Revision 10301
Added by Aaron Marcuse-Kubitza over 11 years ago
| inputs/Madidi/IndividualObservation/postprocess.sql | ||
|---|---|---|
| 1 | 1 |
SELECT util.search_path_append('util');
|
| 2 | 2 |
|
| 3 |
SELECT mk_derived_col((:table_str, 'FieldFamilyFullName#originalFamily'), $$"FieldFamilyFullName"$$); |
|
| 3 |
SELECT mk_derived_col((:table_str, 'originalFamily'), $$family$$); |
|
| inputs/Madidi/IndividualObservation/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/Madidi/IndividualObservation/test.xml.ref | ||
|---|---|---|
| 9 | 9 |
<location> |
| 10 | 10 |
<parent_id> |
| 11 | 11 |
<location> |
| 12 |
<authorlocationcode>$PlotName</authorlocationcode>
|
|
| 13 |
<sourceaccessioncode>$PlotID</sourceaccessioncode>
|
|
| 12 |
<authorlocationcode>$locationName</authorlocationcode>
|
|
| 13 |
<sourceaccessioncode>$locationID</sourceaccessioncode>
|
|
| 14 | 14 |
</location> |
| 15 | 15 |
</parent_id> |
| 16 |
<authorlocationcode>$Sequence</authorlocationcode>
|
|
| 16 |
<authorlocationcode>$subplot</authorlocationcode>
|
|
| 17 | 17 |
<locationevent> |
| 18 | 18 |
<parent_id> |
| 19 | 19 |
<locationevent> |
| ... | ... | |
| 21 | 21 |
<location> |
| 22 | 22 |
<authorlocationcode> |
| 23 | 23 |
<_if name="if subplot"> |
| 24 |
<cond>$Sequence</cond>
|
|
| 25 |
<then>$PlotName</then>
|
|
| 24 |
<cond>$subplot</cond>
|
|
| 25 |
<then>$locationName</then>
|
|
| 26 | 26 |
</_if> |
| 27 | 27 |
</authorlocationcode> |
| 28 | 28 |
<sourceaccessioncode> |
| 29 | 29 |
<_if name="if subplot"> |
| 30 |
<cond>$Sequence</cond>
|
|
| 31 |
<then>$PlotID</then>
|
|
| 30 |
<cond>$subplot</cond>
|
|
| 31 |
<then>$locationID</then>
|
|
| 32 | 32 |
</_if> |
| 33 | 33 |
</sourceaccessioncode> |
| 34 | 34 |
</location> |
| 35 | 35 |
</location_id> |
| 36 |
<authoreventcode>$PlotInventoryName</authoreventcode>
|
|
| 36 |
<authoreventcode>$authorEventCode</authoreventcode>
|
|
| 37 | 37 |
</locationevent> |
| 38 | 38 |
</parent_id> |
| 39 | 39 |
<taxonoccurrence> |
| 40 | 40 |
<aggregateoccurrence> |
| 41 |
<notes>$TreeNotes</notes>
|
|
| 41 |
<notes>$occurrenceRemarks</notes>
|
|
| 42 | 42 |
<plantobservation> |
| 43 |
<authorplantcode>$Tree</authorplantcode>
|
|
| 43 |
<authorplantcode>$individualCode</authorplantcode>
|
|
| 44 | 44 |
<specimenreplicate> |
| 45 |
<catalognumber_dwc>$SpecimenID</catalognumber_dwc>
|
|
| 46 |
<collectionnumber>$CollectionNumber</collectionnumber>
|
|
| 45 |
<catalognumber_dwc>$accessionNumber</catalognumber_dwc>
|
|
| 46 |
<collectionnumber>$collectorNumber</collectionnumber>
|
|
| 47 | 47 |
<institution_id> |
| 48 | 48 |
<sourcelist> |
| 49 |
<name>$Institutions</name> |
|
| 49 |
<name>$specimenHolderInstitutions</name>
|
|
| 50 | 50 |
<sourcename> |
| 51 | 51 |
<name> |
| 52 | 52 |
<_split> |
| 53 | 53 |
<separator>[,;] *</separator> |
| 54 |
<value>$Institutions</value> |
|
| 54 |
<value>$specimenHolderInstitutions</value>
|
|
| 55 | 55 |
</_split> |
| 56 | 56 |
</name> |
| 57 | 57 |
</sourcename> |
| ... | ... | |
| 59 | 59 |
</institution_id> |
| 60 | 60 |
</specimenreplicate> |
| 61 | 61 |
<stemobservation> |
| 62 |
<authorstemcode>$Trunk</authorstemcode>
|
|
| 63 |
<diameterbreastheight_m><_cm_to_m><value>$Diameter</value></_cm_to_m></diameterbreastheight_m>
|
|
| 64 |
<height_m>$TotalHeight</height_m>
|
|
| 65 |
<tag>$Tag</tag>
|
|
| 62 |
<authorstemcode>$authorStemCode</authorstemcode>
|
|
| 63 |
<diameterbreastheight_m><_cm_to_m><value>$diameterBreastHeight_cm</value></_cm_to_m></diameterbreastheight_m>
|
|
| 64 |
<height_m>$height_m</height_m>
|
|
| 65 |
<tag>$tag</tag>
|
|
| 66 | 66 |
</stemobservation> |
| 67 | 67 |
</plantobservation> |
| 68 | 68 |
</aggregateoccurrence> |
| 69 |
<authortaxoncode>$Tree</authortaxoncode>
|
|
| 70 |
<collector_id><party><fullname>$CollectorString</fullname></party></collector_id>
|
|
| 71 |
<growthform>$HabitName</growthform>
|
|
| 69 |
<authortaxoncode>$individualCode</authortaxoncode>
|
|
| 70 |
<collector_id><party><fullname>$recordedBy</fullname></party></collector_id>
|
|
| 71 |
<growthform>$growthForm</growthform>
|
|
| 72 | 72 |
<taxondetermination> |
| 73 | 73 |
<taxonverbatim_id> |
| 74 | 74 |
<taxonverbatim> |
| ... | ... | |
| 76 | 76 |
<taxonlabel> |
| 77 | 77 |
<parent_id> |
| 78 | 78 |
<taxonlabel> |
| 79 |
<rank>$CurrentDetRank</rank>
|
|
| 79 |
<rank>$taxonRank</rank>
|
|
| 80 | 80 |
<parent_id> |
| 81 | 81 |
<taxonlabel> |
| 82 | 82 |
<rank>cultivar</rank> |
| ... | ... | |
| 98 | 98 |
<parent_id> |
| 99 | 99 |
<taxonlabel> |
| 100 | 100 |
<rank>family</rank> |
| 101 |
<taxonepithet>$FieldFamilyFullName</taxonepithet>
|
|
| 101 |
<taxonepithet>$family</taxonepithet>
|
|
| 102 | 102 |
</taxonlabel> |
| 103 | 103 |
</parent_id> |
| 104 | 104 |
</taxonlabel> |
| ... | ... | |
| 115 | 115 |
</parent_id> |
| 116 | 116 |
</taxonlabel> |
| 117 | 117 |
</parent_id> |
| 118 |
<rank>$CurrentDetRank</rank>
|
|
| 118 |
<rank>$taxonRank</rank>
|
|
| 119 | 119 |
<taxonomicname> |
| 120 | 120 |
<_merge_prefix> |
| 121 |
<prefix><_taxon_family_require_std><family>$FieldFamilyFullName</family></_taxon_family_require_std></prefix>
|
|
| 122 |
<value>$CurrentDet</value>
|
|
| 121 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
|
|
| 122 |
<value>$scientificName</value>
|
|
| 123 | 123 |
</_merge_prefix> |
| 124 | 124 |
</taxonomicname> |
| 125 | 125 |
</taxonlabel> |
| 126 | 126 |
</taxonlabel_id> |
| 127 |
<family>$FieldFamilyFullName</family>
|
|
| 128 |
