapacity_cmol_kg</cationexchangecapacity_cmol_kg>
|
|
| 22 |
<clay_fraction><_percent_to_fraction><value>$clay_percent</value></_percent_to_fraction></clay_fraction>
|
|
| 23 |
<organic_fraction><_percent_to_fraction><value>$organic_percent</value></_percent_to_fraction></organic_fraction>
|
|
| 24 |
<ph>$ph</ph>
|
|
| 25 |
<sand_fraction><_percent_to_fraction><value>$sand_percent</value></_percent_to_fraction></sand_fraction>
|
|
| 26 |
<silt_fraction><_percent_to_fraction><value>$silt_percent</value></_percent_to_fraction></silt_fraction>
|
|
| 27 |
<texture>$texture</texture>
|
|
| 28 | 28 |
</soilsample> |
| 29 | 29 |
</locationevent> |
| 30 | 30 |
</location> |
| inputs/CVS/observation_/VegBIEN.csv | ||
|---|---|---|
| 1 |
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
PLOT_ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 3 |
authorObsCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else", |
|
| 4 |
PLOT_ID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 5 |
PLOT_ID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 6 |
methodNarrative,/location/locationevent/*_id/method/name, |
|
| 7 |
PROJECT_ID,/location/locationevent/*_id/project/sourceaccessioncode, |
|
| 8 |
authorObsCode,"/location/locationevent/_if[@name=""if subplot""]/else/authoreventcode", |
|
| 9 |
OBSERVATION_ID,"/location/locationevent/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 10 |
OBSERVATION_ID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 11 |
authorObsCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 12 |
obsEndDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 13 |
obsStartDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 14 |
PLOT_ID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
|
| 15 |
authorObsCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/authoreventcode", |
|
| 16 |
obsEndDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/1", |
|
| 17 |
obsStartDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/1", |
|
| 18 |
OBSERVATION_ID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/sourceaccessioncode", |
|
| 19 |
OBSERVATION_ID,/location/locationevent/locationevent:[@fkey=parent_id]/sourceaccessioncode, |
|
| 20 |
OBSERVATION_ID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 21 |
PLOT_ID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 22 |
authorObsCode,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 23 |
obsEndDate,/location/locationevent/obsenddate/_alt/1, |
|
| 24 |
obsStartDate,/location/locationevent/obsstartdate/_alt/1, |
|
| 25 |
baseSaturation,/location/locationevent/soilsample/basesaturation_fraction/_percent_to_fraction/value, |
|
| 26 |
exchangeCapacity,/location/locationevent/soilsample/cationexchangecapacity_cmol_kg, |
|
| 27 |
soilClay,/location/locationevent/soilsample/clay_fraction/_percent_to_fraction/value, |
|
| 28 |
soilOrganic,/location/locationevent/soilsample/organic_fraction/_percent_to_fraction/value, |
|
| 29 |
soilPH,/location/locationevent/soilsample/ph, |
|
| 30 |
soilSand,/location/locationevent/soilsample/sand_fraction/_percent_to_fraction/value, |
|
| 31 |
soilSilt,/location/locationevent/soilsample/silt_fraction/_percent_to_fraction/value, |
|
| 32 |
soilTexture,/location/locationevent/soilsample/texture, |
|
| 33 |
PLOT_ID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 34 |
PLOT_ID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
|
| 35 |
COVERMETHOD_ID,,** No join mapping for *COVERMETHOD_ID ** |
|
| 36 |
PREVIOUSOBS_ID,,** No join mapping for *PREVIOUSOBS_ID ** |
|
| 37 |
SOILOBS_ID,,** No join mapping for *SOILOBS_ID ** |
|
| 38 |
SOILTAXON_ID,,** No join mapping for *SOILTAXON_ID ** |
|
| 39 |
STRATUMMETHOD_ID,,** No join mapping for *STRATUMMETHOD_ID ** |
|
| 40 |
accessionCode,,** No join mapping for *accessionCode ** |
|
| 41 |
autoTaxonCover,,** No join mapping for *autoTaxonCover ** |
|
| 42 |
basalArea,,** No join mapping for *basalArea ** |
|
| 43 |
bryophyteQuality,,** No join mapping for *bryophyteQuality ** |
|
| 44 |
coverDispersion,,** No join mapping for *coverDispersion ** |
|
| 45 |
cust_cvs_Al_ppm,,** No join mapping for *cust_cvs_Al_ppm ** |
|
| 46 |
cust_cvs_B_ppm,,** No join mapping for *cust_cvs_B_ppm ** |
|
| 47 |
cust_cvs_Ca_over_Mg_ppm,,** No join mapping for *cust_cvs_Ca_over_Mg_ppm ** |
|
| 48 |
cust_cvs_Ca_ppm,,** No join mapping for *cust_cvs_Ca_ppm ** |
|
| 49 |
cust_cvs_CanopyHeight,,** No join mapping for *cust_cvs_CanopyHeight ** |
|
| 50 |
cust_cvs_CowardinSystem,,** No join mapping for *cust_cvs_CowardinSystem ** |
|
| 51 |
cust_cvs_Cu_ppm,,** No join mapping for *cust_cvs_Cu_ppm ** |
|
| 52 |
cust_cvs_Density,,** No join mapping for *cust_cvs_Density ** |
|
| 53 |
cust_cvs_Fe_ppm,,** No join mapping for *cust_cvs_Fe_ppm ** |
|
| 54 |
cust_cvs_GPSLocationX,,** No join mapping for *cust_cvs_GPSLocationX ** |
|
| 55 |
cust_cvs_GPSLocationY,,** No join mapping for *cust_cvs_GPSLocationY ** |
|
| 56 |
cust_cvs_K_ppm,,** No join mapping for *cust_cvs_K_ppm ** |
|
| 57 |
cust_cvs_Lab,,** No join mapping for *cust_cvs_Lab ** |
|
| 58 |
cust_cvs_LeafPhenology,,** No join mapping for *cust_cvs_LeafPhenology ** |
|
| 59 |
cust_cvs_LeafType,,** No join mapping for *cust_cvs_LeafType ** |
|
| 60 |
cust_cvs_LocationSource,,** No join mapping for *cust_cvs_LocationSource ** |
|
| 61 |
cust_cvs_Mg_ppm,,** No join mapping for *cust_cvs_Mg_ppm ** |
|
| 62 |
cust_cvs_Mn_ppm,,** No join mapping for *cust_cvs_Mn_ppm ** |
|
| 63 |
cust_cvs_N,,** No join mapping for *cust_cvs_N ** |
|
| 64 |
cust_cvs_Na_ppm,,** No join mapping for *cust_cvs_Na_ppm ** |
|
| 65 |
cust_cvs_Ownership,,** No join mapping for *cust_cvs_Ownership ** |
|
| 66 |
cust_cvs_P,,** No join mapping for *cust_cvs_P ** |
|
| 67 |
cust_cvs_S,,** No join mapping for *cust_cvs_S ** |
|
| 68 |
cust_cvs_Zn_ppm,,** No join mapping for *cust_cvs_Zn_ppm ** |
|
| 69 |
cust_cvs_collectionName,,** No join mapping for *cust_cvs_collectionName ** |
|
| 70 |
cust_cvs_compassType,,** No join mapping for *cust_cvs_compassType ** |
|
| 71 |
cust_cvs_lengthSoilProbe,,** No join mapping for *cust_cvs_lengthSoilProbe ** |
|
| 72 |
cust_cvs_mcnab_LFI,,** No join mapping for *cust_cvs_mcnab_LFI ** |
|
| 73 |
cust_cvs_mcnab_LFI_135,,** No join mapping for *cust_cvs_mcnab_LFI_135 ** |
|
| 74 |
cust_cvs_mcnab_LFI_180,,** No join mapping for *cust_cvs_mcnab_LFI_180 ** |
|
| 75 |
cust_cvs_mcnab_LFI_225,,** No join mapping for *cust_cvs_mcnab_LFI_225 ** |
|
| 76 |
cust_cvs_mcnab_LFI_270,,** No join mapping for *cust_cvs_mcnab_LFI_270 ** |
|
| 77 |
cust_cvs_mcnab_LFI_315,,** No join mapping for *cust_cvs_mcnab_LFI_315 ** |
|
| 78 |
cust_cvs_mcnab_LFI_45,,** No join mapping for *cust_cvs_mcnab_LFI_45 ** |
|
| 79 |
cust_cvs_mcnab_LFI_90,,** No join mapping for *cust_cvs_mcnab_LFI_90 ** |
|
| 80 |
cust_cvs_mcnab_LFI_asp,,** No join mapping for *cust_cvs_mcnab_LFI_asp ** |
|
| 81 |
cust_cvs_mcnab_TSI,,** No join mapping for *cust_cvs_mcnab_TSI ** |
|
| 82 |
cust_cvs_mcnab_TSI_135,,** No join mapping for *cust_cvs_mcnab_TSI_135 ** |
|
| 83 |
cust_cvs_mcnab_TSI_180,,** No join mapping for *cust_cvs_mcnab_TSI_180 ** |
|
| 84 |
cust_cvs_mcnab_TSI_225,,** No join mapping for *cust_cvs_mcnab_TSI_225 ** |
|
| 85 |
cust_cvs_mcnab_TSI_270,,** No join mapping for *cust_cvs_mcnab_TSI_270 ** |
|
| 86 |
cust_cvs_mcnab_TSI_315,,** No join mapping for *cust_cvs_mcnab_TSI_315 ** |
|
| 87 |
cust_cvs_mcnab_TSI_45,,** No join mapping for *cust_cvs_mcnab_TSI_45 ** |
|
| 88 |
cust_cvs_mcnab_TSI_90,,** No join mapping for *cust_cvs_mcnab_TSI_90 ** |
|
| 89 |
cust_cvs_mcnab_TSI_asp,,** No join mapping for *cust_cvs_mcnab_TSI_asp ** |
|
| 90 |
cust_cvs_percentBedrock,,** No join mapping for *cust_cvs_percentBedrock ** |
|
| 91 |
cust_cvs_percentBoulder,,** No join mapping for *cust_cvs_percentBoulder ** |
|
| 92 |
cust_cvs_percentCWD,,** No join mapping for *cust_cvs_percentCWD ** |
|
| 93 |
cust_cvs_percentDuff,,** No join mapping for *cust_cvs_percentDuff ** |
|
| 94 |
cust_cvs_percentFWD,,** No join mapping for *cust_cvs_percentFWD ** |
|
| 95 |
cust_cvs_percentGravelCobble,,** No join mapping for *cust_cvs_percentGravelCobble ** |
|
| 96 |
cust_cvs_percentHistosol,,** No join mapping for *cust_cvs_percentHistosol ** |
|
| 97 |
cust_cvs_percentLitter,,** No join mapping for *cust_cvs_percentLitter ** |
|
| 98 |
cust_cvs_percentMineralSoil,,** No join mapping for *cust_cvs_percentMineralSoil ** |
|
| 99 |
cust_cvs_percentNonVasc,,** No join mapping for *cust_cvs_percentNonVasc ** |
|
| 100 |
cust_cvs_percentOther,,** No join mapping for *cust_cvs_percentOther ** |
|
| 101 |
cust_cvs_percentOtherName,,** No join mapping for *cust_cvs_percentOtherName ** |
|
| 102 |
cust_cvs_percentWater,,** No join mapping for *cust_cvs_percentWater ** |
|
| 103 |
cust_cvs_percent_Ca,,** No join mapping for *cust_cvs_percent_Ca ** |
|
| 104 |
cust_cvs_percent_H,,** No join mapping for *cust_cvs_percent_H ** |
|
| 105 |
cust_cvs_percent_K,,** No join mapping for *cust_cvs_percent_K ** |
|
| 106 |
cust_cvs_percent_Mg,,** No join mapping for *cust_cvs_percent_Mg ** |
|
| 107 |
cust_cvs_percent_Na,,** No join mapping for *cust_cvs_percent_Na ** |
|
| 108 |
cust_cvs_percent_Othr,,** No join mapping for *cust_cvs_percent_Othr ** |
|
| 109 |
cust_cvs_postDsgPoly,,** No join mapping for *cust_cvs_postDsgPoly ** |
|
| 110 |
cust_cvs_samplingLevel,,** No join mapping for *cust_cvs_samplingLevel ** |
|
| 111 |
cust_cvs_stemSamplingNarrative,,** No join mapping for *cust_cvs_stemSamplingNarrative ** |
|
| 112 |
cust_cvs_stemsSampled,,** No join mapping for *cust_cvs_stemsSampled ** |
|
| 113 |
cust_cvs_taxaRichness,,** No join mapping for *cust_cvs_taxaRichness ** |
|
| 114 |
cust_eep_plotLastPlantedDate,,** No join mapping for *cust_eep_plotLastPlantedDate ** |
|
| 115 |
cust_eep_plotNotSampled,,** No join mapping for *cust_eep_plotNotSampled ** |
|
| 116 |
cust_eep_plotNotSampledReason,,** No join mapping for *cust_eep_plotNotSampledReason ** |
|
| 117 |
dateAccuracy,,** No join mapping for *dateAccuracy ** |
|
| 118 |
dateEntered,,** No join mapping for *dateEntered ** |
|
| 119 |
dba_notes,,** No join mapping for *dba_notes ** |
|
| 120 |
dba_src_ID,,** No join mapping for *dba_src_ID ** |
|
| 121 |
dominantStratum,,** No join mapping for *dominantStratum ** |
|
| 122 |
effortLevel,,** No join mapping for *effortLevel ** |
|
| 123 |
entry_IntensiveModuleList,,** No join mapping for *entry_IntensiveModuleList ** |
|
| 124 |
entry_ares_herbs,,** No join mapping for *entry_ares_herbs ** |
|
| 125 |
entry_ares_trees,,** No join mapping for *entry_ares_trees ** |
|
| 126 |
entry_currentLandUse,,** No join mapping for *entry_currentLandUse ** |
|
| 127 |
entry_depth,,** No join mapping for *entry_depth ** |
|
| 128 |
entry_elevationUnits,,** No join mapping for *entry_elevationUnits ** |
|
| 129 |
entry_formerLandUse,,** No join mapping for *entry_formerLandUse ** |
|
| 130 |
entry_identificationNarrative,,** No join mapping for *entry_identificationNarrative ** |
|
| 131 |
entry_moduleSizeX,,** No join mapping for *entry_moduleSizeX ** |
|
| 132 |
entry_moduleSizeY,,** No join mapping for *entry_moduleSizeY ** |
|
| 133 |
entry_moduleSize_Overall,,** No join mapping for *entry_moduleSize_Overall ** |
|
| 134 |
entry_numberOfModules,,** No join mapping for *entry_numberOfModules ** |
|
| 135 |
entry_photosTaken,,** No join mapping for *entry_photosTaken ** |
|
| 136 |
entry_physClass,,** No join mapping for *entry_physClass ** |
|
| 137 |
entry_plot,,** No join mapping for *entry_plot ** |
|
| 138 |
entry_plot_X,,** No join mapping for *entry_plot_X ** |
|
| 139 |
entry_plot_Y,,** No join mapping for *entry_plot_Y ** |
|
| 140 |
entry_soilModulesSampled,,** No join mapping for *entry_soilModulesSampled ** |
|
| 141 |
entry_subsequentObsNum,,** No join mapping for *entry_subsequentObsNum ** |
|
| 142 |
entry_taxonomicAuthorityDate,,** No join mapping for *entry_taxonomicAuthorityDate ** |
|
| 143 |
entry_taxonomicAuthority_ID,,** No join mapping for *entry_taxonomicAuthority_ID ** |
|
| 144 |
entry_team,,** No join mapping for *entry_team ** |
|
| 145 |
errors,,** No join mapping for *errors ** |
|
| 146 |
fieldCover,,** No join mapping for *fieldCover ** |
|
| 147 |
fieldHt,,** No join mapping for *fieldHt ** |
|
| 148 |
floatingCover,,** No join mapping for *floatingCover ** |
|
| 149 |
floristicQuality,,** No join mapping for *floristicQuality ** |
|
| 150 |
growthform1Cover,,** No join mapping for *growthform1Cover ** |
|
| 151 |
growthform1Type,,** No join mapping for *growthform1Type ** |
