Revision 10386
Added by Aaron Marcuse-Kubitza over 11 years ago
| inputs/BRIT/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
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| 0 | 3 | |
| inputs/BRIT/specimen_flat/postprocess.sql | ||
|---|---|---|
| 1 | 1 |
SELECT util.search_path_append('util');
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| 2 | 2 |
|
| 3 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY (specimen_id)$$);
|
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| 3 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("dataProviderRecordID")$$);
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| 4 | 4 |
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| 5 | 5 |
|
| 6 | 6 |
-- map_nulls() derived cols |
| ... | ... | |
| 14 | 14 |
LANGUAGE sql IMMUTABLE |
| 15 | 15 |
COST 100; |
| 16 | 16 |
|
| 17 |
SELECT mk_derived_col((:table_str, 'diameterBreastHeight_min_cm'), $$map_nulls__nonzero("DBH_Min" )$$); -- runtime: 0.2 s ("Time: 172.094 ms") @starscream
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| 18 |
SELECT mk_derived_col((:table_str, 'diameterBreastHeight_max_cm'), $$map_nulls__nonzero("DBH_Max" )$$); -- runtime: 0.2 s ("Time: 161.774 ms") @starscream
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| 19 |
SELECT mk_derived_col((:table_str, 'height_min_m' ), $$map_nulls__nonzero("Height_Min")$$); -- runtime: 0.2 s ("Time: 153.984 ms") @starscream
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| 20 |
SELECT mk_derived_col((:table_str, 'height_max_m' ), $$map_nulls__nonzero("Height_Max")$$); -- runtime: 0.2 s ("Time: 207.515 ms") @starscream
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| 17 |
SELECT mk_derived_col((:table_str, 'diameterBreastHeight_min_cm'), $$map_nulls__nonzero("diameterBreastHeight_min_cm_verbatim")$$); -- runtime: 0.2 s ("Time: 172.094 ms") @starscream
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| 18 |
SELECT mk_derived_col((:table_str, 'diameterBreastHeight_max_cm'), $$map_nulls__nonzero("diameterBreastHeight_max_cm_verbatim")$$); -- runtime: 0.2 s ("Time: 161.774 ms") @starscream
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| 19 |
SELECT mk_derived_col((:table_str, 'height_min_m' ), $$map_nulls__nonzero("height_min_m_verbatim" )$$); -- runtime: 0.2 s ("Time: 153.984 ms") @starscream
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| 20 |
SELECT mk_derived_col((:table_str, 'height_max_m' ), $$map_nulls__nonzero("height_max_m_verbatim" )$$); -- runtime: 0.2 s ("Time: 207.515 ms") @starscream
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| 21 | 21 |
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| 22 | 22 |
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| 23 | 23 |
SELECT mk_derived_col((:table_str, 'occurrenceRemarks'), |
| 24 |
$$CASE WHEN "Locality_Description" IS NOT NULL THEN "Notes_Plant" END$$)
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| 24 |
$$CASE WHEN "locality__area__main" IS NOT NULL THEN "occurrenceRemarks_verbatim" END$$)
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| 25 | 25 |
; -- runtime: 0.3 s ("Time: 311.190 ms") @starscream
|
| 26 | 26 |
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| 27 |
SELECT mk_derived_col((:table_str, 'diameterBreastHeight_cm'), $$_avg("DBH_Min" , "DBH_Max" )$$); -- runtime: 0.3 s ("Time: 326.615 ms") @starscream
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| 28 |
SELECT mk_derived_col((:table_str, 'height_m'), $$_avg("Height_Min", "Height_Max")$$); -- runtime: 0.3 s ("Time: 346.548 ms") @starscream
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| 27 |
SELECT mk_derived_col((:table_str, 'diameterBreastHeight_cm'), $$_avg("diameterBreastHeight_min_cm_verbatim", "diameterBreastHeight_max_cm_verbatim")$$); -- runtime: 0.3 s ("Time: 326.615 ms") @starscream
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| 28 |