<taxonomicname>$CurrentDet</taxonomicname>
|
|
| 129 |
<verbatimrank>$CurrentDetRank</verbatimrank>
|
|
| 127 |
<family>$family</family>
|
|
| 128 |
<taxonomicname>$scientificName</taxonomicname>
|
|
| 129 |
<verbatimrank>$taxonRank</verbatimrank>
|
|
| 130 | 130 |
</taxonverbatim> |
| 131 | 131 |
</taxonverbatim_id> |
| 132 |
<taxonfit>$CurrentDetQualifier</taxonfit>
|
|
| 132 |
<taxonfit>$identificationQualifier</taxonfit>
|
|
| 133 | 133 |
</taxondetermination> |
| 134 | 134 |
<taxondetermination> |
| 135 | 135 |
<isoriginal>true</isoriginal> |
| 136 | 136 |
<taxonverbatim_id> |
| 137 | 137 |
<taxonverbatim> |
| 138 |
<author>$FieldNameAuthors</author>
|
|
| 139 |
<family>$FieldFamilyFullName#originalFamily</family>
|
|
| 140 |
<morphoname>$MorphoSpeciesName</morphoname>
|
|
| 141 |
<taxonname>$FieldNameFullName</taxonname>
|
|
| 138 |
<author>$originalScientificNameAuthorship</author>
|
|
| 139 |
<family>$originalFamily</family> |
|
| 140 |
<morphoname>$morphoname</morphoname>
|
|
| 141 |
<taxonname>$originalTaxonName</taxonname>
|
|
| 142 | 142 |
</taxonverbatim> |
| 143 | 143 |
</taxonverbatim_id> |
| 144 | 144 |
</taxondetermination> |
| ... | ... | |
| 146 | 146 |
</locationevent> |
| 147 | 147 |
<sourceaccessioncode> |
| 148 | 148 |
<_join> |
| 149 |
<1>$PlotID</1>
|
|
| 150 |
<2>$Sequence</2>
|
|
| 149 |
<1>$locationID</1>
|
|
| 150 |
<2>$subplot</2>
|
|
| 151 | 151 |
</_join> |
| 152 | 152 |
</sourceaccessioncode> |
| 153 |
<sublocationxposition_m>$SubplotX</sublocationxposition_m>
|
|
| 154 |
<sublocationyposition_m>$SubplotY</sublocationyposition_m>
|
|
| 153 |
<sublocationxposition_m>$subplotX</sublocationxposition_m>
|
|
| 154 |
<sublocationyposition_m>$subplotY</sublocationyposition_m>
|
|
| 155 | 155 |
</location> |
| 156 | 156 |
</path> |
| 157 | 157 |
</_simplifyPath> |
| inputs/Madidi/IndividualObservation/VegBIEN.csv | ||
|---|---|---|
| 1 |
Madidi,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
SpecimenID,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
Institutions,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 4 |
Sequence,"/location/_if[@name=""if subplot""]/cond/_exists", |
|
| 5 |
PlotName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
|
| 6 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 7 |
PlotInventoryName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else", |
|
| 8 |
SpecimenID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
| 9 |
SpecimenID,"/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", |
|
| 10 |
Institutions,"/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", |
|
| 11 |
SpecimenID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
|
| 12 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 13 |
PlotName,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
|
| 14 |
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 15 |
Sequence,/location/authorlocationcode, |
|
| 16 |
CollectionNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 17 |
Sequence,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists", |
|
| 18 |
PlotInventoryName,"/location/locationevent/_if[@name=""if subplot""]/else/authoreventcode", |
|
| 19 |
PlotInventoryName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 20 |
Sequence,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/cond/_first/2", |
|
| 21 |
PlotName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then", |
|
| 22 |
Sequence,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond/_first/2", |
|
| 23 |
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
|
| 24 |
PlotInventoryName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/authoreventcode", |
|
| 25 |
CurrentDetQualifier,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/taxonfit", |
|
| 26 |
TreeNotes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1, |
|
| 27 |
Tree,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/1, |
|
| 28 |
CollectionNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2, |
|
| 29 |
SpecimenID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
|
| 30 |
CollectionNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else", |
|
| 31 |
SpecimenID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 32 |
Institutions,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2", |
|
| 33 |
Institutions,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value", |
|
| 34 |
Trunk,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode, |
|
| 35 |
Diameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value, |
|
| 36 |
TotalHeight,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m, |
|
| 37 |
Tag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
|
| 38 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 39 |
PlotInventoryName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 40 |
PlotName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 41 |
Tree,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/1", |
|
| 42 |
Tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
|
| 43 |
CollectionNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
| 44 |
FieldNameFullName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/1", |
|
| 45 |
CurrentDet,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
|
| 46 |
CollectorString,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
|
| 47 |
HabitName,/location/locationevent/taxonoccurrence/growthform, |
|
| 48 |
CollectionNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 49 |
CurrentDetRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 50 |
FieldFamilyFullName,"/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", |
|
| 51 |
CurrentDetRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 52 |
CurrentDetRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank", |
|
| 53 |
FieldFamilyFullName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 54 |
CurrentDet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 55 |
CurrentDetRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 56 |
FieldFamilyFullName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 57 |
CurrentDet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
|
| 58 |
CurrentDetRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 59 |
CurrentDetQualifier,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit, |
|
| 60 |
FieldNameAuthors,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/author, |
|
| 61 |
FieldFamilyFullName#originalFamily,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/family, |
|
| 62 |
MorphoSpeciesName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/morphoname, |
|
| 63 |
FieldNameFullName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonname, |
|
| 64 |
SpecimenID,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
|
| 65 |
CollectionNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then", |
|
| 66 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 67 |
Sequence,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/cond/_exists", |
|
| 68 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
|
| 69 |
Sequence,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/2", |
|
| 70 |
SubplotX,/location/sublocationxposition_m, |
|
| 71 |
SubplotY,/location/sublocationyposition_m, |
|
| 72 |
AreaRachilla1,,** No non-empty join mapping for UNUSED#AreaRachilla1 ** |
|
| 73 |
AreaRachilla2,,** No non-empty join mapping for UNUSED#AreaRachilla2 ** |
|
| 74 |
AreaRachilla3,,** No non-empty join mapping for UNUSED#AreaRachilla3 ** |
|
| 75 |
AreaRachilla4,,** No non-empty join mapping for UNUSED#AreaRachilla4 ** |
|
| 76 |
AreaRachilla5,,** No non-empty join mapping for UNUSED#AreaRachilla5 ** |
|
| 77 |
AreaRachis1,,** No non-empty join mapping for UNUSED#AreaRachis1 ** |
|
| 78 |
AreaRachis2,,** No non-empty join mapping for UNUSED#AreaRachis2 ** |
|
| 79 |
AreaRachis3,,** No non-empty join mapping for UNUSED#AreaRachis3 ** |
|
| 80 |
AreaRachis4,,** No non-empty join mapping for UNUSED#AreaRachis4 ** |
|
| 81 |
AreaRachis5,,** No non-empty join mapping for UNUSED#AreaRachis5 ** |
|
| 82 |
BoleHeight,,** No join mapping for *BoleHeight ** |
|
| 83 |
CauseOfDeath1,,** No non-empty join mapping for UNUSED#CauseOfDeath1 ** |
|
| 84 |
CauseOfDeath2,,** No non-empty join mapping for UNUSED#CauseOfDeath2 ** |
|
| 85 |
CauseOfDeath3,,** No non-empty join mapping for UNUSED#CauseOfDeath3 ** |
|
| 86 |
CauseOfDeath4,,** No non-empty join mapping for UNUSED#CauseOfDeath4 ** |
|
| 87 |
CauseOfDeath5,,** No non-empty join mapping for UNUSED#CauseOfDeath5 ** |
|
| 88 |
Circumference,,** No join mapping for *Circumference ** |
|
| 89 |
CollectorAbbrev,,** No non-empty join mapping for DUPLICATE#of:CollectorString#CollectorAbbrev ** |
|
| 90 |
CollectorStringShortened,,** No non-empty join mapping for DUPLICATE#of:CollectorString#CollectorStringShortened ** |
|
| 91 |
CommonName,,** No join mapping for vernacularName ** |
|
| 92 |
CompoundLeaf,,** No non-empty join mapping for UNUSED#CompoundLeaf ** |
|
| 93 |
CompoundLeafID,,** No non-empty join mapping for UNUSED#CompoundLeafID ** |
|
| 94 |
CrownPositionName,,** No join mapping for *CrownPositionName ** |
|
| 95 |
CrownShapeName,,** No join mapping for *CrownShapeName ** |
|
| 96 |
CurrentDetFamily,,"** No non-empty join mapping for OMIT#CurrentDetFamily ** Omitted because includes *family* author, which TNRS can’t handle" |
|
| 97 |
DNASample,,** No join mapping for *DNASample ** |
|
| 98 |
Decomposition,,** No non-empty join mapping for UNUSED#Decomposition ** |
|
| 99 |
DiameterWithBark,,** No non-empty join mapping for UNUSED#DiameterWithBark ** |
|
| 100 |
DiameterWithoutBark,,** No non-empty join mapping for UNUSED#DiameterWithoutBark ** |
|
| 101 |
DirectionOfFall,,** No non-empty join mapping for UNUSED#DirectionOfFall ** |
|
| 102 |
DryWeight,,** No non-empty join mapping for UNUSED#DryWeight ** |
|
| 103 |
FieldFamilyHTML,,"** No non-empty join mapping for OMIT#FieldFamilyHTML ** Omitted because includes *family* author, which TNRS can’t handle" |
|
| 104 |
FieldNameHTML,,** No non-empty join mapping for OMIT#FieldNameHTML ** Adds HTML formatting to FieldNameFullName+FieldNameAuthors |
|
| 105 |
HeightButtresses,,** No non-empty join mapping for UNUSED#HeightButtresses ** |
|
| 106 |
InstitutionString,,** No join mapping for *InstitutionString ** |
|
| 107 |
IsAlive,,** No join mapping for *IsAlive ** |
|
| 108 |
LeafPhoto1,,** No non-empty join mapping for UNUSED#LeafPhoto1 ** |
|
| 109 |
LeafPhoto2,,** No non-empty join mapping for UNUSED#LeafPhoto2 ** |
|
| 110 |
LeafPhoto3,,** No non-empty join mapping for UNUSED#LeafPhoto3 ** |
|
| 111 |
LeafPhoto4,,** No non-empty join mapping for UNUSED#LeafPhoto4 ** |
|
| 112 |
LeafPhoto5,,** No non-empty join mapping for UNUSED#LeafPhoto5 ** |
|
| 113 |
LianaPresenceName,,** No join mapping for *LianaPresenceName ** |
|
| 114 |
MortalityType,,** No non-empty join mapping for UNUSED#MortalityType ** |
