Revision 7162
Added by Aaron Marcuse-Kubitza almost 12 years ago
| inputs/JBM/Specimen/VegBIEN.csv | ||
|---|---|---|
| 37 | 37 |
id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 38 | 38 |
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 39 | 39 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 40 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 41 |
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1", |
|
| 42 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 43 |
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 44 | 40 |
specificEpithet,"/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", |
| 45 | 41 |
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]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
| 46 | 42 |
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", |
| inputs/UBC/Specimen/test.xml.ref | ||
|---|---|---|
| 82 | 82 |
<taxonverbatim> |
| 83 | 83 |
<taxonlabel_id> |
| 84 | 84 |
<taxonlabel> |
| 85 |
<matched_label_id> |
|
| 86 |
<taxonlabel> |
|
| 87 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 88 |
<taxonomicname> |
|
| 89 |
<_merge_prefix> |
|
| 90 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 91 |
<value> |
|
| 92 |
<_alt> |
|
| 93 |
<1>$scientificName</1> |
|
| 94 |
<2> |
|
| 95 |
<_join_words> |
|
| 96 |
<1> |
|
| 97 |
<_join_words> |
|
| 98 |
<2>$genus</2> |
|
| 99 |
<3>$specificEpithet</3> |
|
| 100 |
<5> |
|
| 101 |
<_join_words> |
|
| 102 |
<1> |
|
| 103 |
<_if name="if has infraspecificEpithet"> |
|
| 104 |
<cond>$infraspecificEpithet</cond> |
|
| 105 |
<then>$taxonRank</then> |
|
| 106 |
</_if> |
|
| 107 |
</1> |
|
| 108 |
<2>$infraspecificEpithet</2> |
|
| 109 |
</_join_words> |
|
| 110 |
</5> |
|
| 111 |
</_join_words> |
|
| 112 |
</1> |
|
| 113 |
<2>$scientificNameAuthorship</2> |
|
| 114 |
</_join_words> |
|
| 115 |
</2> |
|
| 116 |
</_alt> |
|
| 117 |
</value> |
|
| 118 |
</_merge_prefix> |
|
| 119 |
</taxonomicname> |
|
| 120 |
</taxonlabel> |
|
| 121 |
</matched_label_id> |
|
| 122 | 85 |
<creationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></creationdate> |
| 123 | 86 |
<parent_id> |
| 124 | 87 |
<taxonlabel> |
| ... | ... | |
| 308 | 271 |
</path> |
| 309 | 272 |
</_setDefault> |
| 310 | 273 |
</VegBIEN> |
| 311 |
Inserted 41 new rows into database |
|
| 274 |
Inserted 38 new rows into database |
|
| inputs/SpeciesLink/Specimen/VegBIEN.csv | ||
|---|---|---|
| 145 | 145 |
conceptual_darwin_2003_1_0_IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 146 | 146 |
dwc_curatorial_IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 147 | 147 |
dwc_terms_identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 148 |
conceptual_darwin_2003_1_0_Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 149 |
dwc_dwcore_Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 150 |
dwc_terms_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 151 |
conceptual_darwin_2003_1_0_ScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1", |
|
| 152 |
dwc_dwcore_ScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1", |
|
| 153 |
dwc_terms_scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1", |
|
| 154 |
conceptual_darwin_2003_1_0_Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 155 |
dwc_dwcore_Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 156 |
dwc_terms_genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 157 |
conceptual_darwin_2003_1_0_Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 158 |
dwc_dwcore_SpecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 159 |
dwc_terms_specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 160 |
conceptual_darwin_2003_1_0_Subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4", |
|
| 161 |
dwc_dwcore_InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 162 |
dwc_terms_infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 163 |
dwc_dwcore_InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2", |
|
| 164 |
dwc_terms_infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2", |
|
| 165 |
dwc_terms_scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2/_alt/1", |
|
| 166 |
conceptual_darwin_2003_1_0_ScientificNameAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2/_alt/2", |
|
| 167 |
dwc_dwcore_AuthorYearOfScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2/_alt/3", |
|
| 168 | 148 |
dwc_terms_dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value, |
| 169 | 149 |
conceptual_darwin_2003_1_0_DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 170 | 150 |
conceptual_darwin_2003_1_0_MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
|---|---|---|
| 97 | 97 |
PlotObsID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
| 98 | 98 |
PlotObsID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
| 99 | 99 |
det_by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 100 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 101 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 102 |
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 103 |
infra_ep_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 104 |
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 105 |
infra_ep_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2", |
|
| 106 |
auth,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",Brad: This is the author of the scientificName. |
|
| 107 | 100 |
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
| 108 | 101 |
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
| 109 | 102 |
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]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
| ... | ... | |
| 126 | 119 |
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 127 | 120 |
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
| 128 | 121 |
cfaff,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank." |
| 129 |
OrigFamily,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,Brad: OMIT |
|
| 130 |
OrigGenus,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2, |
|
| 131 |
OrigSpecies,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3,Brad: OMIT |
|
| 132 | 122 |
OrigSpecies,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",Brad: OMIT |
| 133 | 123 |
OrigGenus,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
| 134 | 124 |
OrigFamily,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",Brad: OMIT |
| inputs/SALVIAS/plotMetadata_/test.xml.ref | ||
|---|---|---|
| 189 | 189 |
</path> |
| 190 | 190 |
</_setDefault> |
| 191 | 191 |
</VegBIEN> |
| 192 |
Inserted 16 new rows into database |
|
| 192 |
Inserted 15 new rows into database |
|
| inputs/U/Specimen/test.xml.ref | ||
|---|---|---|