SELECT mk_derived_col((:table_str, 'height_m'), $$_avg("height_min_m_verbatim" , "height_max_m_verbatim" )$$); -- runtime: 0.3 s ("Time: 346.548 ms") @starscream
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| 29 | 29 |
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| 30 | 30 |
SELECT mk_derived_col((:table_str, 'recordedBy'), |
| 31 |
$$_join("Collector_Abbrev_Name", "Collection_Team")$$)
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$$_join("recordedBy_primary", "recordedBy_additional")$$)
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| 32 | 32 |
; -- runtime: 0.3 s ("Time: 281.817 ms") @starscream
|
| 33 | 33 |
SELECT mk_derived_col((:table_str, 'locality'), |
| 34 |
$$_join("Locality_Summary", "Locality_Description", "Locality_Site_Specific")$$)
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| 34 |
$$_join("locality__area__prefix", "locality__area__main", "locality__spot")$$)
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| 35 | 35 |
; -- runtime: 0.3 s ("Time: 254.771 ms") @starscream
|
| inputs/BRIT/specimen_flat/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
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| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
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| 0 | 3 | |
| inputs/BRIT/specimen_flat/map.csv | ||
|---|---|---|
| 59 | 59 |
Year_Identified,yearIdentified,, |
| 60 | 60 |
Month_Identified,monthIdentified,, |
| 61 | 61 |
Day_Identified,dayIdentified,, |
| 62 |
diameterBreastHeight_min_cm,diameterBreastHeight_min_cm,, |
|
| 63 |
diameterBreastHeight_max_cm,diameterBreastHeight_max_cm,, |
|
| 64 |
height_min_m,height_min_m,, |
|
| 65 |
height_max_m,height_max_m,, |
|
| 66 |
occurrenceRemarks,occurrenceRemarks,, |
|
| 67 |
diameterBreastHeight_cm,diameterBreastHeight_cm,, |
|
| 68 |
height_m,height_m,, |
|
| 69 |
recordedBy,recordedBy,, |
|
| 70 |
locality,locality,, |
|
| inputs/BRIT/specimen_flat/test.xml.ref | ||
|---|---|---|
| 9 | 9 |
<location> |
| 10 | 10 |
<authorlocationcode> |
| 11 | 11 |
<_alt> |
| 12 |
<1>$specimen_id</1>
|
|
| 12 |
<1>$dataProviderRecordID</1>
|
|
| 13 | 13 |
<2> |
| 14 | 14 |
<_join> |
| 15 |
<1>$Institution_Code</1>
|
|
| 16 |
<3>$Catalog_Number</3>
|
|
| 15 |
<1>$specimenHolderInstitutions</1>
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|
| 16 |
<3>$accessionNumber</3>
|
|
| 17 | 17 |
</_join> |
| 18 | 18 |
</2> |
| 19 | 19 |
</_alt> |
| 20 | 20 |
</authorlocationcode> |
| 21 | 21 |
<elevation_m> |
| 22 | 22 |
<_avg> |
| 23 |
<1>$Elevation_Min</1>
|
|
| 24 |
<2>$Elevation_Max</2>
|
|
| 23 |
<1>$minimumElevationInMeters</1>
|
|
| 24 |
<2>$maximumElevationInMeters</2>
|
|
| 25 | 25 |
</_avg> |
| 26 | 26 |
</elevation_m> |
| 27 | 27 |
<iscultivated> |
| ... | ... | |
| 29 | 29 |
<locationnarrative> |
| 30 | 30 |
<_join> |
| 31 | 31 |
<1>$locality</1> |
| 32 |
<3>$Habitat_Description</3>
|
|
| 32 |
<3>$habitat</3>
|
|
| 33 | 33 |
</_join> |
| 34 | 34 |
</locationnarrative> |
| 35 | 35 |
</_locationnarrative_is_cultivated> |
| 36 | 36 |
</iscultivated> |
| 37 | 37 |
<locationevent> |
| 38 |
<method_id><method><name>$Collection_Method</name></method></method_id>
|
|
| 39 |
<project_id><project><projectname>$Project_Name</projectname></project></project_id>
|
|
| 38 |
<method_id><method><name>$samplingProtocol</name></method></method_id>
|
|
| 39 |
<project_id><project><projectname>$projectName</projectname></project></project_id>
|
|
| 40 | 40 |
<taxonoccurrence> |
| 41 | 41 |
<aggregateoccurrence> |
| 42 | 42 |
<collectiondate> |
| 43 | 43 |
<_alt> |
| 44 |
<1>$Date_of_Collection</1>
|
|
| 44 |
<1>$dateCollected</1>
|
|
| 45 | 45 |
<2> |
| 46 | 46 |
<_date> |
| 47 | 47 |
<day> |
| 48 | 48 |
<_nullIf> |
| 49 | 49 |
<null>0</null> |
| 50 | 50 |
<type>float</type> |
| 51 |
<value>$Day_Collected</value>
|
|
| 51 |
<value>$dayCollected</value>
|
|