|
| 115 |
MultipleFalls,,** No non-empty join mapping for UNUSED#MultipleFalls ** |
|
| 116 |
NitrogenContent,,** No non-empty join mapping for UNUSED#NitrogenContent ** |
|
| 117 |
NumberFolioles1,,** No non-empty join mapping for UNUSED#NumberFolioles1 ** |
|
| 118 |
NumberFolioles2,,** No non-empty join mapping for UNUSED#NumberFolioles2 ** |
|
| 119 |
NumberFolioles3,,** No non-empty join mapping for UNUSED#NumberFolioles3 ** |
|
| 120 |
NumberFolioles4,,** No non-empty join mapping for UNUSED#NumberFolioles4 ** |
|
| 121 |
NumberFolioles5,,** No non-empty join mapping for UNUSED#NumberFolioles5 ** |
|
| 122 |
NumberFoliolules1,,** No non-empty join mapping for UNUSED#NumberFoliolules1 ** |
|
| 123 |
NumberFoliolules2,,** No non-empty join mapping for UNUSED#NumberFoliolules2 ** |
|
| 124 |
NumberFoliolules3,,** No non-empty join mapping for UNUSED#NumberFoliolules3 ** |
|
| 125 |
NumberFoliolules4,,** No non-empty join mapping for UNUSED#NumberFoliolules4 ** |
|
| 126 |
NumberFoliolules5,,** No non-empty join mapping for UNUSED#NumberFoliolules5 ** |
|
| 127 |
NumberOfLeaves,,** No non-empty join mapping for UNUSED#NumberOfLeaves ** |
|
| 128 |
OrientationXDegrees,,** No join mapping for *OrientationXDegrees ** |
|
| 129 |
OrientationYDegrees,,** No join mapping for *OrientationYDegrees ** |
|
| 130 |
Phenology1,,** No join mapping for *Phenology1 ** |
|
| 131 |
Phenology2,,** No join mapping for *Phenology2 ** |
|
| 132 |
Phenology3,,** No join mapping for *Phenology3 ** |
|
| 133 |
Phenology4,,** No join mapping for *Phenology4 ** |
|
| 134 |
RachisPhoto1,,** No non-empty join mapping for UNUSED#RachisPhoto1 ** |
|
| 135 |
RachisPhoto2,,** No non-empty join mapping for UNUSED#RachisPhoto2 ** |
|
| 136 |
RachisPhoto3,,** No non-empty join mapping for UNUSED#RachisPhoto3 ** |
|
| 137 |
RachisPhoto4,,** No non-empty join mapping for UNUSED#RachisPhoto4 ** |
|
| 138 |
RachisPhoto5,,** No non-empty join mapping for UNUSED#RachisPhoto5 ** |
|
| 139 |
RemainingTrunkHeight,,** No non-empty join mapping for UNUSED#RemainingTrunkHeight ** |
|
| 140 |
RepresentativeCollectionNumber,,** No join mapping for *RepresentativeCollectionNumber ** |
|
| 141 |
RepresentativeSpecimenCollectorAbbreviation,,** No join mapping for *RepresentativeSpecimenCollectorAbbreviation ** |
|
| 142 |
RepresentativeSpecimenID,,** No join mapping for *RepresentativeSpecimenID ** |
|
| 143 |
RepresentativeSpecimenSeniorCollector,,** No join mapping for *RepresentativeSpecimenSeniorCollector ** |
|
| 144 |
SLAArea1,,** No non-empty join mapping for UNUSED#SLAArea1 ** |
|
| 145 |
SLAArea10,,** No non-empty join mapping for UNUSED#SLAArea10 ** |
|
| 146 |
SLAArea11,,** No non-empty join mapping for UNUSED#SLAArea11 ** |
|
| 147 |
SLAArea12,,** No non-empty join mapping for UNUSED#SLAArea12 ** |
|
| 148 |
SLAArea13,,** No non-empty join mapping for UNUSED#SLAArea13 ** |
|
| 149 |
SLAArea14,,** No non-empty join mapping for UNUSED#SLAArea14 ** |
|
| 150 |
SLAArea15,,** No non-empty join mapping for UNUSED#SLAArea15 ** |
|
| 151 |
SLAArea2,,** No non-empty join mapping for UNUSED#SLAArea2 ** |
|
| 152 |
SLAArea3,,** No non-empty join mapping for UNUSED#SLAArea3 ** |
|
| 153 |
SLAArea4,,** No non-empty join mapping for UNUSED#SLAArea4 ** |
|
| 154 |
SLAArea5,,** No non-empty join mapping for UNUSED#SLAArea5 ** |
|
| 155 |
SLAArea6,,** No non-empty join mapping for UNUSED#SLAArea6 ** |
|
| 156 |
SLAArea7,,** No non-empty join mapping for UNUSED#SLAArea7 ** |
|
| 157 |
SLAArea8,,** No non-empty join mapping for UNUSED#SLAArea8 ** |
|
| 158 |
SLAArea9,,** No non-empty join mapping for UNUSED#SLAArea9 ** |
|
| 159 |
SeniorCollector,,** No non-empty join mapping for DUPLICATE#of:CollectorString#SeniorCollector ** |
|
| 160 |
SubplotX2,,** No join mapping for *SubplotX2 ** |
|
| 161 |
SubplotY2,,** No join mapping for *SubplotY2 ** |
|
| 162 |
Thickness1,,** No non-empty join mapping for UNUSED#Thickness1 ** |
|
| 163 |
Thickness10,,** No non-empty join mapping for UNUSED#Thickness10 ** |
|
| 164 |
Thickness11,,** No non-empty join mapping for UNUSED#Thickness11 ** |
|
| 165 |
Thickness12,,** No non-empty join mapping for UNUSED#Thickness12 ** |
|
| 166 |
Thickness13,,** No non-empty join mapping for UNUSED#Thickness13 ** |
|
| 167 |
Thickness14,,** No non-empty join mapping for UNUSED#Thickness14 ** |
|
| 168 |
Thickness15,,** No non-empty join mapping for UNUSED#Thickness15 ** |
|
| 169 |
Thickness2,,** No non-empty join mapping for UNUSED#Thickness2 ** |
|
| 170 |
Thickness3,,** No non-empty join mapping for UNUSED#Thickness3 ** |
|
| 171 |
Thickness4,,** No non-empty join mapping for UNUSED#Thickness4 ** |
|
| 172 |
Thickness5,,** No non-empty join mapping for UNUSED#Thickness5 ** |
|
| 173 |
Thickness6,,** No non-empty join mapping for UNUSED#Thickness6 ** |
|
| 174 |
Thickness7,,** No non-empty join mapping for UNUSED#Thickness7 ** |
|
| 175 |
Thickness8,,** No non-empty join mapping for UNUSED#Thickness8 ** |
|
| 176 |
Thickness9,,** No non-empty join mapping for UNUSED#Thickness9 ** |
|
| 177 |
TotArea1,,** No non-empty join mapping for UNUSED#TotArea1 ** |
|
| 178 |
TotArea10,,** No non-empty join mapping for UNUSED#TotArea10 ** |
|
| 179 |
TotArea11,,** No non-empty join mapping for UNUSED#TotArea11 ** |
|
| 180 |
TotArea12,,** No non-empty join mapping for UNUSED#TotArea12 ** |
|
| 181 |
TotArea13,,** No non-empty join mapping for UNUSED#TotArea13 ** |
