Revision 10597
Added by Aaron Marcuse-Kubitza over 11 years ago
| inputs/U/Specimen/postprocess.sql | ||
|---|---|---|
| 2 | 2 |
|
| 3 | 3 |
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| 4 | 4 |
SELECT mk_derived_col((:table_str, 'county'), |
| 5 |
$$_alt("Gazetteer", "Newgazett")$$)
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|
| 5 |
$$_alt("county.main", "county.alt")$$)
|
|
| 6 | 6 |
; -- runtime: 0.5 s ("Time: 610.516 ms") @starscream
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| 7 | 7 |
|
| 8 | 8 |
SELECT mk_derived_col((:table_str, 'recordedBy'), |
| 9 |
$$_join("Collector", "Addcoll")$$)
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|
| 9 |
$$_join("recordedBy_primary", "recordedBy_additional")$$)
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|
| 10 | 10 |
; -- runtime: 2 s ("Time: 2273.582 ms") @starscream
|
| inputs/U/Specimen/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
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| 0 | 3 | |
| inputs/U/Specimen/map.csv | ||
|---|---|---|
| 32 | 32 |
Phenology,reproductiveCondition,, |
| 33 | 33 |
Notes,occurrenceRemarks,, |
| 34 | 34 |
:U,specimenHolderInstitutions,, |
| 35 |
county,county,, |
|
| 36 |
recordedBy,recordedBy,, |
|
| inputs/U/Specimen/test.xml.ref | ||
|---|---|---|
| 9 | 9 |
<location> |
| 10 | 10 |
<authorlocationcode> |
| 11 | 11 |
<_alt> |
| 12 |
<1>$ID</1> |
|
| 12 |
<1>$dataProviderRecordID</1>
|
|
| 13 | 13 |
<2> |
| 14 | 14 |
<_join> |
| 15 | 15 |
<1>U</1> |
| 16 |
<3>$Barcode</3>
|
|
| 16 |
<3>$accessionNumber</3>
|
|
| 17 | 17 |
</_join> |
| 18 | 18 |
</2> |
| 19 | 19 |
</_alt> |
| ... | ... | |
| 22 | 22 |
<_locationnarrative_is_cultivated> |
| 23 | 23 |
<locationnarrative> |
| 24 | 24 |
<_join> |
| 25 |
<2>$Locnotes</2>
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|
| 26 |
<3>$Ecology</3>
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|
| 25 |
<2>$verbatimLocality</2>
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|
| 26 |
<3>$habitat</3>
|
|
| 27 | 27 |
</_join> |
| 28 | 28 |
</locationnarrative> |
| 29 | 29 |
</_locationnarrative_is_cultivated> |
| ... | ... | |
| 37 | 37 |
<_nullIf> |
| 38 | 38 |
<null>0</null> |
| 39 | 39 |
<type>float</type> |
| 40 |
<value>$Colldd</value>
|
|
| 40 |
<value>$dayCollected</value>
|
|
| 41 | 41 |
</_nullIf> |
| 42 | 42 |
</day> |
| 43 | 43 |
<month> |
| 44 | 44 |
<_nullIf> |
| 45 | 45 |
<null>0</null> |
| 46 | 46 |
<type>float</type> |
| 47 |
<value>$Collmm</value>
|
|
| 47 |
<value>$monthCollected</value>
|
|
| 48 | 48 |
</_nullIf> |
| 49 | 49 |
</month> |
| 50 | 50 |
<year> |
| 51 | 51 |
<_nullIf> |
| 52 | 52 |
<null>0</null> |
| 53 | 53 |
<type>float</type> |
| 54 |
<value>$Collyy</value>
|
|
| 54 |
<value>$yearCollected</value>
|
|
| 55 | 55 |
</_nullIf> |
| 56 | 56 |
</year> |
| 57 | 57 |
</_date> |
| 58 | 58 |
</collectiondate> |
| 59 |
<notes>$Notes</notes>
|
|
| 59 |
<notes>$occurrenceRemarks</notes>
|
|
| 60 | 60 |
<plantobservation> |
| 61 |
<authorplantcode>$Number</authorplantcode> |
|
| 62 |
<reproductivecondition>$Phenology</reproductivecondition>
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|
| 61 |
<authorplantcode>$collectorNumber</authorplantcode>
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|
| 62 |
<reproductivecondition>$reproductiveCondition</reproductivecondition>
|
|
| 63 | 63 |
<specimenreplicate> |
| 64 |
<catalognumber_dwc>$Barcode</catalognumber_dwc>
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|
| 65 |
<collectionnumber>$Number</collectionnumber> |
|
| 64 |
<catalognumber_dwc>$accessionNumber</catalognumber_dwc>
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|
| 65 |
<collectionnumber>$collectorNumber</collectionnumber>
|
|
| 66 | 66 |
<institution_id> |
| 67 | 67 |
<sourcelist> |
| 68 | 68 |
<name>U</name> |
| ... | ... | |
| 76 | 76 |
</sourcename> |
| 77 | 77 |
</sourcelist> |
| 78 | 78 |
</institution_id> |
| 79 |
<sourceaccessioncode>$ID</sourceaccessioncode> |
|
| 79 |
<sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>
|
|
| 80 | 80 |
</specimenreplicate> |
| 81 | 81 |
</plantobservation> |
| 82 | 82 |
</aggregateoccurrence> |
| 83 | 83 |
<collector_id><party><fullname>$recordedBy</fullname></party></collector_id> |
| 84 |
<sourceaccessioncode>$ID</sourceaccessioncode> |
|
| 84 |
<sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>
|
|
| 85 | 85 |
<taxondetermination> |
| 86 |
<party_id><party><fullname>$Detby</fullname></party></party_id>
|
|
| 86 |
<party_id><party><fullname>$identifiedBy</fullname></party></party_id>
|
|
| 87 | 87 |
<taxonverbatim_id> |
| 88 | 88 |
<taxonverbatim> |
| 89 | 89 |
<taxonlabel_id> |
| ... | ... | |
| 108 | 108 |
<parent_id> |