| 52 | 52 |
</_nullIf> |
| 53 | 53 |
</day> |
| 54 | 54 |
<month> |
| 55 | 55 |
<_nullIf> |
| 56 | 56 |
<null>0</null> |
| 57 | 57 |
<type>float</type> |
| 58 |
<value>$Month_Collected</value>
|
|
| 58 |
<value>$monthCollected</value>
|
|
| 59 | 59 |
</_nullIf> |
| 60 | 60 |
</month> |
| 61 | 61 |
<year> |
| 62 | 62 |
<_nullIf> |
| 63 | 63 |
<null>0</null> |
| 64 | 64 |
<type>float</type> |
| 65 |
<value>$Year_Collected</value>
|
|
| 65 |
<value>$yearCollected</value>
|
|
| 66 | 66 |
</_nullIf> |
| 67 | 67 |
</year> |
| 68 | 68 |
</_date> |
| ... | ... | |
| 71 | 71 |
</collectiondate> |
| 72 | 72 |
<notes>$occurrenceRemarks</notes> |
| 73 | 73 |
<plantobservation> |
| 74 |
<authorplantcode>$Collection_Number</authorplantcode>
|
|
| 75 |
<reproductivecondition>$Phenology_Stage</reproductivecondition>
|
|
| 74 |
<authorplantcode>$collectorNumber</authorplantcode>
|
|
| 75 |
<reproductivecondition>$reproductiveCondition</reproductivecondition>
|
|
| 76 | 76 |
<specimenreplicate> |
| 77 |
<catalognumber_dwc>$Catalog_Number</catalognumber_dwc>
|
|
| 78 |
<collectionnumber>$Collection_Number</collectionnumber>
|
|
| 77 |
<catalognumber_dwc>$accessionNumber</catalognumber_dwc>
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|
| 78 |
<collectionnumber>$collectorNumber</collectionnumber>
|
|
| 79 | 79 |
<institution_id> |
| 80 | 80 |
<sourcelist> |
| 81 |
<name>$Institution_Code</name>
|
|
| 81 |
<name>$specimenHolderInstitutions</name>
|
|
| 82 | 82 |
<sourcename> |
| 83 | 83 |
<name> |
| 84 | 84 |
<_split> |
| 85 | 85 |
<separator>[,;] *</separator> |
| 86 |
<value>$Institution_Code</value>
|
|
| 86 |
<value>$specimenHolderInstitutions</value>
|
|
| 87 | 87 |
</_split> |
| 88 | 88 |
</name> |
| 89 | 89 |
</sourcename> |
| 90 | 90 |
</sourcelist> |
| 91 | 91 |
</institution_id> |
| 92 |
<sourceaccessioncode>$specimen_id</sourceaccessioncode>
|
|
| 92 |
<sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>
|
|
| 93 | 93 |
</specimenreplicate> |
| 94 | 94 |
<stemobservation> |
| 95 | 95 |
<diameterbreastheight_m><_cm_to_m><value>$diameterBreastHeight_cm</value></_cm_to_m></diameterbreastheight_m> |
| ... | ... | |
| 98 | 98 |
</plantobservation> |
| 99 | 99 |
</aggregateoccurrence> |
| 100 | 100 |
<collector_id><party><fullname>$recordedBy</fullname></party></collector_id> |
| 101 |
<sourceaccessioncode>$specimen_id</sourceaccessioncode>
|
|
| 101 |
<sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>
|
|
| 102 | 102 |
<taxondetermination> |
| 103 |
<party_id><party><fullname>$Determined_By_Name</fullname></party></party_id>
|
|
| 103 |
<party_id><party><fullname>$identifiedBy</fullname></party></party_id>
|
|
| 104 | 104 |
<taxonverbatim_id> |
| 105 | 105 |
<taxonverbatim> |
| 106 | 106 |
<taxonlabel_id> |
| ... | ... | |
| 122 | 122 |
<parent_id> |
| 123 | 123 |
<taxonlabel> |
| 124 | 124 |
<rank>species</rank> |
| 125 |
<taxonepithet>$Specific_Epithet</taxonepithet>
|
|
| 125 |
<taxonepithet>$specificEpithet</taxonepithet>
|
|
| 126 | 126 |
<parent_id> |
| 127 | 127 |
<taxonlabel> |
| 128 | 128 |
<rank>genus</rank> |
| 129 |
<taxonepithet>$Genus_Name</taxonepithet>
|
|
| 129 |
<taxonepithet>$genus</taxonepithet>
|
|
| 130 | 130 |
<parent_id> |
| 131 | 131 |
<taxonlabel> |
| 132 | 132 |
<rank>family</rank> |
| 133 |
<taxonepithet>$Family_Name</taxonepithet>
|
|
| 133 |
<taxonepithet>$family</taxonepithet>
|
|
| 134 | 134 |
<parent_id> |
| 135 | 135 |
<taxonlabel> |
| 136 | 136 |
<rank>order</rank> |
| 137 |
<taxonepithet>$Order_Name</taxonepithet>
|
|
| 137 |
<taxonepithet>$order</taxonepithet>
|
|
| 138 | 138 |
<parent_id> |
| 139 | 139 |
<taxonlabel> |
| 140 | 140 |
<rank>class</rank> |
| 141 |
<taxonepithet>$Class_Name</taxonepithet>
|
|
| 141 |
<taxonepithet>$class</taxonepithet>
|
|
| 142 | 142 |
<parent_id> |
| 143 | 143 |
<taxonlabel> |
| 144 | 144 |
<rank>phylum</rank> |
| 145 |
<taxonepithet>$Division_Name</taxonepithet>