|
| 182 |
TotArea14,,** No non-empty join mapping for UNUSED#TotArea14 ** |
|
| 183 |
TotArea15,,** No non-empty join mapping for UNUSED#TotArea15 ** |
|
| 184 |
TotArea2,,** No non-empty join mapping for UNUSED#TotArea2 ** |
|
| 185 |
TotArea3,,** No non-empty join mapping for UNUSED#TotArea3 ** |
|
| 186 |
TotArea4,,** No non-empty join mapping for UNUSED#TotArea4 ** |
|
| 187 |
TotArea5,,** No non-empty join mapping for UNUSED#TotArea5 ** |
|
| 188 |
TotArea6,,** No non-empty join mapping for UNUSED#TotArea6 ** |
|
| 189 |
TotArea7,,** No non-empty join mapping for UNUSED#TotArea7 ** |
|
| 190 |
TotArea8,,** No non-empty join mapping for UNUSED#TotArea8 ** |
|
| 191 |
TotArea9,,** No non-empty join mapping for UNUSED#TotArea9 ** |
|
| 192 |
TreeLeaf3Notes,,** No non-empty join mapping for UNUSED#TreeLeaf3Notes ** |
|
| 193 |
TreeMortalityNotes,,** No non-empty join mapping for UNUSED#TreeMortalityNotes ** |
|
| 194 |
TreeTrunkNotes,,** No non-empty join mapping for UNUSED#TreeTrunkNotes ** |
|
| 195 |
VesselArea,,** No non-empty join mapping for UNUSED#VesselArea ** |
|
| 196 |
VesselNumber,,** No non-empty join mapping for UNUSED#VesselNumber ** |
|
| 197 |
Volume1,,** No non-empty join mapping for UNUSED#Volume1 ** |
|
| 198 |
Volume2,,** No non-empty join mapping for UNUSED#Volume2 ** |
|
| 199 |
WasCollected,,** No join mapping for *WasCollected ** |
|
| 200 |
Weight1,,** No non-empty join mapping for UNUSED#Weight1 ** |
|
| 201 |
Weight10,,** No non-empty join mapping for UNUSED#Weight10 ** |
|
| 202 |
Weight11,,** No non-empty join mapping for UNUSED#Weight11 ** |
|
| 203 |
Weight12,,** No non-empty join mapping for UNUSED#Weight12 ** |
|
| 204 |
Weight13,,** No non-empty join mapping for UNUSED#Weight13 ** |
|
| 205 |
Weight14,,** No non-empty join mapping for UNUSED#Weight14 ** |
|
| 206 |
Weight15,,** No non-empty join mapping for UNUSED#Weight15 ** |
|
| 207 |
Weight2,,** No non-empty join mapping for UNUSED#Weight2 ** |
|
| 208 |
Weight3,,** No non-empty join mapping for UNUSED#Weight3 ** |
|
| 209 |
Weight4,,** No non-empty join mapping for UNUSED#Weight4 ** |
|
| 210 |
Weight5,,** No non-empty join mapping for UNUSED#Weight5 ** |
|
| 211 |
Weight6,,** No non-empty join mapping for UNUSED#Weight6 ** |
|
| 212 |
Weight7,,** No non-empty join mapping for UNUSED#Weight7 ** |
|
| 213 |
Weight8,,** No non-empty join mapping for UNUSED#Weight8 ** |
|
| 214 |
Weight9,,** No non-empty join mapping for UNUSED#Weight9 ** |
|
| 215 |
WeightOfBranch,,** No non-empty join mapping for UNUSED#WeightOfBranch ** |
|
| 216 |
WeightRachilla1,,** No non-empty join mapping for UNUSED#WeightRachilla1 ** |
|
| 217 |
WeightRachilla2,,** No non-empty join mapping for UNUSED#WeightRachilla2 ** |
|
| 218 |
WeightRachilla3,,** No non-empty join mapping for UNUSED#WeightRachilla3 ** |
|
| 219 |
WeightRachilla4,,** No non-empty join mapping for UNUSED#WeightRachilla4 ** |
|
| 220 |
WeightRachilla5,,** No non-empty join mapping for UNUSED#WeightRachilla5 ** |
|
| 221 |
WeightRachis1,,** No non-empty join mapping for UNUSED#WeightRachis1 ** |
|
| 222 |
WeightRachis2,,** No non-empty join mapping for UNUSED#WeightRachis2 ** |
|
| 223 |
WeightRachis3,,** No non-empty join mapping for UNUSED#WeightRachis3 ** |
|
| 224 |
WeightRachis4,,** No non-empty join mapping for UNUSED#WeightRachis4 ** |
|
| 225 |
WeightRachis5,,** No non-empty join mapping for UNUSED#WeightRachis5 ** |
|
| 226 |
WidthButtresses,,** No non-empty join mapping for UNUSED#WidthButtresses ** |
|
| 227 |
row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 228 | 2 | |
| inputs/Madidi/LocationObservation/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/Madidi/LocationObservation/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<authorlocationcode>$Plot Name</authorlocationcode>
|
|
| 11 |
<sourceaccessioncode>$PlotName</sourceaccessioncode>
|
|
| 12 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$Locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
|
|
| 10 |
<authorlocationcode>$locationName</authorlocationcode>
|
|
| 11 |
<sourceaccessioncode>$locationID</sourceaccessioncode>
|
|
| 12 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
|
|
| 13 | 13 |
<locationevent> |
| 14 | 14 |
<project_id> |
| 15 | 15 |
<project> |
| 16 |
<projectname>$Expedition Name</projectname>
|
|
| 17 |
<sourceaccessioncode>$Expedition Number</sourceaccessioncode>
|
|
| 16 |
<projectname>$projectName</projectname>
|
|
| 17 |
<sourceaccessioncode>$projectID</sourceaccessioncode>
|
|
| 18 | 18 |
</project> |
| 19 | 19 |
</project_id> |
| 20 |
<authoreventcode>$PlotInventoryName</authoreventcode>
|
|
| 21 |
<commclass><commdetermination><commconcept_id><commconcept><commname_id><commname><commname>$Vegetation Type</commname></commname></commname_id></commconcept></commconcept_id></commdetermination></commclass>
|
|
| 20 |
<authoreventcode>$authorEventCode</authoreventcode>
|
|
| 21 |
<commclass><commdetermination><commconcept_id><commconcept><commname_id><commname><commname>$communityID</commname></commname></commname_id></commconcept></commconcept_id></commdetermination></commclass>
|
|
| 22 | 22 |
<soilsample> |
| 23 |
<acidity_fraction><_percent_to_fraction><value>$Interchangeable Acidity</value></_percent_to_fraction></acidity_fraction>
|
|
| 24 |
<calcium_fraction><_percent_to_fraction><value>$Interchangable Calcium</value></_percent_to_fraction></calcium_fraction>
