Revision 5832
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/.NCBI/nodes/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
NCBI,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists", |
|
| 2 | 3 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
| 3 | 4 |
name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/6", |
| 4 | 5 |
parent tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_taxonlabel_set_parent_id/parent_id/taxonlabel/sourceaccessioncode, |
| inputs/.NCBI/nodes/test.xml.ref | ||
|---|---|---|
| 11 | 11 |
<taxonverbatim> |
| 12 | 12 |
<taxonlabel_id> |
| 13 | 13 |
<taxonlabel> |
| 14 |
<matched_label_id> |
|
| 15 |
<taxonlabel> |
|
| 16 |
<creator_id> |
|
| 17 |
<party> |
|
| 18 |
<creator_id>0</creator_id> |
|
| 19 |
<organizationname>TNRS</organizationname> |
|
| 20 |
</party> |
|
| 21 |
</creator_id> |
|
| 22 |
<taxonomicname>$name_txt</taxonomicname> |
|
| 23 |
</taxonlabel> |
|
| 24 |
</matched_label_id> |
|
| 25 | 14 |
<_taxonlabel_set_parent_id><parent_id><taxonlabel><sourceaccessioncode>$parent tax_id</sourceaccessioncode></taxonlabel></parent_id></_taxonlabel_set_parent_id> |
| 26 | 15 |
<rank>$rank</rank> |
| 27 | 16 |
<sourceaccessioncode>$tax_id</sourceaccessioncode> |
| ... | ... | |
| 54 | 43 |
</path> |
| 55 | 44 |
</_simplifyPath> |
| 56 | 45 |
</VegBIEN> |
| 57 |
Inserted 8 new rows into database |
|
| 46 |
Inserted 5 new rows into database |
|
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 129 | 129 |
individualID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else", |
| 130 | 130 |
occurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 131 | 131 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 132 |
taxonName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists", |
|
| 132 | 133 |
verbatimScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists", |
| 133 | 134 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family", |
| 134 | 135 |
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_join_words/2/_alt/1", |
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 129 | 129 |
individualID,"//taxonoccurrence/sourceaccessioncode/_if[@name=""if organism in AggregateOccurrence""]/else", |
| 130 | 130 |
occurrenceID,//taxonoccurrence/sourceaccessioncode, |
| 131 | 131 |
identifiedBy,//taxonoccurrence/taxondetermination[]/*_id/party/fullname, |
| 132 |
taxonName,"//*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists", |
|
| 132 | 133 |
verbatimScientificName,"//*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists", |
| 133 | 134 |
family,"//*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel/taxonomicname", |
| 134 | 135 |
scientificName,"//*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel/taxonomicname", |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: Don't create matched taxonlabel if taxonName was provided. This fixes a bug where an NCBI node was incorrectly pointing to a TNRS name, when the reference should only be the other way around. This may also fix the TNRS slowdown, if it was caused by circular matched_label_id references.