|
|
| 145 |
<taxonepithet>$phylum</taxonepithet>
|
|
| 146 | 146 |
<parent_id> |
| 147 | 147 |
<taxonlabel> |
| 148 | 148 |
<rank>kingdom</rank> |
| 149 |
<taxonepithet>$Kingdom_Name</taxonepithet>
|
|
| 149 |
<taxonepithet>$kingdom</taxonepithet>
|
|
| 150 | 150 |
</taxonlabel> |
| 151 | 151 |
</parent_id> |
| 152 | 152 |
</taxonlabel> |
| ... | ... | |
| 169 | 169 |
</parent_id> |
| 170 | 170 |
</taxonlabel> |
| 171 | 171 |
</parent_id> |
| 172 |
<taxonepithet>$Infra_Epithet</taxonepithet>
|
|
| 172 |
<taxonepithet>$infraspecificEpithet</taxonepithet>
|
|
| 173 | 173 |
</taxonlabel> |
| 174 | 174 |
</parent_id> |
| 175 | 175 |
<taxonomicname> |
| 176 | 176 |
<_merge_prefix> |
| 177 |
<prefix><_taxon_family_require_std><family>$Family_Name</family></_taxon_family_require_std></prefix>
|
|
| 177 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
|
|
| 178 | 178 |
<value> |
| 179 | 179 |
<_alt> |
| 180 |
<1>$Scientific_Name</1>
|
|
| 180 |
<1>$scientificName</1>
|
|
| 181 | 181 |
<2> |
| 182 | 182 |
<_join_words> |
| 183 | 183 |
<1> |
| 184 | 184 |
<_join_words> |
| 185 |
<2><_filter_genus><value>$Genus_Name</value></_filter_genus></2>
|
|
| 186 |
<3>$Specific_Epithet</3>
|
|
| 187 |
<5>$Infra_Epithet</5>
|
|
| 185 |
<2><_filter_genus><value>$genus</value></_filter_genus></2>
|
|
| 186 |
<3>$specificEpithet</3>
|
|
| 187 |
<5>$infraspecificEpithet</5>
|
|
| 188 | 188 |
</_join_words> |
| 189 | 189 |
</1> |
| 190 |
<2>$Sp_Authority</2>
|
|
| 190 |
<2>$scientificNameAuthorship</2>
|
|
| 191 | 191 |
</_join_words> |
| 192 | 192 |
</2> |
| 193 | 193 |
</_alt> |
| ... | ... | |
| 196 | 196 |
</taxonomicname> |
| 197 | 197 |
</taxonlabel> |
| 198 | 198 |
</taxonlabel_id> |
| 199 |
<author>$Sp_Authority</author>
|
|
| 200 |
<family>$Family_Name</family>
|
|
| 201 |
<genus>$Genus_Name</genus>
|
|
| 202 |
<specific_epithet>$Specific_Epithet</specific_epithet>
|
|
| 203 |
<taxonomicname>$Scientific_Name</taxonomicname>
|
|
| 199 |
<author>$scientificNameAuthorship</author>
|
|
| 200 |
<family>$family</family>
|
|
| 201 |
<genus>$genus</genus>
|
|
| 202 |
<specific_epithet>$specificEpithet</specific_epithet>
|
|
| 203 |
<taxonomicname>$scientificName</taxonomicname>
|
|
| 204 | 204 |
</taxonverbatim> |
| 205 | 205 |
</taxonverbatim_id> |
| 206 | 206 |
<determinationdate> |
| 207 | 207 |
<_alt> |
| 208 |
<1><_dateRangeStart><value>$Determined_By_Date</value></_dateRangeStart></1>
|
|
| 208 |
<1><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></1>
|
|
| 209 | 209 |
<2> |
| 210 | 210 |
<_date> |
| 211 | 211 |
<day> |
| 212 | 212 |
<_nullIf> |
| 213 | 213 |
<null>0</null> |
| 214 | 214 |
<type>float</type> |
| 215 |
<value>$Day_Identified</value>
|
|
| 215 |
<value>$dayIdentified</value>
|
|
| 216 | 216 |
</_nullIf> |
| 217 | 217 |
</day> |
| 218 | 218 |
<month> |
| 219 | 219 |
<_nullIf> |
| 220 | 220 |
<null>0</null> |
| 221 | 221 |
<type>float</type> |
| 222 |
<value>$Month_Identified</value>
|
|
| 222 |
<value>$monthIdentified</value>
|
|
| 223 | 223 |
</_nullIf> |
| 224 | 224 |
</month> |
| 225 | 225 |
<year> |
| 226 | 226 |
<_nullIf> |
| 227 | 227 |
<null>0</null> |
| 228 | 228 |
<type>float</type> |
| 229 |
<value>$Year_Identified</value>
|
|
| 229 |
<value>$yearIdentified</value>
|
|
| 230 | 230 |
</_nullIf> |
| 231 | 231 |
</year> |
| 232 | 232 |
</_date> |
| ... | ... | |
| 242 | 242 |
<3> |
| 243 | 243 |
<_label> |
| 244 | 244 |
<label>habitat</label> |
| 245 |
<value>$Habitat_Description</value>
|
|
| 245 |
<value>$habitat</value>
|
|
| 246 | 246 |
</_label> |
| 247 | 247 |
</3> |
| 248 | 248 |
</_merge> |
| ... | ... | |
| 252 | 252 |
<place> |
| 253 | 253 |
<coordinates_id> |
| 254 | 254 |
<coordinates> |
| 255 |
<coordsaccuracy_m><_noCV><value>$Coordinate_Uncertainity</value></_noCV></coordsaccuracy_m>
|
|
| 255 |
<coordsaccuracy_m><_noCV><value>$coordinateUncertaintyInMeters</value></_noCV></coordsaccuracy_m>