|
|
| 25 |
<carbon_fraction><_percent_to_fraction><value>$Organic Carbon</value></_percent_to_fraction></carbon_fraction>
|
|
| 26 |
<cationexchangecapacity_cmol_kg>$CIC</cationexchangecapacity_cmol_kg>
|
|
| 27 |
<clay_fraction><_percent_to_fraction><value>$Clay</value></_percent_to_fraction></clay_fraction>
|
|
| 28 |
<conductivity>$Electric conductivity</conductivity>
|
|
| 29 |
<magnesium_fraction><_percent_to_fraction><value>$Interchangeable Magnesium</value></_percent_to_fraction></magnesium_fraction>
|
|
| 30 |
<nitrogen_fraction><_percent_to_fraction><value>$Total Nitrogen</value></_percent_to_fraction></nitrogen_fraction>
|
|
| 31 |
<organic_fraction><_percent_to_fraction><value>$Organic material</value></_percent_to_fraction></organic_fraction>
|
|
| 32 |
<ph>$pH disolved</ph>
|
|
| 33 |
<phosphorus_fraction><_percent_to_fraction><value>$Available Phosphor</value></_percent_to_fraction></phosphorus_fraction>
|
|
| 34 |
<potassium_fraction><_percent_to_fraction><value>$Interchangeable Potassium</value></_percent_to_fraction></potassium_fraction>
|
|
| 35 |
<sand_fraction><_percent_to_fraction><value>$Sand</value></_percent_to_fraction></sand_fraction>
|
|
| 36 |
<silt_fraction><_percent_to_fraction><value>$Silt</value></_percent_to_fraction></silt_fraction>
|
|
| 37 |
<sodium_fraction><_percent_to_fraction><value>$Interchangeable Sodium</value></_percent_to_fraction></sodium_fraction>
|
|
| 38 |
<texture>$Textural Class</texture>
|
|
| 23 |
<acidity_fraction><_percent_to_fraction><value>$acidity_percent</value></_percent_to_fraction></acidity_fraction>
|
|
| 24 |
<calcium_fraction><_percent_to_fraction><value>$calcium_percent</value></_percent_to_fraction></calcium_fraction>
|
|
| 25 |
<carbon_fraction><_percent_to_fraction><value>$carbon_percent</value></_percent_to_fraction></carbon_fraction>
|
|
| 26 |
<cationexchangecapacity_cmol_kg>$cationExchangeCapacity_cmol_kg</cationexchangecapacity_cmol_kg>
|
|
| 27 |
<clay_fraction><_percent_to_fraction><value>$clay_percent</value></_percent_to_fraction></clay_fraction>
|
|
| 28 |
<conductivity>$conductivity</conductivity> |
|
| 29 |
<magnesium_fraction><_percent_to_fraction><value>$magnesium_percent</value></_percent_to_fraction></magnesium_fraction>
|
|
| 30 |
<nitrogen_fraction><_percent_to_fraction><value>$nitrogen_percent</value></_percent_to_fraction></nitrogen_fraction>
|
|
| 31 |
<organic_fraction><_percent_to_fraction><value>$organic_percent</value></_percent_to_fraction></organic_fraction>
|
|
| 32 |
<ph>$ph</ph>
|
|
| 33 |
<phosphorus_fraction><_percent_to_fraction><value>$phosphorus_percent</value></_percent_to_fraction></phosphorus_fraction>
|
|
| 34 |
<potassium_fraction><_percent_to_fraction><value>$potassium_percent</value></_percent_to_fraction></potassium_fraction>
|
|
| 35 |
<sand_fraction><_percent_to_fraction><value>$sand_percent</value></_percent_to_fraction></sand_fraction>
|
|
| 36 |
<silt_fraction><_percent_to_fraction><value>$silt_percent</value></_percent_to_fraction></silt_fraction>
|
|
| 37 |
<sodium_fraction><_percent_to_fraction><value>$sodium_percent</value></_percent_to_fraction></sodium_fraction>
|
|
| 38 |
<texture>$texture</texture>
|
|
| 39 | 39 |
</soilsample> |
| 40 | 40 |
</locationevent> |
| 41 | 41 |
<locationnarrative> |
| 42 | 42 |
<_merge> |
| 43 |
<1>$Locality</1> |
|
| 44 |
<4> |
|
| 45 |
<_alt> |
|
| 46 |
<0>$Notes</0> |
|
| 47 |
<1>$Notes 2</1> |
|
| 48 |
</_alt> |
|
| 49 |
</4> |
|
| 43 |
<1>$locality</1> |
|
| 44 |
<4>$locationRemarks</4> |
|
| 50 | 45 |
</_merge> |
| 51 | 46 |
</locationnarrative> |
| 52 | 47 |
<locationplace> |
| ... | ... | |
| 58 | 53 |
<_nullIf> |
| 59 | 54 |
<null>0</null> |
| 60 | 55 |
<type>float</type> |
| 61 |
<value>$LatitudeDecDeg</value>
|
|
| 56 |
<value>$decimalLatitude</value>
|
|
| 62 | 57 |
</_nullIf> |
| 63 | 58 |
</latitude_deg> |
| 64 | 59 |
<longitude_deg> |
| 65 | 60 |
<_nullIf> |
| 66 | 61 |
<null>0</null> |
| 67 | 62 |
<type>float</type> |
| 68 |
<value>$LongitudeDecDeg</value>
|
|
| 63 |
<value>$decimalLongitude</value>
|
|
| 69 | 64 |
</_nullIf> |
| 70 | 65 |
</longitude_deg> |
| 71 | 66 |
</coordinates> |
| ... | ... | |
| 80 | 75 |
<_nullIf> |
| 81 | 76 |
<null>0</null> |
| 82 | 77 |
<type>float</type> |
| 83 |
<value>$LatitudeDecDeg</value>
|
|
| 78 |
<value>$decimalLatitude</value>
|
|
| 84 | 79 |
</_nullIf> |
| 85 | 80 |
</latitude_deg> |
| 86 | 81 |
<longitude_deg> |
| 87 | 82 |
<_nullIf> |
| 88 | 83 |
<null>0</null> |
| 89 | 84 |
<type>float</type> |
| 90 |
<value>$LongitudeDecDeg</value>
|
|
| 85 |
<value>$decimalLongitude</value>
|
|
| 91 | 86 |
</_nullIf> |
| 92 | 87 |
</longitude_deg> |
| 93 | 88 |
</coordinates> |
| ... | ... | |
| 97 | 92 |
</place> |
| 98 | 93 |
</place_id> |
| 99 | 94 |
</locationplace> |
| 100 |
<slopegradient_fraction>$Slope</slopegradient_fraction>
|
|
| 95 |
<slopegradient_fraction>$slopeGradient</slopegradient_fraction>
|
|
| 101 | 96 |
</location> |
| 102 | 97 |
</path> |
| 103 | 98 |
</_simplifyPath> |
| inputs/Madidi/LocationObservation/VegBIEN.csv | ||
|---|---|---|
| 1 |
Madidi,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
Plot Name,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
|
| 3 |
PlotName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 4 |
PlotInventoryName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else", |
|
| 5 |
PlotName,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 6 |