|
| 152 |
growthform2Cover,,** No join mapping for *growthform2Cover ** |
|
| 153 |
growthform2Type,,** No join mapping for *growthform2Type ** |
|
| 154 |
growthform3Cover,,** No join mapping for *growthform3Cover ** |
|
| 155 |
growthform3Type,,** No join mapping for *growthform3Type ** |
|
| 156 |
homogeneity,,** No join mapping for *homogeneity ** |
|
| 157 |
hydrologicRegime,,** No join mapping for *hydrologicRegime ** |
|
| 158 |
landscapeNarrative,,** No join mapping for *landscapeNarrative ** |
|
| 159 |
lichenQuality,,** No join mapping for *lichenQuality ** |
|
| 160 |
nameOther,,** No join mapping for *nameOther ** |
|
| 161 |
nonvascularCover,,** No join mapping for *nonvascularCover ** |
|
| 162 |
nonvascularHt,,** No join mapping for *nonvascularHt ** |
|
| 163 |
notesMgt,,** No join mapping for *notesMgt ** |
|
| 164 |
notesPublic,,** No join mapping for *notesPublic ** |
|
| 165 |
numberOfTaxa,,** No join mapping for *numberOfTaxa ** |
|
| 166 |
observationNarrative,,** No join mapping for *observationNarrative ** |
|
| 167 |
organicDepth,,** No join mapping for *organicDepth ** |
|
| 168 |
originalData,,** No join mapping for *originalData ** |
|
| 169 |
percentBareSoil,,** No join mapping for *percentBareSoil ** |
|
| 170 |
percentBedRock,,** No join mapping for *percentBedRock ** |
|
| 171 |
percentLitter,,** No join mapping for *percentLitter ** |
|
| 172 |
percentOther,,** No join mapping for *percentOther ** |
|
| 173 |
percentRockGravel,,** No join mapping for *percentRockGravel ** |
|
| 174 |
percentWater,,** No join mapping for *percentWater ** |
|
| 175 |
percentWood,,** No join mapping for *percentWood ** |
|
| 176 |
phenologicAspect,,** No join mapping for *phenologicAspect ** |
|
| 177 |
plotValidationLevel,,** No join mapping for *plotValidationLevel ** |
|
| 178 |
representativeness,,** No join mapping for *representativeness ** |
|
| 179 |
revisions,,** No join mapping for *revisions ** |
|
| 180 |
shoreDistance,,** No join mapping for *shoreDistance ** |
|
| 181 |
shrubCover,,** No join mapping for *shrubCover ** |
|
| 182 |
shrubHt,,** No join mapping for *shrubHt ** |
|
| 183 |
soilCoarse,,** No join mapping for *soilCoarse ** |
|
| 184 |
soilColor,,** No join mapping for *soilColor ** |
|
| 185 |
soilDepth,,** No join mapping for *soilDepth ** |
|
| 186 |
soilDepthBottom,,** No join mapping for *soilDepthBottom ** |
|
| 187 |
soilDepthTop,,** No join mapping for *soilDepthTop ** |
|
| 188 |
soilDescription,,** No join mapping for *soilDescription ** |
|
| 189 |
soilDrainage,,** No join mapping for *soilDrainage ** |
|
| 190 |
soilHorizon,,** No join mapping for *soilHorizon ** |
|
| 191 |
soilMapUnit,,** No join mapping for *soilMapUnit ** |
|
| 192 |
soilMoistureRegime,,** No join mapping for *soilMoistureRegime ** |
|
| 193 |
soilObs_dba_src_ID,,** No join mapping for *soilObs_dba_src_ID ** |
|
| 194 |
soilTaxonComplex,,** No join mapping for *soilTaxonComplex ** |
|
| 195 |
soilTaxonSrc,,** No join mapping for *soilTaxonSrc ** |
|
| 196 |
standMaturity,,** No join mapping for *standMaturity ** |
|
| 197 |
stemObservationArea,,** No join mapping for *stemObservationArea ** |
|
| 198 |
stemSampleMethod,,** No join mapping for *stemSampleMethod ** |
|
| 199 |
stemSizeLimit,,** No join mapping for *stemSizeLimit ** |
|
| 200 |
submergedCover,,** No join mapping for *submergedCover ** |
|
| 201 |
submergedHt,,** No join mapping for *submergedHt ** |
|
| 202 |
successionalStatus,,** No join mapping for *successionalStatus ** |
|
| 203 |
taxonObservationArea,,** No join mapping for *taxonObservationArea ** |
|
| 204 |
totalCover,,** No join mapping for *totalCover ** |
|
| 205 |
treeCover,,** No join mapping for *treeCover ** |
|
| 206 |
treeHt,,** No join mapping for *treeHt ** |
|
| 207 |
waterDepth,,** No join mapping for *waterDepth ** |
|
| 208 |
waterSalinity,,** No join mapping for *waterSalinity ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 209 | 2 | |
| inputs/CVS/run | ||
|---|---|---|
| 1 | 1 |
#!/bin/bash -e |
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
|
|
| 2 | 3 |
|
| 3 | 4 |
# `make .../reinstall` runtime: 25 min ("25m30.587s") @starscream
|
| 4 | 5 |
# 45 min ("43m40.625s") @vegbiendev
|
| inputs/CVS/taxonObservation_/postprocess.sql | ||
|---|---|---|
| 1 | 1 |
SELECT util.search_path_append('util');
|
| 2 | 2 |
|
| 3 |
SELECT create_if_not_exists($$CREATE INDEX $$||:table_str||%'_parent'||$$ ON $$||:table_str||$$ ("OBSERVATION_ID")$$); -- runtime: 1 s ("795.083 ms") @starscream
|
|
| 3 |
SELECT create_if_not_exists($$CREATE INDEX $$||:table_str||%'_parent'||$$ ON $$||:table_str||$$ ("eventID")$$); -- runtime: 1 s ("795.083 ms") @starscream
|
|
| 4 | 4 |
|
| 5 | 5 |
|
| 6 | 6 |
UPDATE :table SET |
| 7 |
denorm_kingdom = "Kingdom"
|
|
| 8 |
WHERE denorm_kingdom != "Kingdom"/*implies both NOT NULL*/ -- applies to 1 row (PLANTCONCEPT_ID 92372)
|
|
| 7 |
kingdom = "DUPLICATE#of:denorm_kingdom#Kingdom"
|
|
| 8 |
WHERE kingdom != "DUPLICATE#of:denorm_kingdom#Kingdom"/*implies both NOT NULL*/ -- applies to 1 row (**PLANTCONCEPT_ID 92372)
|
|
| 9 | 9 |
; -- rerun time: 0.5 s ("710.176 ms") @starscream; runtime: 2 s ("2211.789 ms") @starscream
|
| 10 | 10 |
|
| 11 | 11 |
UPDATE :table SET |
| 12 |
denorm_genus = trim(denorm_genus, '{}') -- applies to 6 rows
|
|
| 13 |
WHERE denorm_genus LIKE '{%}' -- applies to 6 rows
|
|
| 12 |
genus_main = trim(genus_main, '{}') -- applies to 6 rows
|
|
| 13 |
WHERE genus_main LIKE '{%}' -- applies to 6 rows
|
|
| 14 | 14 |
; -- rerun time: 0.5 s ("492.670 ms") @starscream; runtime: 0.5 s ("543.942 ms") @starscream
|
| inputs/CVS/taxonObservation_/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CVS/taxonObservation_/test.xml.ref | ||
|---|---|---|
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 | 10 |
<locationevent> |
| 11 |
<sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode>
|
|
| 11 |
<sourceaccessioncode>$eventID</sourceaccessioncode>
|
|
| 12 | 12 |
<locationevent fkey="parent_id"> |
| 13 |
<sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode>
|
|
| 13 |
<sourceaccessioncode>$eventID</sourceaccessioncode>
|
|
| 14 | 14 |
<taxonoccurrence> |
| 15 | 15 |
<aggregateoccurrence> |
| 16 |
<collectiondate>$collectionDate</collectiondate>