| 92 | 92 |
<taxonverbatim> |
| 93 | 93 |
<taxonlabel_id> |
| 94 | 94 |
<taxonlabel> |
| 95 |
<matched_label_id> |
|
| 96 |
<taxonlabel> |
|
| 97 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 98 |
<taxonomicname> |
|
| 99 |
<_merge_prefix> |
|
| 100 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix> |
|
| 101 |
<value>$Genus</value> |
|
| 102 |
</_merge_prefix> |
|
| 103 |
</taxonomicname> |
|
| 104 |
</taxonlabel> |
|
| 105 |
</matched_label_id> |
|
| 106 | 95 |
<creationdate> |
| 107 | 96 |
<_date> |
| 108 | 97 |
<year> |
| ... | ... | |
| 264 | 253 |
</path> |
| 265 | 254 |
</_setDefault> |
| 266 | 255 |
</VegBIEN> |
| 267 |
Inserted 35 new rows into database |
|
| 256 |
Inserted 32 new rows into database |
|
| inputs/GBIF/Specimen/test.xml.ref | ||
|---|---|---|
| 52 | 52 |
<taxonverbatim> |
| 53 | 53 |
<taxonlabel_id> |
| 54 | 54 |
<taxonlabel> |
| 55 |
<matched_label_id> |
|
| 56 |
<taxonlabel> |
|
| 57 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 58 |
<taxonomicname> |
|
| 59 |
<_merge_prefix> |
|
| 60 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix> |
|
| 61 |
<value> |
|
| 62 |
<_join_words> |
|
| 63 |
<1> |
|
| 64 |
<_alt> |
|
| 65 |
<1>$ScientificName</1> |
|
| 66 |
<2> |
|
| 67 |
<_join_words> |
|
| 68 |
<2>$Genus</2> |
|
| 69 |
<3>$SpecificEpithet</3> |
|
| 70 |
<5>$InfraspecificEpithet</5> |
|
| 71 |
</_join_words> |
|
| 72 |
</2> |
|
| 73 |
</_alt> |
|
| 74 |
</1> |
|
| 75 |
<2>$AuthorOfScientificName</2> |
|
| 76 |
</_join_words> |
|
| 77 |
</value> |
|
| 78 |
</_merge_prefix> |
|
| 79 |
</taxonomicname> |
|
| 80 |
</taxonlabel> |
|
| 81 |
</matched_label_id> |
|
| 82 | 55 |
<parent_id> |
| 83 | 56 |
<taxonlabel> |
| 84 | 57 |
<parent_id> |
| ... | ... | |
| 160 | 133 |
<taxonverbatim> |
| 161 | 134 |
<taxonlabel_id> |
| 162 | 135 |
<taxonlabel> |
| 163 |
<matched_label_id> |
|
| 164 |
<taxonlabel> |
|
| 165 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 166 |
<taxonomicname> |
|
| 167 |
<_merge_prefix> |
|
| 168 |
<prefix><_taxon_family_require_std><family>$GBIFFamilyOriginal</family></_taxon_family_require_std></prefix> |
|
| 169 |
<value> |
|
| 170 |
<_alt> |
|
| 171 |
<1>$ScientificNameOriginal</1> |
|
| 172 |
<2>$GBIFGenusOriginal</2> |
|
| 173 |
</_alt> |
|
| 174 |
</value> |
|
| 175 |
</_merge_prefix> |
|
| 176 |
</taxonomicname> |
|
| 177 |
</taxonlabel> |
|
| 178 |
</matched_label_id> |
|
| 179 | 136 |
<parent_id> |
| 180 | 137 |
<taxonlabel> |
| 181 | 138 |
<parent_id> |
| ... | ... | |
| 299 | 256 |
</path> |
| 300 | 257 |
</_setDefault> |
| 301 | 258 |
</VegBIEN> |
| 302 |
Inserted 47 new rows into database |
|
| 259 |
Inserted 42 new rows into database |
|
| inputs/QFA/Specimen/test.xml.ref | ||
|---|---|---|
| 98 | 98 |
<taxonverbatim> |
| 99 | 99 |
<taxonlabel_id> |
| 100 | 100 |
<taxonlabel> |
| 101 |
<matched_label_id> |
|
| 102 |
<taxonlabel> |
|
| 103 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 104 |
<taxonomicname> |
|
| 105 |
<_merge_prefix> |
|
| 106 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 107 |
<value> |
|
| 108 |
<_alt> |
|
| 109 |
<1>$scientificName</1> |
|
| 110 |
<2> |
|
| 111 |
<_join_words> |
|
| 112 |
<1> |
|
| 113 |
<_join_words> |
|
| 114 |
<2>$genus</2> |
|
| 115 |
<3>$specificEpithet</3> |
|
| 116 |
<5> |
|
| 117 |
<_join_words> |
|
| 118 |
<1> |
|
| 119 |
<_if name="if has infraspecificEpithet"> |
|
| 120 |
<cond>$infraspecificEpithet</cond> |
|
| 121 |
<then>$taxonRank</then> |
|
| 122 |
</_if> |
|
| 123 |
</1> |
|
| 124 |
<2>$infraspecificEpithet</2> |
|
| 125 |
</_join_words> |
|
| 126 |
</5> |
|
| 127 |
</_join_words> |
|
| 128 |
</1> |
|
| 129 |
<2>$scientificNameAuthorship</2> |
|
| 130 |
</_join_words> |
|
| 131 |
</2> |
|
| 132 |
</_alt> |
|
| 133 |
</value> |
|
| 134 |
</_merge_prefix> |
|
| 135 |
</taxonomicname> |
|
| 136 |
</taxonlabel> |
|
| 137 |
</matched_label_id> |
|
| 138 | 101 |
<creationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></creationdate> |
| 139 | 102 |
<parent_id> |
| 140 | 103 |
<taxonlabel> |
| ... | ... | |
| 322 | 285 |
</path> |
| 323 | 286 |
</_setDefault> |
| 324 | 287 |
</VegBIEN> |
| 325 |
Inserted 45 new rows into database |
|
| 288 |
Inserted 42 new rows into database |
|
| inputs/UBC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 37 | 37 |
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 38 | 38 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 39 | 39 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 40 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 41 |
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1", |
|
| 42 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 43 |
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 44 |
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 45 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 46 |
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2", |
|
| 47 |
scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
|
| 48 | 40 |
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value, |
| 49 | 41 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
| 50 | 42 |
specificEpithet,"/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", |
| inputs/HIBG/Specimen/test.xml.ref | ||
|---|---|---|
| 82 | 82 |
<taxonverbatim> |
| 83 | 83 |
<taxonlabel_id> |
| 84 | 84 |
<taxonlabel> |
| 85 |
<matched_label_id> |
|
| 86 |
<taxonlabel> |
|
| 87 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 88 |
<taxonomicname> |
|
| 89 |
<_merge_prefix> |
|
| 90 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 91 |
<value> |
|
| 92 |
<_alt> |
|
| 93 |
<1>$scientificName</1> |
|
| 94 |
<2> |
|
| 95 |
<_join_words> |
|
| 96 |
<1> |
|
| 97 |
<_join_words> |
|
| 98 |
<2>$genus</2> |
|
| 99 |
<3>$specificEpithet</3> |
|
| 100 |
<5> |
|
| 101 |
<_join_words> |
|
| 102 |
<1> |
|
| 103 |
<_if name="if has infraspecificEpithet"> |
|
| 104 |
<cond>$infraspecificEpithet</cond> |
|
| 105 |
<then>$taxonRank</then> |
|
| 106 |
</_if> |
|
| 107 |
</1> |
|
| 108 |
<2>$infraspecificEpithet</2> |
|
| 109 |
</_join_words> |
|
| 110 |
</5> |
|
| 111 |
</_join_words> |
|
| 112 |
</1> |
|
| 113 |
<2>$scientificNameAuthorship</2> |
|
| 114 |
</_join_words> |
|
| 115 |
</2> |
|
| 116 |
</_alt> |
|
| 117 |
</value> |
|
| 118 |
</_merge_prefix> |
|
| 119 |
</taxonomicname> |
|
| 120 |
</taxonlabel> |
|
| 121 |
</matched_label_id> |
|
| 122 | 85 |
<creationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></creationdate> |
| 123 | 86 |
<parent_id> |
| 124 | 87 |
<taxonlabel> |
| ... | ... | |
| 309 | 272 |
</path> |
| 310 | 273 |
</_setDefault> |
| 311 | 274 |
</VegBIEN> |
| 312 |
Inserted 39 new rows into database |
|