Plot Name,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
|
| 7 |
PlotName,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 8 |
Locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 9 |
Expedition Name,/location/locationevent/*_id/project/projectname, |
|
| 10 |
Expedition Number,/location/locationevent/*_id/project/sourceaccessioncode, |
|
| 11 |
PlotInventoryName,"/location/locationevent/_if[@name=""if subplot""]/else/authoreventcode", |
|
| 12 |
PlotInventoryName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 13 |
Plot Name,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then", |
|
| 14 |
PlotName,"/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 |
PlotInventoryName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/authoreventcode", |
|
| 16 |
Vegetation Type,/location/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname, |
|
| 17 |
Interchangeable Acidity,/location/locationevent/soilsample/acidity_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
|
| 18 |
Interchangable Calcium,/location/locationevent/soilsample/calcium_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
|
| 19 |
Organic Carbon,/location/locationevent/soilsample/carbon_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
|
| 20 |
CIC,/location/locationevent/soilsample/cationexchangecapacity_cmol_kg, |
|
| 21 |
Clay,/location/locationevent/soilsample/clay_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
|
| 22 |
Electric conductivity,/location/locationevent/soilsample/conductivity, |
|
| 23 |
Interchangeable Magnesium,/location/locationevent/soilsample/magnesium_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
|
| 24 |
Total Nitrogen,/location/locationevent/soilsample/nitrogen_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
|
| 25 |
Organic material,/location/locationevent/soilsample/organic_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
|
| 26 |
pH disolved,/location/locationevent/soilsample/ph, |
|
| 27 |
Available Phosphor,/location/locationevent/soilsample/phosphorus_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
|
| 28 |
Interchangeable Potassium,/location/locationevent/soilsample/potassium_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
|
| 29 |
Sand,/location/locationevent/soilsample/sand_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
|
| 30 |
Silt,/location/locationevent/soilsample/silt_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
|
| 31 |
Interchangeable Sodium,/location/locationevent/soilsample/sodium_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
|
| 32 |
Textural Class,/location/locationevent/soilsample/texture, |
|
| 33 |
Plot Name,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 34 |
PlotInventoryName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 35 |
PlotName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 36 |
Locality,/location/locationnarrative/_merge/1, |
|
| 37 |
Notes,/location/locationnarrative/_merge/4, |
|
| 38 |
Notes 2,/location/locationnarrative/_merge/4, |
|
| 39 |
LatitudeDecDeg,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 40 |
LongitudeDecDeg,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 41 |
LatitudeDecDeg,"/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" |
|
| 42 |
LongitudeDecDeg,"/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" |
|
| 43 |
Slope,/location/slopegradient_fraction/_alt/1, |
|
| 44 |
PlotName,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 45 |
PlotName,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
|
| 46 |
Collaborators,,** No join mapping for *Collaborators ** |
|
| 47 |
Collaborators (OLD),,** No join mapping for *Collaborators (OLD) ** |
|
| 48 |
Funding agency,,** No join mapping for *Funding agency ** |
|
| 49 |
Installed and evaluated by,,** No join mapping for *Installed and evaluated by ** |
|
| 50 |
Installed and evaluated by (OLD),,** No join mapping for *Installed and evaluated by (OLD) ** |
|
| 51 |
Local Plot Number,,** No join mapping for *Local Plot Number ** |
|
| 52 |
Locality Description,,** No join mapping for *Locality Description ** |
|
| 53 |
Number of Trees,,** No join mapping for *Number of Trees ** |
|
| 54 |
Number of Trunks,,** No join mapping for *Number of Trunks ** |
|
| 55 |
Other Epilocs (OLD),,** No join mapping for *Other Epilocs (OLD) ** |
|
| 56 |
Other epilocs,,** No join mapping for *Other epilocs ** |
|
| 57 |
Plot Compass Direction,,** No join mapping for *Plot Compass Direction ** |
|
| 58 |
PlotID,,** No non-empty join mapping for DUPLICATE#of:PlotName#PlotID ** |
|
| 59 |
Political Location,,** No join mapping for *Political Location ** |
|
| 60 |
Qualifier Available Phosphor,,** No join mapping for *Qualifier Available Phosphor ** |
|
| 61 |
Qualifier Interchangeable Acidity,,** No join mapping for *Qualifier Interchangeable Acidity ** |
|
| 62 |
Qualifier Interchangeable Calcium,,** No join mapping for *Qualifier Interchangeable Calcium ** |
|
| 63 |
Textural Class (select),,** No join mapping for *Textural Class (select) ** |
|
| 64 |
Topographic location,,** No join mapping for *Topographic location ** |
|
| 65 |
row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 66 | 2 | |
| inputs/Madidi/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
|
|
| 0 | 3 | |
| inputs/Madidi/Location/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/Madidi/Location/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<authorlocationcode>$PlotName</authorlocationcode>