|
|
| 256 | 256 |
<latitude_deg> |
| 257 | 257 |
<_nullIf> |
| 258 | 258 |
<null>0</null> |
| 259 | 259 |
<type>float</type> |
| 260 |
<value>$Latitude</value> |
|
| 260 |
<value>$decimalLatitude</value>
|
|
| 261 | 261 |
</_nullIf> |
| 262 | 262 |
</latitude_deg> |
| 263 | 263 |
<longitude_deg> |
| 264 | 264 |
<_nullIf> |
| 265 | 265 |
<null>0</null> |
| 266 | 266 |
<type>float</type> |
| 267 |
<value>$Longitude</value> |
|
| 267 |
<value>$decimalLongitude</value>
|
|
| 268 | 268 |
</_nullIf> |
| 269 | 269 |
</longitude_deg> |
| 270 | 270 |
</coordinates> |
| 271 | 271 |
</coordinates_id> |
| 272 |
<continent>$Continent_Name</continent>
|
|
| 273 |
<country>$Country_Name</country>
|
|
| 274 |
<county>$Subregion_Name</county>
|
|
| 272 |
<continent>$continent</continent>
|
|
| 273 |
<country>$country</country>
|
|
| 274 |
<county>$county</county>
|
|
| 275 | 275 |
<matched_place_id> |
| 276 | 276 |
<place> |
| 277 | 277 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
| ... | ... | |
| 282 | 282 |
<_nullIf> |
| 283 | 283 |
<null>0</null> |
| 284 | 284 |
<type>float</type> |
| 285 |
<value>$Latitude</value> |
|
| 285 |
<value>$decimalLatitude</value>
|
|
| 286 | 286 |
</_nullIf> |
| 287 | 287 |
</latitude_deg> |
| 288 | 288 |
<longitude_deg> |
| 289 | 289 |
<_nullIf> |
| 290 | 290 |
<null>0</null> |
| 291 | 291 |
<type>float</type> |
| 292 |
<value>$Longitude</value> |
|
| 292 |
<value>$decimalLongitude</value>
|
|
| 293 | 293 |
</_nullIf> |
| 294 | 294 |
</longitude_deg> |
| 295 | 295 |
</coordinates> |
| 296 | 296 |
</coordinates_id> |
| 297 |
<country>$Country_Name</country>
|
|
| 298 |
<county>$Subregion_Name</county>
|
|
| 299 |
<stateprovince>$Region_Name</stateprovince>
|
|
| 297 |
<country>$country</country>
|
|
| 298 |
<county>$county</county>
|
|
| 299 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 300 | 300 |
</place> |
| 301 | 301 |
</matched_place_id> |
| 302 |
<stateprovince>$Region_Name</stateprovince>
|
|
| 302 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 303 | 303 |
</place> |
| 304 | 304 |
</place_id> |
| 305 | 305 |
</locationplace> |
| inputs/BRIT/specimen_flat/VegBIEN.csv | ||
|---|---|---|
| 1 |
BRIT,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
Catalog_Number,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
specimen_id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
Institution_Code,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 5 |
specimen_id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
|
| 6 |
Catalog_Number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
| 7 |
Catalog_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 |
specimen_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 |
Catalog_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", |
|
| 11 |
Elevation_Min,/location/elevation_m/_alt/2/_avg/1,Assuming units based on the range and precision of values |
|
| 12 |
Elevation_Max,/location/elevation_m/_alt/2/_avg/2,Assuming units based on the range and precision of values |
|
| 13 |
Collection_Number,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 14 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 15 |
Habitat_Description,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 16 |
Collection_Method,/location/locationevent/*_id/method/name, |
|
| 17 |
Project_Name,/location/locationevent/*_id/project/projectname, |
|
| 18 |
Determined_By_Date,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value", |
|
| 19 |
Day_Identified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
|
| 20 |
Month_Identified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
|
| 21 |
Year_Identified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
|
| 22 |
Date_of_Collection,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
|
| 23 |
Day_Collected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