| 275 |
Inserted 37 new rows into database |
|
| inputs/MT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 20 | 20 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_alt/2/_map:[cultivated=t,wild=f,*=]/value", |
| 21 | 21 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
| 22 | 22 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 23 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 24 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 25 | 23 |
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]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
| 26 | 24 |
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", |
| 27 | 25 |
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]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
| inputs/MT/Specimen/test.xml.ref | ||
|---|---|---|
| 61 | 61 |
<taxonverbatim> |
| 62 | 62 |
<taxonlabel_id> |
| 63 | 63 |
<taxonlabel> |
| 64 |
<matched_label_id> |
|
| 65 |
<taxonlabel> |
|
| 66 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 67 |
<taxonomicname> |
|
| 68 |
<_merge_prefix> |
|
| 69 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 70 |
<value>$genus</value> |
|
| 71 |
</_merge_prefix> |
|
| 72 |
</taxonomicname> |
|
| 73 |
</taxonlabel> |
|
| 74 |
</matched_label_id> |
|
| 75 | 64 |
<parent_id> |
| 76 | 65 |
<taxonlabel> |
| 77 | 66 |
<parent_id> |
| ... | ... | |
| 136 | 125 |
</path> |
| 137 | 126 |
</_setDefault> |
| 138 | 127 |
</VegBIEN> |
| 139 |
Inserted 26 new rows into database |
|
| 128 |
Inserted 24 new rows into database |
|
| inputs/test_taxonomic_names/Taxon/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
test_taxonomic_names,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 | 2 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
| 3 |
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1", |
|
| 4 | 3 |
scientificNameID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
| 5 | 4 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
| 6 | 5 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
| inputs/test_taxonomic_names/Taxon/test.xml.ref | ||
|---|---|---|
| 14 | 14 |
<taxonverbatim> |
| 15 | 15 |
<taxonlabel_id> |
| 16 | 16 |
<taxonlabel> |
| 17 |
<matched_label_id> |
|
| 18 |
<taxonlabel> |
|
| 19 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 20 |
<taxonomicname>$scientificName</taxonomicname> |
|
| 21 |
</taxonlabel> |
|
| 22 |
</matched_label_id> |
|
| 23 | 17 |
<sourceaccessioncode>$scientificNameID</sourceaccessioncode> |
| 24 | 18 |
<taxonomicname>$scientificName</taxonomicname> |
| 25 | 19 |
</taxonlabel> |
| ... | ... | |
| 36 | 30 |
</path> |
| 37 | 31 |
</_setDefault> |
| 38 | 32 |
</VegBIEN> |
| 39 |
Inserted 8 new rows into database |
|
| 33 |
Inserted 5 new rows into database |
|
| inputs/XAL/Specimen/VegBIEN.csv | ||
|---|---|---|
| 27 | 27 |
darwin:Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| 28 | 28 |
darwin:CollectorNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 29 | 29 |
darwin:IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 30 |
darwin:Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 31 |
darwin:ScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1", |
|
| 32 |
darwin:Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 33 |
darwin:Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 34 |
darwin:Subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4", |
|
| 35 |
darwin:ScientificNameAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
|
| 36 | 30 |
darwin:DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 37 | 31 |
darwin:MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| 38 | 32 |
darwin:YearIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| inputs/NCU/Specimen/VegBIEN.csv | ||
|---|---|---|
| 36 | 36 |
firstCollectorRemarks,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Actually the collector's number, not remarks" |
| 37 | 37 |
Cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/2/_nullIf:[null=""-1""]/value", |
| 38 | 38 |
SpecimenPK,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 39 |
CurrentScientificNameWithAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1", |
|
| 40 |
CurrentScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1", |
|
| 41 | 39 |
CurrentScientificNameWithAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
| 42 | 40 |
CurrentScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
| 43 | 41 |
CurrentScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
| 44 | 42 |
CurrentScientificNameWithAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
| 45 |
OriginalTaxonLabel,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 46 | 43 |
OriginalTaxonLabel,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
| 47 | 44 |
OriginalTaxonLabel,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonomicname, |
| 48 | 45 |
CatalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
| inputs/NCU/Specimen/test.xml.ref | ||
|---|---|---|
| 84 | 84 |
<taxonverbatim> |
| 85 | 85 |
<taxonlabel_id> |
| 86 | 86 |
<taxonlabel> |
| 87 |
<matched_label_id> |
|
| 88 |
<taxonlabel> |
|
| 89 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 90 |
<taxonomicname> |
|
| 91 |
<_alt> |
|
| 92 |
<1>$CurrentScientificNameWithAuthor</1> |
|
| 93 |
<2>$CurrentScientificName</2> |
|
| 94 |
</_alt> |
|
| 95 |
</taxonomicname> |
|
| 96 |
</taxonlabel> |
|
| 97 |
</matched_label_id> |
|
| 98 | 87 |
<taxonomicname> |
| 99 | 88 |
<_alt> |
| 100 | 89 |
<1>$CurrentScientificNameWithAuthor</1> |
| ... | ... | |
| 112 | 101 |
<isoriginal>true</isoriginal> |
| 113 | 102 |
<taxonverbatim_id> |
| 114 | 103 |
<taxonverbatim> |
| 115 |
<taxonlabel_id> |
|
| 116 |
<taxonlabel> |
|
| 117 |
<matched_label_id> |
|
| 118 |
<taxonlabel> |
|
| 119 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 120 |
<taxonomicname>$OriginalTaxonLabel</taxonomicname> |
|
| 121 |
</taxonlabel> |
|
| 122 |
</matched_label_id> |
|
| 123 |
<taxonomicname>$OriginalTaxonLabel</taxonomicname> |
|
| 124 |
</taxonlabel> |
|
| 125 |
</taxonlabel_id> |
|
| 104 |
<taxonlabel_id><taxonlabel><taxonomicname>$OriginalTaxonLabel</taxonomicname></taxonlabel></taxonlabel_id> |
|
| 126 | 105 |
<taxonomicname>$OriginalTaxonLabel</taxonomicname> |
| 127 | 106 |
</taxonverbatim> |
| 128 | 107 |
</taxonverbatim_id> |
| ... | ... | |
| 197 | 176 |
</path> |
| 198 | 177 |
</_setDefault> |
| 199 | 178 |
</VegBIEN> |
| 200 |
Inserted 40 new rows into database |
|
| 179 |
Inserted 36 new rows into database |
|
| inputs/bien2_traits/TraitObservation/VegBIEN.csv | ||
|---|---|---|
| 11 | 11 |
Habit,/location/locationevent/taxonoccurrence/growthform, |
| 12 | 12 |