|
|
| 11 |
<sourceaccessioncode>$PlotID</sourceaccessioncode>
|
|
| 12 |
<area_m2><_ha_to_m2><value>$Area</value></_ha_to_m2></area_m2>
|
|
| 10 |
<authorlocationcode>$locationName</authorlocationcode>
|
|
| 11 |
<sourceaccessioncode>$locationID</sourceaccessioncode>
|
|
| 12 |
<area_m2><_ha_to_m2><value>$plotArea_ha</value></_ha_to_m2></area_m2>
|
|
| 13 | 13 |
<elevation_m> |
| 14 | 14 |
<_avg> |
| 15 |
<1>$MinimumElevationMeters</1>
|
|
| 16 |
<2>$MaximumElevationMeters</2>
|
|
| 15 |
<1>$minimumElevationInMeters</1>
|
|
| 16 |
<2>$maximumElevationInMeters</2>
|
|
| 17 | 17 |
</_avg> |
| 18 | 18 |
</elevation_m> |
| 19 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$LocalityDescription</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
|
|
| 20 |
<landform>$Topography</landform>
|
|
| 19 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
|
|
| 20 |
<landform>$landform</landform>
|
|
| 21 | 21 |
<locationnarrative> |
| 22 | 22 |
<_merge> |
| 23 |
<1>$LocalityDescription</1>
|
|
| 24 |
<4>$Note</4>
|
|
| 23 |
<1>$locality</1>
|
|
| 24 |
<4>$locationRemarks</4>
|
|
| 25 | 25 |
</_merge> |
| 26 | 26 |
</locationnarrative> |
| 27 | 27 |
<locationplace> |
| ... | ... | |
| 33 | 33 |
<_nullIf> |
| 34 | 34 |
<null>0</null> |
| 35 | 35 |
<type>float</type> |
| 36 |
<value>$LatitudeDecDeg</value>
|
|
| 36 |
<value>$decimalLatitude</value>
|
|
| 37 | 37 |
</_nullIf> |
| 38 | 38 |
</latitude_deg> |
| 39 | 39 |
<longitude_deg> |
| 40 | 40 |
<_nullIf> |
| 41 | 41 |
<null>0</null> |
| 42 | 42 |
<type>float</type> |
| 43 |
<value>$LongitudeDecDeg</value>
|
|
| 43 |
<value>$decimalLongitude</value>
|
|
| 44 | 44 |
</_nullIf> |
| 45 | 45 |
</longitude_deg> |
| 46 | 46 |
</coordinates> |
| 47 | 47 |
</coordinates_id> |
| 48 |
<country>$CountryName</country>
|
|
| 49 |
<county>$LowerName</county>
|
|
| 48 |
<country>$country</country>
|
|
| 49 |
<county>$county</county>
|
|
| 50 | 50 |
<matched_place_id> |
| 51 | 51 |
<place> |
| 52 | 52 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
| ... | ... | |
| 57 | 57 |
<_nullIf> |
| 58 | 58 |
<null>0</null> |
| 59 | 59 |
<type>float</type> |
| 60 |
<value>$LatitudeDecDeg</value>
|
|
| 60 |
<value>$decimalLatitude</value>
|
|
| 61 | 61 |
</_nullIf> |
| 62 | 62 |
</latitude_deg> |
| 63 | 63 |
<longitude_deg> |
| 64 | 64 |
<_nullIf> |
| 65 | 65 |
<null>0</null> |
| 66 | 66 |
<type>float</type> |
| 67 |
<value>$LongitudeDecDeg</value>
|
|
| 67 |
<value>$decimalLongitude</value>
|
|
| 68 | 68 |
</_nullIf> |
| 69 | 69 |
</longitude_deg> |
| 70 | 70 |
</coordinates> |
| 71 | 71 |
</coordinates_id> |
| 72 |
<country>$CountryName</country>
|
|
| 73 |
<county>$LowerName</county>
|
|
| 74 |
<stateprovince>$UpperName</stateprovince>
|
|
| 72 |
<country>$country</country>
|
|
| 73 |
<county>$county</county>
|
|
| 74 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 75 | 75 |
</place> |
| 76 | 76 |
</matched_place_id> |
| 77 |
<stateprovince>$UpperName</stateprovince>
|
|
| 77 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 78 | 78 |
</place> |
| 79 | 79 |
</place_id> |
| 80 | 80 |
</locationplace> |
| inputs/Madidi/Location/VegBIEN.csv | ||
|---|---|---|
| 1 |
Madidi,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
PlotName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
|
| 3 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 5 |
PlotName,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
|
| 6 |
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 7 |
Area,/location/area_m2/_ha_to_m2/value, |
|
| 8 |
MinimumElevationMeters,/location/elevation_m/_alt/2/_avg/1, |
|
| 9 |
MaximumElevationMeters,/location/elevation_m/_alt/2/_avg/2, |
|
| 10 |
LocalityDescription,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 11 |
Topography,/location/landform, |
|
| 12 |
PlotName,"/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 |
PlotID,"/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 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 15 |
PlotName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 16 |
LocalityDescription,/location/locationnarrative/_merge/1, |
|
| 17 |
Note,/location/locationnarrative/_merge/4, |
|
| 18 |
LatitudeDecDeg,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 19 |
LongitudeDecDeg,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 20 |
CountryName,/location/locationplace/*_id/place/country, |
|
| 21 |
LowerName,/location/locationplace/*_id/place/county, |
|
| 22 |
LatitudeDecDeg,"/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" |
|
| 23 |
LongitudeDecDeg,"/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" |
|
| 24 |
CountryName,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 25 |
LowerName,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 26 |
UpperName,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 27 |
UpperName,/location/locationplace/*_id/place/stateprovince, |
|
| 28 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 29 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
|
| 30 |
FirstSurveyDate,,** No join mapping for *FirstSurveyDate ** |
|
| 31 |
OrientationXDegrees,,** No join mapping for *OrientationXDegrees ** |
|
| 32 |
OrientationYDegrees,,** No join mapping for *OrientationYDegrees ** |
|
| 33 |
row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 34 | 2 | |
Also available in: Unified diff
inputs/Madidi/: switched to new-style import