|
|
| 17 |
<notes>$notes</notes>
|
|
| 16 |
<collectiondate>$dateCollected</collectiondate>
|
|
| 17 |
<notes>$occurrenceRemarks</notes>
|
|
| 18 | 18 |
<plantobservation> |
| 19 |
<authorplantcode>$collectionNumber</authorplantcode>
|
|
| 19 |
<authorplantcode>$collectorNumber</authorplantcode>
|
|
| 20 | 20 |
<specimenreplicate> |
| 21 |
<catalognumber_dwc>$museumAccessionNumber</catalognumber_dwc>
|
|
| 22 |
<collectionnumber>$collectionNumber</collectionnumber>
|
|
| 21 |
<catalognumber_dwc>$accessionNumber</catalognumber_dwc>
|
|
| 22 |
<collectionnumber>$collectorNumber</collectionnumber>
|
|
| 23 | 23 |
</specimenreplicate> |
| 24 |
<stemobservation><sourceaccessioncode>$stemLocation_ID</sourceaccessioncode></stemobservation>
|
|
| 24 |
<stemobservation><sourceaccessioncode>$stemID</sourceaccessioncode></stemobservation> |
|
| 25 | 25 |
</plantobservation> |
| 26 | 26 |
</aggregateoccurrence> |
| 27 |
<authortaxoncode>$collectionNumber</authortaxoncode>
|
|
| 28 |
<sourceaccessioncode>$TAXONOBSERVATION_ID</sourceaccessioncode>
|
|
| 27 |
<authortaxoncode>$collectorNumber</authortaxoncode>
|
|
| 28 |
<sourceaccessioncode>$taxonOccurrenceID</sourceaccessioncode>
|
|
| 29 | 29 |
<taxondetermination> |
| 30 | 30 |
<taxonverbatim_id> |
| 31 | 31 |
<taxonverbatim> |
| ... | ... | |
| 33 | 33 |
<taxonlabel> |
| 34 | 34 |
<parent_id> |
| 35 | 35 |
<taxonlabel> |
| 36 |
<rank>$taxonLevel</rank>
|
|
| 36 |
<rank>$taxonRank</rank>
|
|
| 37 | 37 |
<parent_id> |
| 38 | 38 |
<taxonlabel> |
| 39 | 39 |
<rank>cultivar</rank> |
| ... | ... | |
| 49 | 49 |
<parent_id> |
| 50 | 50 |
<taxonlabel> |
| 51 | 51 |
<rank>species</rank> |
| 52 |
<taxonepithet>$denorm_species</taxonepithet>
|
|
| 52 |
<taxonepithet>$specificEpithet</taxonepithet>
|
|
| 53 | 53 |
<parent_id> |
| 54 | 54 |
<taxonlabel> |
| 55 | 55 |
<rank>genus</rank> |
| ... | ... | |
| 57 | 57 |
<parent_id> |
| 58 | 58 |
<taxonlabel> |
| 59 | 59 |
<rank>family</rank> |
| 60 |
<taxonepithet>$denorm_family</taxonepithet>
|
|
| 60 |
<taxonepithet>$family</taxonepithet> |
|
| 61 | 61 |
<parent_id> |
| 62 | 62 |
<taxonlabel> |
| 63 | 63 |
<rank>order</rank> |
| 64 |
<taxonepithet>$Order</taxonepithet>
|
|
| 64 |
<taxonepithet>$order</taxonepithet>
|
|
| 65 | 65 |
<parent_id> |
| 66 | 66 |
<taxonlabel> |
| 67 | 67 |
<rank>class</rank> |
| 68 |
<taxonepithet>$Class</taxonepithet>
|
|
| 68 |
<taxonepithet>$class</taxonepithet>
|
|
| 69 | 69 |
<parent_id> |
| 70 | 70 |
<taxonlabel> |
| 71 | 71 |
<rank>phylum</rank> |
| 72 | 72 |
<parent_id> |
| 73 | 73 |
<taxonlabel> |
| 74 | 74 |
<rank>kingdom</rank> |
| 75 |
<taxonepithet>$denorm_kingdom</taxonepithet>
|
|
| 75 |
<taxonepithet>$kingdom</taxonepithet> |
|
| 76 | 76 |
</taxonlabel> |
| 77 | 77 |
</parent_id> |
| 78 | 78 |
</taxonlabel> |
| ... | ... | |
| 95 | 95 |
</parent_id> |
| 96 | 96 |
</taxonlabel> |
| 97 | 97 |
</parent_id> |
| 98 |
<taxonepithet>$denorm_triName</taxonepithet>
|
|
| 98 |
<taxonepithet>$infraspecificEpithet</taxonepithet>
|
|
| 99 | 99 |
</taxonlabel> |
| 100 | 100 |
</parent_id> |
| 101 |
<rank>$taxonLevel</rank>
|
|
| 101 |
<rank>$taxonRank</rank>
|
|
| 102 | 102 |
<taxonomicname> |
| 103 | 103 |
<_merge_prefix> |
| 104 |
<prefix><_taxon_family_require_std><family>$denorm_family</family></_taxon_family_require_std></prefix>
|
|
| 104 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 105 | 105 |
<value> |
| 106 | 106 |
<_alt> |
| 107 |
<1>$plantNameWithAuthority</1>
|
|
| 107 |
<1>$scientificName</1>
|
|
| 108 | 108 |
<2> |
| 109 | 109 |
<_alt> |
| 110 |
<1>$plantname</1>
|
|
| 110 |
<1>$taxonName</1>
|
|
| 111 | 111 |
<2> |
| 112 | 112 |
<_join_words> |
| 113 | 113 |
<2><_filter_genus><value>$genus</value></_filter_genus></2> |
| 114 |
<3>$denorm_species</3>
|
|
| 114 |
<3>$specificEpithet</3>
|
|
| 115 | 115 |
<5> |
| 116 | 116 |
<_join_words> |
| 117 | 117 |
<1> |
| 118 | 118 |
<_if name="if has infraspecificEpithet"> |
| 119 |
<cond>$denorm_triName</cond>
|
|
| 120 |
<then>$taxonLevel</then>
|
|
| 119 |
<cond>$infraspecificEpithet</cond>
|
|
| 120 |
<then>$taxonRank</then>
|
|
| 121 | 121 |
</_if> |
| 122 | 122 |
</1> |
| 123 |
<2>$denorm_triName</2>
|
|
| 123 |
<2>$infraspecificEpithet</2>
|
|
| 124 | 124 |
</_join_words> |
| 125 | 125 |
</5> |
| 126 | 126 |
</_join_words> |
| ... | ... | |
| 133 | 133 |
</taxonomicname> |
| 134 | 134 |
</taxonlabel> |
| 135 | 135 |
</taxonlabel_id> |
| 136 |
<family>$denorm_family</family>
|
|
| 136 |
<family>$family</family> |
|
| 137 | 137 |
<genus>$genus</genus> |
| 138 |
<specific_epithet>$denorm_species</specific_epithet>
|
|
| 139 |
<taxonname>$plantname</taxonname>
|
|
| 140 |
<taxonomicname>$plantNameWithAuthority</taxonomicname>
|
|
| 141 |
<verbatimrank>$taxonLevel</verbatimrank>
|
|
| 138 |
<specific_epithet>$specificEpithet</specific_epithet>
|
|
| 139 |
<taxonname>$taxonName</taxonname>
|
|
| 140 |
<taxonomicname>$scientificName</taxonomicname>
|
|
| 141 |
<verbatimrank>$taxonRank</verbatimrank>
|
|
| 142 | 142 |
</taxonverbatim> |
| 143 | 143 |
</taxonverbatim_id> |
| 144 |
<determinationdate><_dateRangeStart><value>$interpretationDate</value></_dateRangeStart></determinationdate>
|
|
| 145 |
<determinationtype>$interpretationType</determinationtype>
|
|
| 146 |
<iscurrent__verbatim>$currentInterpretation</iscurrent__verbatim>
|
|
| 147 |
<isoriginal>$originalInterpretation</isoriginal>
|
|
| 148 |
<taxonfit>$taxonFit</taxonfit>
|
|
| 144 |
<determinationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></determinationdate>
|
|
| 145 |
<determinationtype>$identificationType</determinationtype>
|
|
| 146 |
<iscurrent__verbatim>$taxon_determination__is_current</iscurrent__verbatim>
|
|
| 147 |
<isoriginal>$taxon_determination__is_original</isoriginal>
|
|
| 148 |
<taxonfit>$identificationQualifier</taxonfit>
|
|
| 149 | 149 |
</taxondetermination> |
| 150 | 150 |
<taxondetermination> |
| 151 | 151 |
<isoriginal>true</isoriginal> |
| 152 |
<taxonverbatim_id><taxonverbatim><taxonname>$authorPlantName</taxonname></taxonverbatim></taxonverbatim_id>
|
|
| 152 |
<taxonverbatim_id><taxonverbatim><taxonname>$originalTaxonName</taxonname></taxonverbatim></taxonverbatim_id>
|
|
| 153 | 153 |
</taxondetermination> |
| 154 | 154 |
</taxonoccurrence> |
| 155 | 155 |
</locationevent> |