TraitObservationID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 13 | 13 |
TraitObservationID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 14 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 15 |
Taxon,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1", |
|
| 16 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 17 |
SpecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 18 |
InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 19 |
InfraspecificRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 20 |
InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2", |
|
| 21 |
AuthorOfScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
|
| 22 | 14 |
InfraspecificRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
| 23 | 15 |
SpecificEpithet,"/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", |
| 24 | 16 |
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]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
| inputs/bien2_traits/TraitObservation/test.xml.ref | ||
|---|---|---|
| 26 | 26 |
<taxonverbatim> |
| 27 | 27 |
<taxonlabel_id> |
| 28 | 28 |
<taxonlabel> |
| 29 |
<matched_label_id> |
|
| 30 |
<taxonlabel> |
|
| 31 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 32 |
<taxonomicname> |
|
| 33 |
<_merge_prefix> |
|
| 34 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix> |
|
| 35 |
<value> |
|
| 36 |
<_join_words> |
|
| 37 |
<1> |
|
| 38 |
<_alt> |
|
| 39 |
<1>$Taxon</1> |
|
| 40 |
<2> |
|
| 41 |
<_join_words> |
|
| 42 |
<2>$Genus</2> |
|
| 43 |
<3>$SpecificEpithet</3> |
|
| 44 |
<5> |
|
| 45 |
<_join_words> |
|
| 46 |
<1> |
|
| 47 |
<_if name="if has infraspecificEpithet"> |
|
| 48 |
<cond>$InfraspecificEpithet</cond> |
|
| 49 |
<then>$InfraspecificRank</then> |
|
| 50 |
</_if> |
|
| 51 |
</1> |
|
| 52 |
<2>$InfraspecificEpithet</2> |
|
| 53 |
</_join_words> |
|
| 54 |
</5> |
|
| 55 |
</_join_words> |
|
| 56 |
</2> |
|
| 57 |
</_alt> |
|
| 58 |
</1> |
|
| 59 |
<2>$AuthorOfScientificName</2> |
|
| 60 |
</_join_words> |
|
| 61 |
</value> |
|
| 62 |
</_merge_prefix> |
|
| 63 |
</taxonomicname> |
|
| 64 |
</taxonlabel> |
|
| 65 |
</matched_label_id> |
|
| 66 | 29 |
<parent_id> |
| 67 | 30 |
<taxonlabel> |
| 68 | 31 |
<rank>$InfraspecificRank</rank> |
| ... | ... | |
| 187 | 150 |
</path> |
| 188 | 151 |
</_setDefault> |
| 189 | 152 |
</VegBIEN> |
| 190 |
Inserted 33 new rows into database |
|
| 153 |
Inserted 30 new rows into database |
|
| inputs/TEAM/VL/VegBIEN.csv | ||
|---|---|---|
| 28 | 28 |
Names of Collectors,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| 29 | 29 |
Id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 30 | 30 |
Id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 31 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 32 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 33 |
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 34 | 31 |
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
| 35 | 32 |
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]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
| 36 | 33 |
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", |
| inputs/TEAM/VL/test.xml.ref | ||
|---|---|---|
| 49 | 49 |
<taxonverbatim> |
| 50 | 50 |
<taxonlabel_id> |
| 51 | 51 |
<taxonlabel> |
| 52 |
<matched_label_id> |
|
| 53 |
<taxonlabel> |
|
| 54 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 55 |
<taxonomicname> |
|
| 56 |
<_merge_prefix> |
|
| 57 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix> |
|
| 58 |
<value> |
|
| 59 |
<_join_words> |
|
| 60 |
<2>$Genus</2> |
|
| 61 |
<3>$Species</3> |
|
| 62 |
</_join_words> |
|
| 63 |
</value> |
|
| 64 |
</_merge_prefix> |
|
| 65 |
</taxonomicname> |
|
| 66 |
</taxonlabel> |
|
| 67 |
</matched_label_id> |
|
| 68 | 52 |
<parent_id> |
| 69 | 53 |
<taxonlabel> |
| 70 | 54 |
<parent_id> |
| ... | ... | |
| 182 | 166 |
</path> |
| 183 | 167 |
</_setDefault> |
| 184 | 168 |
</VegBIEN> |
| 185 |
Inserted 35 new rows into database |
|
| 169 |
Inserted 32 new rows into database |
|
| inputs/TEAM/VT/VegBIEN.csv | ||
|---|---|---|
| 28 | 28 |
Names of Collectors,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| 29 | 29 |
Id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 30 | 30 |
Id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 31 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 32 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 33 |
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 34 | 31 |
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
| 35 | 32 |
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]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
| 36 | 33 |
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", |
| inputs/TEAM/VT/test.xml.ref | ||
|---|---|---|
| 49 | 49 |
<taxonverbatim> |
| 50 | 50 |
<taxonlabel_id> |
| 51 | 51 |
<taxonlabel> |
| 52 |
<matched_label_id> |
|
| 53 |
<taxonlabel> |
|
| 54 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 55 |
<taxonomicname> |
|
| 56 |
<_merge_prefix> |
|
| 57 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix> |
|
| 58 |
<value> |
|
| 59 |
<_join_words> |
|
| 60 |
<2>$Genus</2> |
|
| 61 |
<3>$Species</3> |
|
| 62 |
</_join_words> |
|
| 63 |
</value> |
|
| 64 |
</_merge_prefix> |
|
| 65 |
</taxonomicname> |
|
| 66 |
</taxonlabel> |
|
| 67 |
</matched_label_id> |
|
| 68 | 52 |
<parent_id> |
| 69 | 53 |
<taxonlabel> |
| 70 | 54 |
<parent_id> |
| ... | ... | |
| 182 | 166 |
</path> |
| 183 | 167 |
</_setDefault> |
| 184 | 168 |
</VegBIEN> |
| 185 |
Inserted 33 new rows into database |
|
| 169 |
Inserted 30 new rows into database |
|
| inputs/ACAD/Specimen/VegBIEN.csv | ||
|---|---|---|
| 37 | 37 |
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 38 | 38 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 39 | 39 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 40 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 41 |
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1", |
|
| 42 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 43 |
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 44 |
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 45 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 46 |
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2", |
|
| 47 |
scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
|
| 48 | 40 |
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value, |
| 49 | 41 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
| 50 | 42 |
specificEpithet,"/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", |
| inputs/ACAD/Specimen/test.xml.ref | ||
|---|---|---|
| 82 | 82 |
<taxonverbatim> |
| 83 | 83 |