|
| 24 |
Month_Collected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
|
| 25 |
Year_Collected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
|
| 26 |
occurrenceRemarks,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1, |
|
| 27 |
Collection_Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2, |
|
| 28 |
Phenology_Stage,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/reproductivecondition, |
|
| 29 |
Catalog_Number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
|
| 30 |
Collection_Number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else", |
|
| 31 |
Catalog_Number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 32 |
specimen_id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 33 |
Institution_Code,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2", |
|
| 34 |
Institution_Code,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value", |
|
| 35 |
specimen_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 36 |
diameterBreastHeight_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value, |
|
| 37 |
height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m, |
|
| 38 |
Collection_Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
| 39 |
Scientific_Name,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
|
| 40 |
recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
|
| 41 |
Collection_Number,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 42 |
specimen_id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 43 |
specimen_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 44 |
Determined_By_Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
|
| 45 |
Specific_Epithet,"/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", |
|
| 46 |
Genus_Name,"/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", |
|
| 47 |
Family_Name,"/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", |
|
| 48 |
Order_Name,"/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", |
|
| 49 |
Class_Name,"/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", |
|
| 50 |
Division_Name,"/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", |
|
| 51 |
Kingdom_Name,"/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", |
|
| 52 |
Infra_Epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet, |
|
| 53 |
Family_Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 54 |
Scientific_Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 55 |
Genus_Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 56 |
Specific_Epithet,/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, |
|
| 57 |
Infra_Epithet,"/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""]/cond", |
|
| 58 |
Infra_Epithet,/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/2, |
|
| 59 |
Sp_Authority,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2, |
|
| 60 |
Sp_Authority,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
|
| 61 |
Family_Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 62 |
Genus_Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 63 |
Specific_Epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 64 |
Scientific_Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
|
| 65 |
Determined_By_Date,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value, |
|
| 66 |
Day_Identified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
|
| 67 |
Month_Identified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
|
| 68 |
Year_Identified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
|
| 69 |
Catalog_Number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
|
| 70 |
Collection_Number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then", |
|
| 71 |
locality,/location/locationnarrative/_merge/1, |
|
| 72 |
Habitat_Description,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
|
| 73 |