| inputs/CVS/taxonObservation_/VegBIEN.csv | ||
|---|---|---|
| 1 |
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
museumAccessionNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
:plot,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/observationtype", |
|
| 4 |
:plot,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/cond/_eq:[right=plot]/left", |
|
| 5 |
museumAccessionNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
| 6 |
museumAccessionNumber,"/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", |
|
| 7 |
museumAccessionNumber,"/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", |
|
| 8 |
TAXONOBSERVATION_ID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 9 |
collectionNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 10 |
OBSERVATION_ID,"/location/locationevent/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 11 |
OBSERVATION_ID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 12 |
OBSERVATION_ID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/sourceaccessioncode", |
|
| 13 |
OBSERVATION_ID,/location/locationevent/locationevent:[@fkey=parent_id]/sourceaccessioncode, |
|
| 14 |
interpretationDate,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value", |
|
| 15 |
taxonFit,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/taxonfit", |
|
| 16 |
collectionDate,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
|
| 17 |
notes,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/notes/_join/1, |
|
| 18 |
collectionNumber,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2, |
|
| 19 |
museumAccessionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
|
| 20 |
collectionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else", |
|
| 21 |
museumAccessionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 22 |
stemLocation_ID,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/sourceaccessioncode, |
|
| 23 |
OBSERVATION_ID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 24 |
stemLocation_ID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_if[@name=""if individual""]/cond/_exists", |
|
| 25 |
collectionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
| 26 |
authorPlantName,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/1", |
|
| 27 |
plantNameWithAuthority,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
|
| 28 |
plantname,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
|
| 29 |
TAXONOBSERVATION_ID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 30 |
collectionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 31 |
TAXONOBSERVATION_ID,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/sourceaccessioncode/_first/1, |
|
| 32 |
taxonLevel,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 33 |
denorm_species,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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","unlike VegBank, this is in fact the epithet, not the full name" |
|
| 34 |
genus,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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", |
|
| 35 |
denorm_family,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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", |
|
| 36 |
Order,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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", |
|
| 37 |
Class,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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", |
|
| 38 |
denorm_kingdom,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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", |
|
| 39 |
denorm_triName,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet, |
|
| 40 |
taxonLevel,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 41 |
taxonLevel,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank", |
|
| 42 |
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 43 |
plantNameWithAuthority,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 44 |
plantname,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
|
| 45 |
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 46 |
denorm_species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,"unlike VegBank, this is in fact the epithet, not the full name" |
|
| 47 |
denorm_triName,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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""]/cond", |
|
| 48 |
taxonLevel,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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", |
|
| 49 |
denorm_triName,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
|
| 50 |
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/family, |
|
| 51 |
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/genus, |
|
| 52 |
denorm_species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/specific_epithet,"unlike VegBank, this is in fact the epithet, not the full name" |
|
| 53 |
plantname,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/taxonname, |
|
| 54 |
plantNameWithAuthority,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/taxonomicname, |
|
| 55 |
taxonLevel,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/verbatimrank, |
|
| 56 |
TAXONOBSERVATION_ID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/_if[@name=""if has taxondetermination""]/cond/_exists", |
|
| 57 |
interpretationDate,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/determinationdate/_alt/1/_dateRangeStart/value, |
|
| 58 |
interpretationType,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/determinationtype, |
|
| 59 |
currentInterpretation,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/iscurrent__verbatim, |
|
| 60 |
originalInterpretation,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/isoriginal, |
|
| 61 |
taxonFit,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/taxonfit, |
|
| 62 |
authorPlantName,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonname, |
|
| 63 |
museumAccessionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
|
| 64 |
collectionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then", |
|
| 65 |
*genus,,"** No join mapping for genus_normalized ** unlike VegBank, does *not* include genus author" |
|
| 66 |
Division,,** No join mapping for division_normalized ** |