<taxonlabel_id> |
| 84 | 84 |
<taxonlabel> |
| 85 |
<matched_label_id> |
|
| 86 |
<taxonlabel> |
|
| 87 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 88 |
<taxonomicname> |
|
| 89 |
<_merge_prefix> |
|
| 90 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 91 |
<value> |
|
| 92 |
<_alt> |
|
| 93 |
<1>$scientificName</1> |
|
| 94 |
<2> |
|
| 95 |
<_join_words> |
|
| 96 |
<1> |
|
| 97 |
<_join_words> |
|
| 98 |
<2>$genus</2> |
|
| 99 |
<3>$specificEpithet</3> |
|
| 100 |
<5> |
|
| 101 |
<_join_words> |
|
| 102 |
<1> |
|
| 103 |
<_if name="if has infraspecificEpithet"> |
|
| 104 |
<cond>$infraspecificEpithet</cond> |
|
| 105 |
<then>$taxonRank</then> |
|
| 106 |
</_if> |
|
| 107 |
</1> |
|
| 108 |
<2>$infraspecificEpithet</2> |
|
| 109 |
</_join_words> |
|
| 110 |
</5> |
|
| 111 |
</_join_words> |
|
| 112 |
</1> |
|
| 113 |
<2>$scientificNameAuthorship</2> |
|
| 114 |
</_join_words> |
|
| 115 |
</2> |
|
| 116 |
</_alt> |
|
| 117 |
</value> |
|
| 118 |
</_merge_prefix> |
|
| 119 |
</taxonomicname> |
|
| 120 |
</taxonlabel> |
|
| 121 |
</matched_label_id> |
|
| 122 | 85 |
<creationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></creationdate> |
| 123 | 86 |
<parent_id> |
| 124 | 87 |
<taxonlabel> |
| ... | ... | |
| 308 | 271 |
</path> |
| 309 | 272 |
</_setDefault> |
| 310 | 273 |
</VegBIEN> |
| 311 |
Inserted 45 new rows into database |
|
| 274 |
Inserted 42 new rows into database |
|
| inputs/.NCBI/nodes/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
NCBI,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 | 2 |
name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists", |
| 3 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 4 | 3 |
parent tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_taxonlabel_set_parent_id/parent_id/taxonlabel/sourceaccessioncode, |
| 5 | 4 |
parent tax_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/cond/_exists", |
| 6 | 5 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
| inputs/.NCBI/nodes/test.xml.ref | ||
|---|---|---|
| 43 | 43 |
</path> |
| 44 | 44 |
</_setDefault> |
| 45 | 45 |
</VegBIEN> |
| 46 |
Inserted 6 new rows into database |
|
| 46 |
Inserted 5 new rows into database |
|
| inputs/WIN/Specimen/VegBIEN.csv | ||
|---|---|---|
| 38 | 38 |
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 39 | 39 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 40 | 40 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 41 |
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1", |
|
| 42 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 43 |
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 44 |
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 45 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 46 |
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2", |
|
| 47 |
scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
|
| 48 | 41 |
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value, |
| 49 | 42 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
| 50 | 43 |
specificEpithet,"/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", |
| inputs/WIN/Specimen/test.xml.ref | ||
|---|---|---|
| 87 | 87 |
<taxonverbatim> |
| 88 | 88 |
<taxonlabel_id> |
| 89 | 89 |
<taxonlabel> |
| 90 |
<matched_label_id> |
|
| 91 |
<taxonlabel> |
|
| 92 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 93 |
<taxonomicname> |
|
| 94 |
<_alt> |
|
| 95 |
<1>$scientificName</1> |
|
| 96 |
<2> |
|
| 97 |
<_join_words> |
|
| 98 |
<1> |
|
| 99 |
<_join_words> |
|
| 100 |
<2>$genus</2> |
|
| 101 |
<3>$specificEpithet</3> |
|
| 102 |
<5> |
|
| 103 |
<_join_words> |
|
| 104 |
<1> |
|
| 105 |
<_if name="if has infraspecificEpithet"> |
|
| 106 |
<cond>$infraspecificEpithet</cond> |
|
| 107 |
<then>$taxonRank</then> |
|
| 108 |
</_if> |
|
| 109 |
</1> |
|
| 110 |
<2>$infraspecificEpithet</2> |
|
| 111 |
</_join_words> |
|
| 112 |
</5> |
|
| 113 |
</_join_words> |
|
| 114 |
</1> |
|
| 115 |
<2>$scientificNameAuthorship</2> |
|
| 116 |
</_join_words> |
|
| 117 |
</2> |
|
| 118 |
</_alt> |
|
| 119 |
</taxonomicname> |
|
| 120 |
</taxonlabel> |
|
| 121 |
</matched_label_id> |
|
| 122 | 90 |
<creationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></creationdate> |
| 123 | 91 |
<parent_id> |
| 124 | 92 |
<taxonlabel> |
| ... | ... | |
| 301 | 269 |
</path> |
| 302 | 270 |
</_setDefault> |
| 303 | 271 |
</VegBIEN> |
| 304 |
Inserted 36 new rows into database |
|
| 272 |
Inserted 34 new rows into database |
|
| inputs/CTFS/StemObservation/VegBIEN.csv | ||
|---|---|---|
| 26 | 26 |
Tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| 27 | 27 |
MeasureID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 28 | 28 |
MeasureID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2", |
| 29 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 30 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 31 |
SpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 32 |
SubSpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4", |
|
| 33 |
SpeciesAuthority,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
|
| 34 | 29 |
SubSpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet", |
| 35 | 30 |
SpeciesName,"/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", |
| 36 | 31 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
| inputs/CTFS/StemObservation/test.xml.ref | ||
|---|---|---|
| 55 | 55 |
<taxonverbatim> |
| 56 | 56 |
<taxonlabel_id> |
| 57 | 57 |
<taxonlabel> |
| 58 |
<matched_label_id> |
|
| 59 |
<taxonlabel> |
|
| 60 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 61 |
<taxonomicname> |
|
| 62 |
<_merge_prefix> |
|
| 63 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix> |
|
| 64 |
<value> |
|
| 65 |
<_join_words> |
|
| 66 |
<1> |
|
| 67 |
<_join_words> |
|
| 68 |
<2>$Genus</2> |
|
| 69 |
<3>$SpeciesName</3> |
|
| 70 |
<4>$SubSpeciesName</4> |
|
| 71 |
</_join_words> |
|
| 72 |
</1> |
|
| 73 |
<2>$SpeciesAuthority</2> |
|
| 74 |
</_join_words> |
|
| 75 |
</value> |
|
| 76 |
</_merge_prefix> |
|
| 77 |
</taxonomicname> |
|
| 78 |
</taxonlabel> |
|
| 79 |
</matched_label_id> |
|
| 80 | 58 |
<parent_id> |
| 81 | 59 |
<taxonlabel> |
| 82 | 60 |
<parent_id> |
| ... | ... | |
| 160 | 138 |
</path> |
| 161 | 139 |
</_setDefault> |
| 162 | 140 |
</VegBIEN> |
| 163 |
Inserted 20 new rows into database |
|
| 141 |
Inserted 18 new rows into database |
|
| inputs/CTFS/TaxonOccurrence/VegBIEN.csv | ||
|---|---|---|
| 11 | 11 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
| 12 | 12 |
SpeciesInvID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 13 | 13 |
SpeciesInvID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1, |
| 14 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 15 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 16 |
SpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 17 |
SubSpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4", |
|
| 18 |
SpeciesAuthority,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
|
| 19 | 14 |
SubSpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet", |
| 20 | 15 |
SpeciesName,"/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", |
| 21 | 16 |
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]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
| inputs/CTFS/TaxonOccurrence/test.xml.ref | ||
|---|---|---|
| 17 | 17 |
<taxonverbatim> |
| 18 | 18 |
<taxonlabel_id> |
| 19 | 19 |
<taxonlabel> |
| 20 |
<matched_label_id> |
|
| 21 |
<taxonlabel> |
|
| 22 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 23 |
<taxonomicname> |
|
| 24 |
<_merge_prefix> |
|
| 25 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix> |
|
| 26 |
<value> |
|
| 27 |
<_join_words> |
|
| 28 |
<1> |
|
| 29 |
<_join_words> |
|
| 30 |
<2>$Genus</2> |
|
| 31 |
<3>$SpeciesName</3> |
|
| 32 |
<4>$SubSpeciesName</4> |
|
| 33 |
</_join_words> |
|
| 34 |
</1> |
|
| 35 |
<2>$SpeciesAuthority</2> |
|
| 36 |
</_join_words> |
|
| 37 |
</value> |
|
| 38 |
</_merge_prefix> |
|
| 39 |
</taxonomicname> |
|
| 40 |
</taxonlabel> |
|
| 41 |
</matched_label_id> |
|
| 42 | 20 |
<parent_id> |
| 43 | 21 |
<taxonlabel> |
| 44 | 22 |
<parent_id> |
| ... | ... | |
| 116 | 94 |
</path> |
| 117 | 95 |
</_setDefault> |
| 118 | 96 |
</VegBIEN> |
| 119 |
Inserted 20 new rows into database |
|
| 97 |
Inserted 17 new rows into database |
|
| inputs/SALVIAS/projects/test.xml.ref | ||
|---|---|---|
| 21 | 21 |
</path> |
| 22 | 22 |
</_setDefault> |
| 23 | 23 |
</VegBIEN> |
| 24 |
Inserted 3 new rows into database |
|
| 24 |
Inserted 2 new rows into database |
|
| inputs/SALVIAS/stems/test.xml.ref | ||
|---|---|---|
| 82 | 82 |
</path> |
| 83 | 83 |
</_setDefault> |
| 84 | 84 |
</VegBIEN> |
| 85 |
Inserted 24 new rows into database |
|
| 85 |
Inserted 14 new rows into database |
|
| inputs/SALVIAS/plotObservations/test.xml.ref | ||
|---|---|---|
| 156 | 156 |
<taxonverbatim> |
| 157 | 157 |
<taxonlabel_id> |
| 158 | 158 |
<taxonlabel> |
| 159 |
<matched_label_id> |
|
| 160 |
<taxonlabel> |
|
| 161 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 162 |
<taxonomicname> |
|
| 163 |
<_merge_prefix> |
|
| 164 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix> |
|
| 165 |
<value> |
|
| 166 |
<_join_words> |
|
| 167 |
<1> |
|
| 168 |
<_join_words> |
|
| 169 |
<2>$Genus</2> |
|
| 170 |
<3>$Species</3> |
|
| 171 |
<5> |
|
| 172 |
<_join_words> |
|
| 173 |
<1> |
|
| 174 |
<_if name="if has infraspecificEpithet"> |
|
| 175 |
<cond>$infra_ep_1</cond> |
|
| 176 |
<then>$infra_rank_1</then> |
|
| 177 |
</_if> |
|
| 178 |
</1> |
|
| 179 |
<2>$infra_ep_1</2> |
|
| 180 |
</_join_words> |
|
| 181 |
</5> |
|
| 182 |
</_join_words> |
|
| 183 |
</1> |
|
| 184 |
<2>$auth</2> |
|
| 185 |
</_join_words> |
|
| 186 |
</value> |
|
| 187 |
</_merge_prefix> |
|
| 188 |
</taxonomicname> |
|
| 189 |
</taxonlabel> |
|
| 190 |
</matched_label_id> |
|
| 191 | 159 |
<parent_id> |
| 192 | 160 |
<taxonlabel> |
| 193 | 161 |
<rank>$infra_rank_1</rank> |
| ... | ... | |
| 277 | 245 |
<taxonverbatim> |
| 278 | 246 |
<taxonlabel_id> |
| 279 | 247 |
<taxonlabel> |
| 280 |
<matched_label_id> |
|
| 281 |
<taxonlabel> |
|
| 282 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 283 |
<taxonomicname> |
|
| 284 |
<_merge_prefix> |
|
| 285 |
<prefix><_taxon_family_require_std><family>$OrigFamily</family></_taxon_family_require_std></prefix> |
|
| 286 |
<value> |
|
| 287 |
<_join_words> |
|
| 288 |
<2>$OrigGenus</2> |
|
| 289 |
<3>$OrigSpecies</3> |
|
| 290 |
</_join_words> |
|
| 291 |
</value> |
|
| 292 |
</_merge_prefix> |
|
| 293 |
</taxonomicname> |
|
| 294 |
</taxonlabel> |
|
| 295 |
</matched_label_id> |
|
| 296 | 248 |
<parent_id> |
| 297 | 249 |
<taxonlabel> |
| 298 | 250 |
<parent_id> |
| ... | ... | |
| 390 | 342 |
</path> |
| 391 | 343 |
</_setDefault> |
| 392 | 344 |
</VegBIEN> |
| 393 |
Inserted 50 new rows into database |
|
| 345 |
Inserted 0 new rows into database |
|
| inputs/U/Specimen/VegBIEN.csv | ||
|---|---|---|
| 28 | 28 |
Number,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 29 | 29 |
ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 30 | 30 |
Detby,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 31 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 32 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 33 | 31 |
Detyy,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| 34 | 32 |
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]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
| 35 | 33 |
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", |
| inputs/GBIF/Specimen/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
| 20 | 20 |
Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| 21 | 21 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 22 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 23 |
ScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1", |
|
| 24 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 25 |
SpecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 26 |
InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 27 |
InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2", |
|
| 28 |
AuthorOfScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
|
| 29 | 22 |
SpecificEpithet,"/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", |
| 30 | 23 |
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]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
| 31 | 24 |
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", |
| ... | ... | |
| 44 | 37 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| 45 | 38 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 46 | 39 |
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
| 47 |
GBIFFamilyOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 48 |
ScientificNameOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
|
| 49 |
GBIFGenusOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2, |
|
| 50 | 40 |
GBIFGenusOriginal,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
| 51 | 41 |
GBIFFamilyOriginal,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet", |
| 52 | 42 |
GBIFFamilyOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
| inputs/QFA/Specimen/VegBIEN.csv | ||
|---|---|---|
| 39 | 39 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
| 40 | 40 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 41 | 41 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 42 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 43 |
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1", |
|
| 44 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 45 |
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 46 |
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 47 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 48 |
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2", |
|
| 49 |
scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
|
| 50 | 42 |
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value, |
| 51 | 43 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
| 52 | 44 |
specificEpithet,"/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", |
| inputs/JBM/Specimen/test.xml.ref | ||
|---|---|---|
| 84 | 84 |
<taxonverbatim> |
| 85 | 85 |
<taxonlabel_id> |
| 86 | 86 |
<taxonlabel> |
| 87 |
<matched_label_id> |
|
| 88 |
<taxonlabel> |
|
| 89 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 90 |
<taxonomicname> |
|
| 91 |
<_merge_prefix> |
|
| 92 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 93 |
<value> |
|
| 94 |
<_alt> |
|
| 95 |
<1>$scientificName</1> |
|
| 96 |
<2> |
|
| 97 |
<_join_words> |
|
| 98 |
<2>$genus</2> |
|
| 99 |
<3>$specificEpithet</3> |
|
| 100 |
</_join_words> |
|
| 101 |
</2> |
|
| 102 |
</_alt> |
|
| 103 |
</value> |
|
| 104 |
</_merge_prefix> |
|
| 105 |
</taxonomicname> |
|
| 106 |
</taxonlabel> |
|
| 107 |
</matched_label_id> |
|
| 108 | 87 |
<parent_id> |
| 109 | 88 |
<taxonlabel> |
| 110 | 89 |
<parent_id> |
| ... | ... | |
| 270 | 249 |
</path> |
| 271 | 250 |
</_setDefault> |
| 272 | 251 |
</VegBIEN> |
| 273 |
Inserted 38 new rows into database |
|
| 252 |
Inserted 35 new rows into database |
|
| inputs/HIBG/Specimen/VegBIEN.csv | ||
|---|---|---|
| 37 | 37 |
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 38 | 38 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 39 | 39 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 40 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 41 |
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1", |
|
| 42 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 43 |
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 44 |
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 45 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 46 |
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2", |
|
| 47 |
scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
|
| 48 | 40 |
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value, |
| 49 | 41 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
| 50 | 42 |
specificEpithet,"/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", |
| inputs/SpeciesLink/Specimen/test.xml.ref | ||
|---|---|---|
| 218 | 218 |
<taxonverbatim> |
| 219 | 219 |
<taxonlabel_id> |
| 220 | 220 |
<taxonlabel> |
| 221 |
<matched_label_id> |
|
| 222 |
<taxonlabel> |
|
| 223 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 224 |
<taxonomicname> |
|
| 225 |
<_merge_prefix> |
|
| 226 |
<prefix> |
|
| 227 |
<_taxon_family_require_std> |
|
| 228 |
<family> |
|
| 229 |
<_alt> |
|
| 230 |
<0>$conceptual_darwin_2003_1_0_Family</0> |
|
| 231 |
<1>$dwc_dwcore_Family</1> |
|
| 232 |
<2>$dwc_terms_family</2> |
|
| 233 |
</_alt> |
|
| 234 |
</family> |
|
| 235 |
</_taxon_family_require_std> |
|
| 236 |
</prefix> |
|
| 237 |
<value> |
|
| 238 |
<_join_words> |
|
| 239 |
<1> |
|
| 240 |
<_alt> |
|
| 241 |
<1> |
|
| 242 |
<_alt> |
|
| 243 |
<0>$conceptual_darwin_2003_1_0_ScientificName</0> |
|
| 244 |
<1>$dwc_dwcore_ScientificName</1> |
|
| 245 |
<2>$dwc_terms_scientificName</2> |
|
| 246 |
</_alt> |
|
| 247 |
</1> |
|
| 248 |
<2> |
|
| 249 |
<_join_words> |
|
| 250 |
<2> |
|
| 251 |
<_alt> |
|
| 252 |
<0>$conceptual_darwin_2003_1_0_Genus</0> |
|
| 253 |
<1>$dwc_dwcore_Genus</1> |
|
| 254 |
<2>$dwc_terms_genus</2> |
|
| 255 |
</_alt> |
|
| 256 |
</2> |
|
| 257 |
<3> |
|
| 258 |
<_alt> |
|
| 259 |
<0>$conceptual_darwin_2003_1_0_Species</0> |
|
| 260 |
<1>$dwc_dwcore_SpecificEpithet</1> |
|
| 261 |
<2>$dwc_terms_specificEpithet</2> |
|
| 262 |
</_alt> |
|
| 263 |
</3> |
|
| 264 |
<4>$conceptual_darwin_2003_1_0_Subspecies</4> |
|
| 265 |
<5> |
|
| 266 |
<_alt> |
|
| 267 |
<0>$dwc_dwcore_InfraspecificEpithet</0> |
|
| 268 |
<1>$dwc_terms_infraspecificEpithet</1> |
|
| 269 |
</_alt> |
|
| 270 |
</5> |
|
| 271 |
</_join_words> |
|
| 272 |
</2> |
|
| 273 |
</_alt> |
|
| 274 |
</1> |
|
| 275 |
<2> |
|
| 276 |
<_alt> |
|
| 277 |
<1>$dwc_terms_scientificNameAuthorship</1> |
|
| 278 |
<2>$conceptual_darwin_2003_1_0_ScientificNameAuthor</2> |
|
| 279 |
<3>$dwc_dwcore_AuthorYearOfScientificName</3> |
|
| 280 |
</_alt> |
|
| 281 |
</2> |
|
| 282 |
</_join_words> |
|
| 283 |
</value> |
|
| 284 |
</_merge_prefix> |
|
| 285 |
</taxonomicname> |
|
| 286 |
</taxonlabel> |
|
| 287 |
</matched_label_id> |
|
| 288 | 221 |
<creationdate> |
| 289 | 222 |
<_alt> |
| 290 | 223 |
<1><_dateRangeStart><value>$dwc_terms_dateIdentified</value></_dateRangeStart></1> |
| ... | ... | |
| 731 | 664 |
</path> |
| 732 | 665 |
</_setDefault> |
| 733 | 666 |
</VegBIEN> |
| 734 |
Inserted 47 new rows into database |
|
| 667 |
Inserted 44 new rows into database |
|
| inputs/bien_web/observation/test.xml.ref | ||
|---|---|---|
| 47 | 47 |
<taxonverbatim> |
| 48 | 48 |
<taxonlabel_id> |
| 49 | 49 |
<taxonlabel> |
| 50 |
<matched_label_id> |
|
| 51 |
<taxonlabel> |
|
| 52 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 53 |
<taxonomicname> |
|
| 54 |
<_merge_prefix> |
|
| 55 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 56 |
<value> |
|
| 57 |
<_alt> |
|
| 58 |
<1>$taxon</1> |
|
| 59 |
<2> |
|
| 60 |
<_join_words> |
|
| 61 |
<1> |
|
| 62 |
<_join_words> |
|
| 63 |
<2>$genus</2> |
|
| 64 |
<3>$species</3> |
|
| 65 |
</_join_words> |
|
| 66 |
</1> |
|
| 67 |
<2>$taxonAuthor</2> |
|
| 68 |
</_join_words> |
|
| 69 |
</2> |
|
| 70 |
</_alt> |
|
| 71 |
</value> |
|
| 72 |
</_merge_prefix> |
|
| 73 |
</taxonomicname> |
|
| 74 |
</taxonlabel> |
|
| 75 |
</matched_label_id> |
|
| 76 | 50 |
<parent_id> |
| 77 | 51 |
<taxonlabel> |
| 78 | 52 |
<parent_id> |
| inputs/bien_web/observation/VegBIEN.csv | ||
|---|---|---|
| 36 | 36 |
isCultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/2", |
| 37 | 37 |
observationID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 38 | 38 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 39 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 40 |
taxon,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1", |
|
| 41 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 42 |
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 43 |
taxonAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
|
| 44 | 39 |
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
| 45 | 40 |
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]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
| 46 | 41 |
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", |
| inputs/NY/Specimen/test.xml.ref | ||
|---|---|---|
| 128 | 128 |
<taxonverbatim> |
| 129 | 129 |
<taxonlabel_id> |
| 130 | 130 |
<taxonlabel> |
| 131 |
<matched_label_id> |
|
| 132 |
<taxonlabel> |
|
| 133 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 134 |
<taxonomicname> |
|
| 135 |
<_merge_prefix> |
|
| 136 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix> |
|
| 137 |
<value> |
|
| 138 |
<_join_words> |
|
| 139 |
<1> |
|
| 140 |
<_alt> |
|
| 141 |
<1>$ScientificName</1> |
|
| 142 |
<2> |
|
| 143 |
<_join_words> |
|
| 144 |
<2>$Genus</2> |
|
| 145 |
<3>$Species</3> |
|
| 146 |
<4>$Subspecies</4> |
|
| 147 |
</_join_words> |
|
| 148 |
</2> |
|
| 149 |
</_alt> |
|
| 150 |
</1> |
|
| 151 |
<2>$ScientificNameAuthor</2> |
|
| 152 |
</_join_words> |
|
| 153 |
</value> |
|
| 154 |
</_merge_prefix> |
|
| 155 |
</taxonomicname> |
|
| 156 |
</taxonlabel> |
|
| 157 |
</matched_label_id> |
|
| 158 | 131 |
<creationdate> |
| 159 | 132 |
<_date> |
| 160 | 133 |
<day> |
| ... | ... | |
| 402 | 375 |
</path> |
| 403 | 376 |
</_setDefault> |
| 404 | 377 |
</VegBIEN> |
| 405 |
Inserted 46 new rows into database |
|
| 378 |
Inserted 43 new rows into database |
|
| inputs/NY/Specimen/VegBIEN.csv | ||
|---|---|---|
| 31 | 31 |
Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| 32 | 32 |
FieldNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",Usage inconsistent with DwC definition |
| 33 | 33 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 34 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family", |
|
| 35 |
ScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1", |
|
| 36 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2", |
|
| 37 |
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
|
| 38 |
Subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4", |
|
| 39 |
ScientificNameAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
|
| 40 | 34 |
DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 41 | 35 |
MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| 42 | 36 |
YearIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| inputs/Madidi/Organism/test.xml.ref | ||
|---|---|---|
| 64 | 64 |
<taxonverbatim> |
| 65 | 65 |
<taxonlabel_id> |
| 66 | 66 |
<taxonlabel> |
| 67 |
<matched_label_id> |
|
| 68 |
<taxonlabel> |
|
| 69 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 70 |
<taxonomicname> |
|
| 71 |
<_merge_prefix> |
|
| 72 |
<prefix><_taxon_family_require_std><family>$Family (revised)</family></_taxon_family_require_std></prefix> |
|
| 73 |
<value> |
|
| 74 |
<_alt> |
|
| 75 |
<1>$Specie+autor</1> |
|
| 76 |
<2> |
|
| 77 |
<_join_words> |
|
| 78 |
<1> |
|
| 79 |
<_alt> |
|
| 80 |
<1>$Species and morphotypes</1> |
|
| 81 |
<2> |
|
| 82 |
<_join_words> |
|
| 83 |
<2>$Genera</2> |
|
| 84 |
<3>$Specific epithet</3> |
|
| 85 |
</_join_words> |
|
| 86 |
</2> |
|
| 87 |
</_alt> |
|
| 88 |
</1> |
|
| 89 |
<2>$Autor (revised)</2> |
|
| 90 |
</_join_words> |
|
| 91 |
</2> |
|
| 92 |
</_alt> |
|
| 93 |
</value> |
|
| 94 |
</_merge_prefix> |
|
| 95 |
</taxonomicname> |
|
| 96 |
</taxonlabel> |
|
| 97 |
</matched_label_id> |
|
| 98 | 67 |
<parent_id> |
| 99 | 68 |
<taxonlabel> |
| 100 | 69 |
<parent_id> |
| ... | ... | |
| 181 | 150 |
<taxonverbatim> |
| 182 | 151 |
<taxonlabel_id> |
| 183 | 152 |
<taxonlabel> |
| 184 |
<matched_label_id> |
|
| 185 |
<taxonlabel> |
|
| 186 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 187 |
<taxonomicname> |
|
| 188 |
<_merge_prefix> |
|
| 189 |
<prefix><_taxon_family_require_std><family>$Field family</family></_taxon_family_require_std></prefix> |
|
| 190 |
<value>$Field name</value> |
|
| 191 |
</_merge_prefix> |
|
| 192 |
</taxonomicname> |
|
| 193 |
</taxonlabel> |
|
| 194 |
</matched_label_id> |
|
| 195 | 153 |
<parent_id> |
| 196 | 154 |
<taxonlabel> |
| 197 | 155 |
<parent_id> |
| ... | ... | |
| 260 | 218 |
</path> |
| 261 | 219 |
</_setDefault> |
| 262 | 220 |
</VegBIEN> |
| 263 |
Inserted 44 new rows into database |
|
| 221 |
Inserted 38 new rows into database |
|
| inputs/SALVIAS-CSV/Organism/test.xml.ref | ||
|---|---|---|
| 184 | 184 |
<taxonverbatim> |
| 185 | 185 |
<taxonlabel_id> |
| 186 | 186 |
<taxonlabel> |
| 187 |
<matched_label_id> |
|
| 188 |
<taxonlabel> |
|
| 189 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 190 |
<taxonomicname> |
|
| 191 |
<_merge_prefix> |
|
| 192 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 193 |
<value> |
|
| 194 |
<_join_words> |
|
| 195 |
<1> |
|
| 196 |
<_join_words> |
|
| 197 |
<2>$genus</2> |
|
| 198 |
<3>$specific_epithet</3> |
|
| 199 |
<5> |
|
| 200 |
<_join_words> |
|
| 201 |
<1> |
|
| 202 |
<_if name="if has infraspecificEpithet"> |
|
| 203 |
<cond>$infra_ep_1</cond> |
|
| 204 |
<then>$infra_rank_1</then> |
|
| 205 |
</_if> |
|
| 206 |
</1> |
|
| 207 |
<2>$infra_ep_1</2> |
|
| 208 |
</_join_words> |
|
| 209 |
</5> |
|
| 210 |
</_join_words> |
|
| 211 |
</1> |
|
| 212 |
<2>$specific_authority</2> |
|
| 213 |
</_join_words> |
|
| 214 |
</value> |
|
| 215 |
</_merge_prefix> |
|
| 216 |
</taxonomicname> |
|
| 217 |
</taxonlabel> |
|
| 218 |
</matched_label_id> |
|
| 219 | 187 |
<parent_id> |
| 220 | 188 |
<taxonlabel> |
| 221 | 189 |
<rank>$infra_rank_1</rank> |
| ... | ... | |
| 305 | 273 |
<taxonverbatim> |
| 306 | 274 |
<taxonlabel_id> |
| 307 | 275 |
<taxonlabel> |
| 308 |
<matched_label_id> |
|
| 309 |
<taxonlabel> |
|
| 310 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 311 |
<taxonomicname> |
|
| 312 |
<_merge_prefix> |
|
| 313 |
<prefix><_taxon_family_require_std><family>$orig_family</family></_taxon_family_require_std></prefix> |
|
| 314 |
<value>$orig_species</value> |
|
| 315 |
</_merge_prefix> |
|
| 316 |
</taxonomicname> |
|
| 317 |
</taxonlabel> |
|
| 318 |
</matched_label_id> |
|
| 319 | 276 |
<parent_id> |
| 320 | 277 |
<taxonlabel> |
| 321 | 278 |
<parent_id> |
| ... | ... | |
| 406 | 363 |
</path> |
| 407 | 364 |
</_setDefault> |
| 408 | 365 |
</VegBIEN> |
| 409 |
Inserted 52 new rows into database |
|
| 366 |
Inserted 45 new rows into database |
|
| inputs/REMIB/Specimen/test.xml.ref | ||
|---|---|---|
| 76 | 76 |
<taxonverbatim> |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: Removed TNRS input taxonlabels meant to cross-link to taxonlabels added by the TNRS import, because TNRS taxondeterminations are now created instead