Coordinate_Uncertainity,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_m/_noCV/value,Assuming units based on the range and precision of values |
|
| 74 |
Latitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 75 |
Longitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 76 |
Continent_Name,/location/locationplace/*_id/place/continent, |
|
| 77 |
Country_Name,/location/locationplace/*_id/place/country, |
|
| 78 |
Subregion_Name,/location/locationplace/*_id/place/county, |
|
| 79 |
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" |
|
| 80 |
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" |
|
| 81 |
Country_Name,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 82 |
Subregion_Name,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 83 |
Region_Name,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 84 |
Region_Name,/location/locationplace/*_id/place/stateprovince, |
|
| 85 |
Auxilirary_Collections,,** No non-empty join mapping for UNUSED#Auxilirary_Collections ** |
|
| 86 |
Basis_Of_Specimen,,** No join mapping for basisOfRecord ** |
|
| 87 |
Closest_Town,,** No non-empty join mapping for UNUSED#Closest_Town ** |
|
| 88 |
Collection_Team,,** No join mapping for recordedBy_additional ** additional collectors |
|
| 89 |
Collector_Abbrev_Name,,** No join mapping for recordedBy_primary ** the primary collector |
|
| 90 |
DBH_Max,,** No join mapping for diameterBreastHeight_max_cm_verbatim ** Assuming units based on the range and precision of values |
|
| 91 |
DBH_Min,,** No join mapping for diameterBreastHeight_min_cm_verbatim ** Assuming units based on the range and precision of values |
|
| 92 |
Dubpliate_Herbarium,,** No non-empty join mapping for UNUSED#Dubpliate_Herbarium ** |
|
| 93 |
Duplicates,,** No join mapping for *Duplicates ** # of duplicates |
|
| 94 |
Global_Unique_Identifier,,** No non-empty join mapping for UNUSED#Global_Unique_Identifier ** |
|
| 95 |
Habitat_Summary,,** No non-empty join mapping for UNUSED#Habitat_Summary ** |
|
| 96 |
Height_Max,,** No join mapping for height_max_m_verbatim ** Assuming units based on the range and precision of values |
|
| 97 |
Height_Min,,** No join mapping for height_min_m_verbatim ** Assuming units based on the range and precision of values |
|
| 98 |
Infra_Rank,,** No join mapping for infraspecificRank ** |
|
| 99 |
Local_Name,,** No join mapping for vernacularName ** |
|
| 100 |
Locality_Description,,** No join mapping for locality__area__main ** |
|
| 101 |
Locality_Site_Specific,,"** No join mapping for locality__spot ** location within area, including landmarks" |
|
| 102 |
Locality_Summary,,** No join mapping for locality__area__prefix ** rarely populated |
|
| 103 |
Notes_Plant,,** No join mapping for occurrenceRemarks_verbatim ** |
|
| 104 |
Research_Site_Name,,** No join mapping for *Research_Site_Name ** |
|
| 105 |
Soil_Description,,** No join mapping for *Soil_Description ** |
|
| 106 |
Subclass_Name,,** No join mapping for *subclass ** |
|
| 107 |
Type_Specimen,,** No non-empty join mapping for UNUSED#Type_Specimen ** |
|
| 108 |
Updated_date,,** No join mapping for modified ** |
|
| 109 |
diameterBreastHeight_max_cm,,** No join mapping for diameterBreastHeight_max_cm ** |
|
| 110 |
diameterBreastHeight_min_cm,,** No join mapping for diameterBreastHeight_min_cm ** |
|
| 111 |
height_max_m,,** No join mapping for height_max_m ** |
|
| 112 |
height_min_m,,** No join mapping for height_min_m ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 113 | 2 | |
| inputs/BRIT/specimen_flat/unmapped_terms.csv | ||
|---|---|---|
| 16 | 16 |
basisOfRecord |
| 17 | 17 |
*Duplicates |
| 18 | 18 |
modified |
| 19 |
diameterBreastHeight_min_cm |
|
| 20 |
diameterBreastHeight_max_cm |
|
| 21 |
height_min_m |
|
| 22 |
height_max_m |
|
Also available in: Unified diff
inputs/BRIT/: switched to new-style import, using the steps at wiki.vegpath.org/Adding_new-style_import_to_a_datasource