|
| 67 |
Kingdom,,** No non-empty join mapping for DUPLICATE#of:denorm_kingdom#Kingdom ** |
|
| 68 |
PLANTCONCEPT_ID,,** No join mapping for *PLANTCONCEPT_ID ** |
|
| 69 |
PLANTNAME_ID,,** No join mapping for *PLANTNAME_ID ** |
|
| 70 |
ROLE_ID,,** No join mapping for *ROLE_ID ** |
|
| 71 |
Subclass,,** No join mapping for *Subclass ** |
|
| 72 |
Subkingdom,,** No join mapping for *Subkingdom ** |
|
| 73 |
TAXONINTERPRETATION_ID,,** No join mapping for *TAXONINTERPRETATION_ID ** |
|
| 74 |
USDAPlantsCode,,** No join mapping for *USDAPlantsCode ** |
|
| 75 |
VascularPlant,,** No join mapping for *VascularPlant ** |
|
| 76 |
collector_ID,,** No non-empty join mapping for UNUSED#collector_ID ** |
|
| 77 |
commonName,,** No join mapping for vernacularName ** |
|
| 78 |
composite family,,** No join mapping for *composite family ** |
|
| 79 |
composite genus,,** No join mapping for *composite genus ** |
|
| 80 |
composite species,,** No join mapping for *composite species ** |
|
| 81 |
composite variety,,** No non-empty join mapping for EQUIV#to:species#composite variety ** full taxonomic name at that rank |
|
| 82 |
currentTaxonInterpPlantConcept_ID,,** No join mapping for *currentTaxonInterpPlantConcept_ID ** |
|
| 83 |
cust_cvs_collectionFlag,,** No join mapping for *cust_cvs_collectionFlag ** |
|
| 84 |
cust_cvs_corner1Presence,,** No join mapping for *cust_cvs_corner1Presence ** |
|
| 85 |
cust_cvs_corner2Presence,,** No join mapping for *cust_cvs_corner2Presence ** |
|
| 86 |
cust_cvs_corner3Presence,,** No join mapping for *cust_cvs_corner3Presence ** |
|
| 87 |
cust_cvs_corner4Presence,,** No join mapping for *cust_cvs_corner4Presence ** |
|
| 88 |
cust_cvs_corner5Presence,,** No join mapping for *cust_cvs_corner5Presence ** |
|
| 89 |
denorm_category,,** No join mapping for *category ** |
|
| 90 |
denorm_division,,"** No join mapping for division_main ** must be _alt-ed with Division because this is missing in 2 rows that have Division, and different from Division in 1 row" |
|
| 91 |
denorm_genus,,** No join mapping for genus_main ** must be _alt-ed with genus because this is missing in 1 row that has genus |
|
| 92 |
denorm_hybridX,,** No join mapping for *hybridX ** |
|
| 93 |
denorm_quadAbbr,,** No join mapping for infraspecificRank2 ** sometimes misparsed as the last + sign in the plantNameWithAuthority |
|
| 94 |
denorm_quadName,,** No join mapping for infraspecificEpithet2 ** sometimes misparsed as the part after the last + sign in the plantNameWithAuthority |
|
| 95 |
denorm_triAbbr,,** No join mapping for infraspecificRank ** |
|
| 96 |
division,,** No join mapping for *division ** |
|
| 97 |
entry_herbLineID,,** No join mapping for *entry_herbLineID ** |
|
| 98 |
entry_sortOrder,,** No join mapping for *entry_sortOrder ** |
|
| 99 |
entry_treeLineID,,** No join mapping for *entry_treeLineID ** |
|
| 100 |
entry_unknownSp,,** No join mapping for *entry_unknownSp ** |
|
| 101 |
exotic,,** No join mapping for *exotic ** |
|
| 102 |
family,,** No non-empty join mapping for DUPLICATE#of:denorm_family#family ** |
|
| 103 |
groupType,,** No join mapping for *groupType ** |
|
| 104 |
growthForm_short,,** No join mapping for *growthForm_short ** |
|
| 105 |
lowestChildRank,,** No join mapping for *lowestChildRank ** |
|
| 106 |
lowestParentConcept_ID,,** No join mapping for *lowestParentConcept_ID ** |
|
| 107 |
lowestParentName,,** No join mapping for *lowestParentName ** |
|
| 108 |
museum_ID,,** No join mapping for *museum_ID ** |
|
| 109 |
notesMgt,,** No join mapping for *notesMgt ** |
|
| 110 |
notesPublic,,** No join mapping for *notesPublic ** |
|
| 111 |
plantCode,,** No join mapping for *plantCode ** |
|
| 112 |
plantConcept_accessionCode,,** No join mapping for *plantConcept_accessionCode ** |
|
| 113 |
plantConcept_dba_src_ID,,** No join mapping for *plantConcept_dba_src_ID ** |
|
| 114 |
plantConcept_entry_sppID,,** No join mapping for *plantConcept_entry_sppID ** |
|
| 115 |
plantConcept_reference_ID,,** No join mapping for *plantConcept_reference_ID ** |
|
| 116 |
plantDescription,,** No join mapping for *plantDescription ** |
|
| 117 |
reference_ID,,** No join mapping for *reference_ID ** |
|
| 118 |
revisions,,** No join mapping for *revisions ** |
|
| 119 |
section,,** No join mapping for *section ** |
|
| 120 |
sensitiveSpeciesFuzzPlot,,** No join mapping for *sensitiveSpeciesFuzzPlot ** |
|
| 121 |
species,,** No join mapping for speciesBinomial ** full taxonomic name at that rank |
|
| 122 |
subgenus,,** No join mapping for subgenus ** |
|
| 123 |
subspecies,,** No non-empty join mapping for EQUIV#to:species#subspecies ** full taxonomic name at that rank |
|
| 124 |
taxonConfidence,,** No join mapping for identificationVerificationStatus ** |
|
| 125 |
taxonInferenceArea,,** No join mapping for *taxonInferenceArea ** |
|
| 126 |
taxonInterpretation_PARTY_ID,,** No join mapping for *taxonInterpretation_PARTY_ID ** |
|
| 127 |
taxonInterpretation_PLANTNAME_ID,,** No join mapping for *taxonInterpretation_PLANTNAME_ID ** |
|
| 128 |
taxonInterpretation_accessionCode,,** No join mapping for *taxonInterpretation_accessionCode ** |
|
| 129 |
taxonInterpretation_dba_src_ID,,** No join mapping for *taxonInterpretation_dba_src_ID ** |
|
| 130 |
taxonObservationNotes,,** No join mapping for *taxonObservationNotes ** |
|
| 131 |
taxonObservation_accessionCode,,** No join mapping for *taxonObservation_accessionCode ** |
|
| 132 |
taxonObservation_dba_src_ID,,** No join mapping for *taxonObservation_dba_src_ID ** |
|
| 133 |
taxonObservation_entry_sppID,,** No join mapping for *taxonObservation_entry_sppID ** |
|
| 134 |
taxonObservation_reference_ID,,** No join mapping for *taxonObservation_reference_ID ** |
|
| 135 |
taxonRank,,** No non-empty join mapping for OMIT#taxonRank ** Omitted because taxonLevel contains this information in text form |
|
| 136 |
temp_taxonUpToDate,,** No join mapping for *temp_taxonUpToDate ** |
|
| 137 |
tribe,,** No join mapping for *tribe ** |
|
| 138 |
usda_code,,** No join mapping for *usda_code ** |
|
| 139 |
usda_growthForm,,** No join mapping for *usda_growthForm ** |
|
| 140 |
variety,,** No non-empty join mapping for EQUIV#to:species#variety ** full taxonomic name at that rank |
|
| 141 |