| 109 | 109 |
<taxonlabel> |
| 110 | 110 |
<rank>genus</rank> |
| 111 |
<taxonepithet>$Genus</taxonepithet>
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|
| 111 |
<taxonepithet>$genus</taxonepithet>
|
|
| 112 | 112 |
<parent_id> |
| 113 | 113 |
<taxonlabel> |
| 114 | 114 |
<rank>family</rank> |
| 115 |
<taxonepithet>$Family</taxonepithet>
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|
| 115 |
<taxonepithet>$family</taxonepithet>
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|
| 116 | 116 |
</taxonlabel> |
| 117 | 117 |
</parent_id> |
| 118 | 118 |
</taxonlabel> |
| ... | ... | |
| 131 | 131 |
</parent_id> |
| 132 | 132 |
<taxonomicname> |
| 133 | 133 |
<_merge_prefix> |
| 134 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
|
|
| 135 |
<value><_filter_genus><value>$Genus</value></_filter_genus></value>
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|
| 134 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
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|
| 135 |
<value><_filter_genus><value>$genus</value></_filter_genus></value>
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|
| 136 | 136 |
</_merge_prefix> |
| 137 | 137 |
</taxonomicname> |
| 138 | 138 |
</taxonlabel> |
| 139 | 139 |
</taxonlabel_id> |
| 140 |
<family>$Family</family>
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|
| 141 |
<genus>$Genus</genus>
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|
| 140 |
<family>$family</family>
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|
| 141 |
<genus>$genus</genus>
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|
| 142 | 142 |
</taxonverbatim> |
| 143 | 143 |
</taxonverbatim_id> |
| 144 | 144 |
<determinationdate> |
| ... | ... | |
| 147 | 147 |
<_nullIf> |
| 148 | 148 |
<null>0</null> |
| 149 | 149 |
<type>float</type> |
| 150 |
<value>$Detyy</value>
|
|
| 150 |
<value>$yearIdentified</value>
|
|
| 151 | 151 |
</_nullIf> |
| 152 | 152 |
</year> |
| 153 | 153 |
</_date> |
| 154 | 154 |
</determinationdate> |
| 155 |
<taxonfit>$cf</taxonfit>
|
|
| 155 |
<taxonfit>$identificationQualifier</taxonfit>
|
|
| 156 | 156 |
</taxondetermination> |
| 157 | 157 |
</taxonoccurrence> |
| 158 | 158 |
</locationevent> |
| 159 | 159 |
<locationnarrative> |
| 160 | 160 |
<_merge> |
| 161 |
<2>$Locnotes</2>
|
|
| 161 |
<2>$verbatimLocality</2>
|
|
| 162 | 162 |
<3> |
| 163 | 163 |
<_label> |
| 164 | 164 |
<label>habitat</label> |
| 165 |
<value>$Ecology</value>
|
|
| 165 |
<value>$habitat</value>
|
|
| 166 | 166 |
</_label> |
| 167 | 167 |
</3> |
| 168 | 168 |
</_merge> |
| ... | ... | |
| 176 | 176 |
<_nullIf> |
| 177 | 177 |
<null>0</null> |
| 178 | 178 |
<type>float</type> |
| 179 |
<value>$Lat</value>
|
|
| 179 |
<value>$decimalLatitude</value>
|
|
| 180 | 180 |
</_nullIf> |
| 181 | 181 |
</latitude_deg> |
| 182 | 182 |
<longitude_deg> |
| 183 | 183 |
<_nullIf> |
| 184 | 184 |
<null>0</null> |
| 185 | 185 |
<type>float</type> |
| 186 |
<value>$Long</value>
|
|
| 186 |
<value>$decimalLongitude</value>
|
|
| 187 | 187 |
</_nullIf> |
| 188 | 188 |
</longitude_deg> |
| 189 | 189 |
</coordinates> |
| 190 | 190 |
</coordinates_id> |
| 191 |
<country>$Country</country>
|
|
| 191 |
<country>$country</country>
|
|
| 192 | 192 |
<county>$county</county> |
| 193 | 193 |
<matched_place_id> |
| 194 | 194 |
<place> |
| ... | ... | |
| 200 | 200 |
<_nullIf> |
| 201 | 201 |
<null>0</null> |
| 202 | 202 |
<type>float</type> |
| 203 |
<value>$Lat</value>
|
|
| 203 |
<value>$decimalLatitude</value>
|
|
| 204 | 204 |
</_nullIf> |
| 205 | 205 |
</latitude_deg> |
| 206 | 206 |
<longitude_deg> |
| 207 | 207 |
<_nullIf> |
| 208 | 208 |
<null>0</null> |
| 209 | 209 |
<type>float</type> |
| 210 |
<value>$Long</value>
|
|
| 210 |
<value>$decimalLongitude</value>
|
|
| 211 | 211 |
</_nullIf> |
| 212 | 212 |
</longitude_deg> |
| 213 | 213 |
</coordinates> |
| 214 | 214 |
</coordinates_id> |
| 215 |
<country>$Country</country>
|
|
| 215 |
<country>$country</country>
|
|
| 216 | 216 |
<county>$county</county> |
| 217 |
<stateprovince>$Majorarea</stateprovince>
|
|
| 217 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 218 | 218 |
</place> |
| 219 | 219 |
</matched_place_id> |
| 220 |
<stateprovince>$Majorarea</stateprovince>
|
|
| 220 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 221 | 221 |
</place> |
| 222 | 222 |
</place_id> |
| 223 | 223 |
</locationplace> |
| inputs/U/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
U,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
Barcode,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
ID,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
:U,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 5 |
ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
|
| 6 |
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
| 7 |
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
|
| 8 |
ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
|
| 9 |
:U,"/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 |
Barcode,"/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 |
Number,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 12 |
Locnotes,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/2, |
|
| 13 |
Ecology,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 14 |
Detyy,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
|
| 15 |
cf,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/taxonfit", |
|
| 16 |
Colldd,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
|
| 17 |
Collmm,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
|
| 18 |
Collyy,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
|
| 19 |
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1, |
|
| 20 |
Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2, |
|
| 21 |
Phenology,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/reproductivecondition, |
|
| 22 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
|
| 23 |
Number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else", |
|
| 24 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 25 |
ID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 26 |
:U,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2", |
|
| 27 |
:U,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value", |
|
| 28 |
ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 29 |
Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
| 30 |
recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
|
| 31 |
ID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 32 |
Number,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 33 |
ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 34 |
Detby,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
|
| 35 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
|
| 36 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet", |
|
| 37 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 38 |
Genus,/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, |
|
| 39 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 40 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 41 |
Detyy,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
|
| 42 |
cf,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit, |
|
| 43 |
Barcode,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
|
| 44 |
Number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then", |
|
| 45 |
Locnotes,/location/locationnarrative/_merge/2, |
|
| 46 |
Ecology,"/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?" |
|
| 47 |
Lat,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 48 |
Long,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 49 |
Country,/location/locationplace/*_id/place/country, |
|
| 50 |
county,/location/locationplace/*_id/place/county, |
|
| 51 |
Lat,"/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" |
|
| 52 |
Long,"/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" |
|
| 53 |
Country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 54 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 55 |
Majorarea,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2,closest equivalent for Guyana/Suriname |
|
| 56 |
Majorarea,/location/locationplace/*_id/place/stateprovince,closest equivalent for Guyana/Suriname |
|
| 57 |
Addcoll,,** No join mapping for recordedBy_additional ** additional collectors |
|
| 58 |
Alt,,** No join mapping for *Alt ** What is this? |
|
| 59 |
Alt2,,** No join mapping for *Alt2 ** What is this? |
|
| 60 |
Collector,,** No join mapping for recordedBy_primary ** the primary collector |
|
| 61 |
Coorsyst,,** No join mapping for *Coorsyst ** |
|
| 62 |
DateInfo,,** No non-empty join mapping for UNUSED#DateInfo ** |
|
| 63 |
EW,,** No join mapping for *EW ** |
|
| 64 |
Gazetteer,,** No join mapping for county.main ** closest equivalent for Guyana/Suriname |
|
| 65 |
NS,,** No join mapping for *NS ** |
|
| 66 |
Newgazett,,"** No join mapping for county.alt ** only used in 1 row. only one of Gazetteer, Newgazett is ever populated." |
|
| 67 |
Prefix,,** No non-empty join mapping for UNUSED#Prefix ** |
|
| 68 |
Suffix,,** No non-empty join mapping for UNUSED#Suffix ** |
|
| 69 |
row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 70 | 2 | |
| inputs/U/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
|
|
| 0 | 3 | |
Also available in: Unified diff
inputs/U/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource