Revision 5513
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/.NCBI/higher_taxa/VegBIEN.csv | ||
|---|---|---|
| 2 | 2 |
parent tax_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has explicit parent""]/cond/_exists", |
| 3 | 3 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has explicit parent""]/else/_if[@name=""if has verbatim name""]/{then/.,else/matched_concept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
|
| 4 | 4 |
name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has explicit parent""]/else/_if[@name=""if has verbatim name""]/{then/.,else/matched_concept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/6",
|
| 5 |
parent tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_taxonconcept_set_parent_id/parent_id/taxonconcept/sourceaccessioncode, |
|
| 5 | 6 |
parent tax_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/taxonconcept/_if[@name=""if has explicit parent""]/cond/_exists", |
| 6 | 7 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/taxonconcept/_if[@name=""if has explicit parent""]/else/rank", |
| 7 | 8 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/taxonconcept/_if[@name=""if has explicit parent""]/else/verbatimrank", |
| 8 |
parent tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/taxonconcept/sourceaccessioncode, |
|
| 9 | 9 |
rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/rank, |
| 10 | 10 |
tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/sourceaccessioncode, |
| 11 | 11 |
name_txt,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonname, |
| inputs/.NCBI/higher_taxa/test.xml.ref | ||
|---|---|---|
| 9 | 9 |
<taxondetermination> |
| 10 | 10 |
<taxonconcept_id> |
| 11 | 11 |
<taxonconcept> |
| 12 |
<parent_id><taxonconcept><sourceaccessioncode>$parent tax_id</sourceaccessioncode></taxonconcept></parent_id>
|
|
| 12 |
<_taxonconcept_set_parent_id><parent_id><taxonconcept><sourceaccessioncode>$parent tax_id</sourceaccessioncode></taxonconcept></parent_id></_taxonconcept_set_parent_id>
|
|
| 13 | 13 |
<rank>$rank</rank> |
| 14 | 14 |
<sourceaccessioncode>$tax_id</sourceaccessioncode> |
| 15 | 15 |
<taxonname>$name_txt</taxonname> |
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 184 | 184 |
acceptedSpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_taxonconcept_set_matched_concept_id/matched_concept_id/taxonconcept/species, |
| 185 | 185 |
acceptedScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_taxonconcept_set_matched_concept_id/matched_concept_id/taxonconcept/taxonomicname, |
| 186 | 186 |
acceptedTaxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_taxonconcept_set_matched_concept_id/matched_concept_id/taxonconcept/verbatimrank, |
| 187 |
parentScientificNameID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_taxonconcept_set_parent_id/parent_id/taxonconcept/sourceaccessioncode, |
|
| 188 |
parentTaxonConceptID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_taxonconcept_set_parent_id/parent_id/taxonconcept/sourceaccessioncode, |
|
| 189 |
parentTaxonID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_taxonconcept_set_parent_id/parent_id/taxonconcept/sourceaccessioncode, |
|
| 187 | 190 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/author, |
| 188 | 191 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/creator_id/_simplifyPath:[next=creator_id]/path/party/givenname/_namePart/first, |
| 189 | 192 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/creator_id/_simplifyPath:[next=creator_id]/path/party/middlename/_namePart/middle, |
| ... | ... | |
| 206 | 209 |
class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=class]/taxonname", |
| 207 | 210 |
phylum,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=phylum]/taxonname", |
| 208 | 211 |
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=kingdom]/taxonname", |
| 209 |
parentScientificNameID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/taxonconcept/sourceaccessioncode, |
|
| 210 |
parentTaxonConceptID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/taxonconcept/sourceaccessioncode, |
|
| 211 |
parentTaxonID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/taxonconcept/sourceaccessioncode, |
|
| 212 | 212 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/parent_id/taxonconcept/taxonname, |
| 213 | 213 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/rank, |
| 214 | 214 |
scientificNameID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/sourceaccessioncode, |
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 184 | 184 |
acceptedSpecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/species, |
| 185 | 185 |
acceptedScientificName,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/taxonomicname, |
| 186 | 186 |
acceptedTaxonRank,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/verbatimrank, |
| 187 |
parentScientificNameID,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/sourceaccessioncode, |
|
| 188 |
parentTaxonConceptID,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/sourceaccessioncode, |
|
| 189 |
parentTaxonID,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/sourceaccessioncode, |
|
| 187 | 190 |
scientificNameAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/author, |
| 188 | 191 |
identifiedBy,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/creator_id/party/givenname, |
| 189 | 192 |
identifiedBy,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/creator_id/party/middlename, |
| ... | ... | |
| 206 | 209 |
class,//taxonconcept/parent_id[rank=class]/taxonname, |
| 207 | 210 |
phylum,//taxonconcept/parent_id[rank=phylum]/taxonname, |
| 208 | 211 |
kingdom,//taxonconcept/parent_id[rank=kingdom]/taxonname, |
| 209 |
parentScientificNameID,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/parent_id/taxonconcept/sourceaccessioncode, |
|
| 210 |
parentTaxonConceptID,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/parent_id/taxonconcept/sourceaccessioncode, |
|
| 211 |
parentTaxonID,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/parent_id/taxonconcept/sourceaccessioncode, |
|
| 212 | 212 |
infraspecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/parent_id/taxonconcept/taxonname, |
| 213 | 213 |
taxonRank,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/rank, |
| 214 | 214 |
scientificNameID,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/sourceaccessioncode, |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: taxonconcept.parent_id when explicit parent provided: Set taxonconcept.parent_id using new _taxonconcept_set_parent_id() after creating the child taxonconcept, so that the parent_id will point to the already-inserted parent taxonconcept instead of creating a new, empty parent taxonconcept. This creates a two-step import, where first the taxonconcepts are imported, and then the parent_ids are matched up. This is necessary for column-based import because all the parent taxonconcepts are imported in a separate iteration from the child taxonconcepts with only their sourceaccessioncode, so this iteration must occur after the child taxonconcept iteration in order to match up with fully-populated taxonconcepts. Row-based import, on the other hand, does not require _taxonconcept_set_parent_id() but does require the taxonconcepts to be provided in dependency order (parents first), which is unfortunately not the case for NCBI.