woody,,** No join mapping for *woody ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 142 | 2 | |
| inputs/CVS/plot_/postprocess.sql | ||
|---|---|---|
| 1 | 1 |
SELECT util.search_path_append('util');
|
| 2 | 2 |
|
| 3 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("PLOT_ID")$$); -- runtime: ~0 ("78.941 ms") @starscream
|
|
| 3 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("locationID")$$); -- runtime: ~0 ("78.941 ms") @starscream
|
|
| 4 | 4 |
|
| 5 | 5 |
|
| 6 | 6 |
-- map_*() derived cols |
| ... | ... | |
| 27 | 27 |
LANGUAGE sql IMMUTABLE |
| 28 | 28 |
COST 100; |
| 29 | 29 |
|
| 30 |
SELECT mk_derived_col((:table_str, 'accessRights'), $$map_access_rights("confidentialityStatus")$$); -- runtime: 0.5 s ("292.078 ms") @starscream
|
|
| 30 |
SELECT mk_derived_col((:table_str, 'accessRights'), $$map_access_rights("accessRights_verbatim")$$); -- runtime: 0.5 s ("292.078 ms") @starscream
|
|
| 31 | 31 |
|
| 32 | 32 |
CREATE OR REPLACE FUNCTION map_fuzzing(value integer) |
| 33 | 33 |
RETURNS double precision AS |
| ... | ... | |
| 50 | 50 |
LANGUAGE sql IMMUTABLE |
| 51 | 51 |
COST 100; |
| 52 | 52 |
|
| 53 |
SELECT mk_derived_col((:table_str, 'coordinateUncertaintyInMeters__from_fuzzing'), $$map_fuzzing("confidentialityStatus")$$); -- runtime: 0.2 s ("199.359 ms") @starscream
|
|
| 53 |
SELECT mk_derived_col((:table_str, 'coordinateUncertaintyInMeters__from_fuzzing'), $$map_fuzzing("accessRights_verbatim")$$); -- runtime: 0.2 s ("199.359 ms") @starscream
|
|
| 54 | 54 |
|
| 55 | 55 |
|
| 56 | 56 |
SELECT mk_derived_col((:table_str, 'coordinateUncertaintyInMeters'), |
| 57 |
$$GREATEST("coordinateUncertaintyInMeters__from_fuzzing", "locationAccuracy")$$)
|
|
| 57 |
$$GREATEST("coordinateUncertaintyInMeters__from_fuzzing", "coordinateUncertaintyInMeters__from_coords")$$)
|
|
| 58 | 58 |
; -- runtime: 0.2 s ("172.425 ms") @starscream
|
| inputs/CVS/plot_/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CVS/plot_/map.csv | ||
|---|---|---|
| 64 | 64 |
quadrangle,*quadrangle,, |
| 65 | 65 |
Geographic Name,*Geographic Name,, |
| 66 | 66 |
River Basin,*River Basin,, |
| 67 |
accessRights,accessRights,, |
|
| 68 |
coordinateUncertaintyInMeters__from_fuzzing,coordinateUncertaintyInMeters__from_fuzzing,, |
|
| 69 |
coordinateUncertaintyInMeters,coordinateUncertaintyInMeters,, |
|
| inputs/CVS/plot_/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<authorlocationcode>$authorPlotCode</authorlocationcode>
|
|
| 11 |
<sourceaccessioncode>$PLOT_ID</sourceaccessioncode>
|
|
| 10 |
<authorlocationcode>$locationName</authorlocationcode>
|
|
| 11 |
<sourceaccessioncode>$locationID</sourceaccessioncode>
|
|
| 12 | 12 |
<accesslevel>$accessRights</accesslevel> |
| 13 |
<area_m2>$area</area_m2>
|
|
| 14 |
<elevation_m>$elevation</elevation_m> |
|
| 15 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locationNarrative</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
|
|
| 13 |
<area_m2>$plotArea_m2</area_m2>
|
|
| 14 |
<elevation_m>$elevationInMeters</elevation_m>
|
|
| 15 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
|
|
| 16 | 16 |
<landform>$landform</landform> |
| 17 |
<locationnarrative>$locationNarrative</locationnarrative>
|
|
| 17 |
<locationnarrative>$locality</locationnarrative>
|
|
| 18 | 18 |
<locationplace> |
| 19 | 19 |
<place_id> |
| 20 | 20 |
<place> |
| 21 | 21 |
<coordinates_id> |
| 22 | 22 |
<coordinates> |
| 23 | 23 |
<coordsaccuracy_m><_noCV><value>$coordinateUncertaintyInMeters</value></_noCV></coordsaccuracy_m> |
| 24 |
<footprintgeometry_dwc>$shape</footprintgeometry_dwc>
|
|
| 24 |
<footprintgeometry_dwc>$footprintWKT</footprintgeometry_dwc>
|
|
| 25 | 25 |
<latitude_deg> |
| 26 | 26 |
<_nullIf> |
| 27 | 27 |
<null>0</null> |
| 28 | 28 |
<type>float</type> |
| 29 |
<value>$latitude</value>
|
|
| 29 |
<value>$decimalLatitude</value>
|
|
| 30 | 30 |
</_nullIf> |
| 31 | 31 |
</latitude_deg> |
| 32 | 32 |
<longitude_deg> |
| 33 | 33 |
<_nullIf> |
| 34 | 34 |
<null>0</null> |
| 35 | 35 |
<type>float</type> |
| 36 |
<value>$longitude</value>
|
|
| 36 |
<value>$decimalLongitude</value>
|
|
| 37 | 37 |
</_nullIf> |
| 38 | 38 |
</longitude_deg> |
| 39 | 39 |
</coordinates> |
| 40 | 40 |
</coordinates_id> |
| 41 | 41 |
<continent>$continent</continent> |
| 42 |
<country>$COUNTRY</country>
|
|
| 42 |
<country>$country</country>
|
|
| 43 | 43 |
<county>$county</county> |
| 44 | 44 |
<matched_place_id> |
| 45 | 45 |
<place> |
| ... | ... | |
| 51 | 51 |
<_nullIf> |
| 52 | 52 |
<null>0</null> |
| 53 | 53 |
<type>float</type> |
| 54 |
<value>$latitude</value>
|
|
| 54 |
<value>$decimalLatitude</value>
|
|
| 55 | 55 |
</_nullIf> |
| 56 | 56 |
</latitude_deg> |
| 57 | 57 |
<longitude_deg> |
| 58 | 58 |
<_nullIf> |
| 59 | 59 |
<null>0</null> |
| 60 | 60 |
<type>float</type> |
| 61 |
<value>$longitude</value>
|
|
| 61 |
<value>$decimalLongitude</value>
|
|
| 62 | 62 |
</_nullIf> |
| 63 | 63 |
</longitude_deg> |
| 64 | 64 |
</coordinates> |
| 65 | 65 |
</coordinates_id> |
| 66 |
<country>$COUNTRY</country>
|
|
| 66 |
<country>$country</country>
|
|
| 67 | 67 |
<county>$county</county> |
| 68 | 68 |
<stateprovince>$stateProvince</stateprovince> |
| 69 | 69 |
</place> |
| ... | ... | |
| 72 | 72 |
</place> |
| 73 | 73 |
</place_id> |
| 74 | 74 |
</locationplace> |
| 75 |
<parent_id><location><sourceaccessioncode>$PARENT_ID</sourceaccessioncode></location></parent_id>
|
|
| 75 |
<parent_id><location><sourceaccessioncode>$parentLocationID</sourceaccessioncode></location></parent_id>
|
|
| 76 | 76 |
<slopeaspect_deg> |
| 77 | 77 |
<_alt> |
| 78 | 78 |
<1><_compass><value>$slopeAspect</value></_compass></1> |
| inputs/CVS/plot_/unmapped_terms.csv | ||
|---|---|---|
| 37 | 37 |
*quadrangle |
| 38 | 38 |
*Geographic Name |
| 39 | 39 |
*River Basin |
| 40 |
coordinateUncertaintyInMeters__from_fuzzing |
|
| inputs/CVS/plot_/VegBIEN.csv | ||
|---|---|---|
| 1 |
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
authorPlotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
|
| 3 |
PLOT_ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 4 |
PLOT_ID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 5 |
authorPlotCode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
|
| 6 |
PLOT_ID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 7 |
accessRights,/location/accesslevel, |
|
| 8 |
area,/location/area_m2,"assuming units are the same as VegBank's corresponding field (""Total area of the plot in m2"", http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename#area)"
|
|
| 9 |
elevation,/location/elevation_m/_alt/1,"assuming units are the same as VegBank's corresponding field (""The elevation of the plot origin in meters above sea level"", http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename#elevation)"
|
|
| 10 |
locationNarrative,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 11 |
landform,/location/landform, |
|
| 12 |
authorPlotCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then", |
|
| 13 |
PLOT_ID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
|
| 14 |
PLOT_ID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 15 |
authorPlotCode,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 16 |
locationNarrative,/location/locationnarrative/_merge/1, |
|
| 17 |
coordinateUncertaintyInMeters,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_m/_noCV/value, |
|
| 18 |
shape,/location/locationplace/*_id/place/*_id/coordinates/footprintgeometry_dwc, |
|
| 19 |
latitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 20 |
longitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 21 |
continent,/location/locationplace/*_id/place/continent, |
|
| 22 |
COUNTRY,/location/locationplace/*_id/place/country, |
|
| 23 |
county,/location/locationplace/*_id/place/county, |
|
| 24 |
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" |
|
| 25 |
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" |
|
| 26 |
COUNTRY,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 27 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 28 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 29 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
|
| 30 |
PARENT_ID,/location/parent_id/location/sourceaccessioncode, |
|
| 31 |
slopeAspect,/location/slopeaspect_deg/_alt/1/_compass/value, |
|
| 32 |
minSlopeAspect,/location/slopeaspect_deg/_alt/2/_avg/1, |
|
| 33 |
maxSlopeAspect,/location/slopeaspect_deg/_alt/2/_avg/2, |
|
| 34 |
slopeGradient,/location/slopegradient_fraction/_alt/1, |
|
| 35 |
minSlopeGradient,/location/slopegradient_fraction/_alt/2/_avg/1, |
|
| 36 |
maxSlopeGradient,/location/slopegradient_fraction/_alt/2/_avg/2, |
|
| 37 |
PLOT_ID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 38 |
PLOT_ID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
|
| 39 |
Geographic Name,,** No join mapping for *Geographic Name ** |
|
| 40 |
REPLACEMENTPLOT_ID,,** No join mapping for *REPLACEMENTPLOT_ID ** |
|
| 41 |
River Basin,,** No join mapping for *River Basin ** |
|
| 42 |
accessionCode,,** No join mapping for *accessionCode ** |
|
| 43 |
area|country|territory,,** No non-empty join mapping for DUPLICATE#of:COUNTRY#area|country|territory ** |
|
| 44 |
authorCoordinateType,,** No join mapping for *authorCoordinateType ** |
|
| 45 |
authorCoordinateUnits,,** No join mapping for *authorCoordinateUnits ** |
|
| 46 |
authorDatum,,** No join mapping for *authorDatum ** |
|
| 47 |
authorE,,** No join mapping for *authorE ** |
|
| 48 |
authorLocation,,** No join mapping for *authorLocation ** |
|
| 49 |
authorN,,** No join mapping for *authorN ** |
|
| 50 |
authorZone,,** No join mapping for *authorZone ** |
|
| 51 |
azimuth,,** No join mapping for *azimuth ** |
|
| 52 |
confidentialityFieldsBlocked,,** No join mapping for *confidentialityFieldsBlocked ** |
|
| 53 |
confidentialityReason,,** No join mapping for *confidentialityReason ** |
|
| 54 |
confidentialityStatus,,** No join mapping for accessRights_verbatim ** |
|
| 55 |
coordinateUncertaintyInMeters__from_fuzzing,,** No join mapping for coordinateUncertaintyInMeters__from_fuzzing ** |
|
| 56 |
county_,,** No non-empty join mapping for DUPLICATE#of:county#county_ ** |
|
| 57 |
cust_cvs_province,,** No join mapping for *cust_cvs_province ** |
|
| 58 |
cust_eep_reach,,** No join mapping for *cust_eep_reach ** |
|
| 59 |
dateentered,,** No join mapping for *dateentered ** |
|
| 60 |
dba_src_ID,,** No join mapping for *dba_src_ID ** |
|
| 61 |
dsgpoly,,** No join mapping for *dsgpoly ** |
|
| 62 |
elevationAccuracy,,** No join mapping for *elevationAccuracy ** |
|
| 63 |
elevationRange,,** No non-empty join mapping for UNUSED#elevationRange ** |
|
| 64 |
layoutNarrative,,** No join mapping for *layoutNarrative ** |
|
| 65 |
locationAccuracy,,"** No join mapping for coordinateUncertaintyInMeters__from_coords ** assuming units are the same as VegBank's corresponding field (""within this many meters of the reported location"", http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename¶ms=plot#locationAccuracy)"
|
|
| 66 |
notesMgt,,** No join mapping for *notesMgt ** |
|
| 67 |
notesPublic,,** No join mapping for *notesPublic ** |
|
| 68 |
permanence,,** No join mapping for *permanence ** |
|
| 69 |
placementMethod,,** No join mapping for *placementMethod ** |
|
| 70 |
plotObsolete,,** No join mapping for *plotObsolete ** |
|
| 71 |
plotRationaleNarrative,,** No join mapping for *plotRationaleNarrative ** |
|
| 72 |
quadrangle,,** No join mapping for *quadrangle ** |
|
| 73 |
realLatitude,,** No non-empty join mapping for UNUSED#realLatitude ** |
|
| 74 |
realLongitude,,** No non-empty join mapping for UNUSED#realLongitude ** |
|
| 75 |
reference_ID,,** No join mapping for *reference_ID ** |
|
| 76 |
region|state|province,,** No non-empty join mapping for DUPLICATE#of:stateProvince#region|state|province ** |
|
| 77 |
revisions,,** No join mapping for *revisions ** |
|
| 78 |
rockType,,** No join mapping for *rockType ** |
|
| 79 |
standSize,,** No join mapping for *standSize ** |
|
| 80 |
submitter_email,,** No join mapping for *submitter_email ** |
|
| 81 |
submitter_givenname,,** No join mapping for *submitter_givenname ** |
|
| 82 |
submitter_surname,,** No join mapping for *submitter_surname ** |
|
| 83 |
surficialDeposits,,** No join mapping for *surficialDeposits ** |
|
| 84 |
topoPosition,,** No join mapping for *topoPosition ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 85 | 2 | |
Also available in: Unified diff
inputs/CVS/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource