Revision 5703
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/.NCBI/higher_taxa/create.sql | ||
|---|---|---|
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SELECT * |
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FROM nodes |
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JOIN names USING (tax_id) |
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WHERE "name class" = 'scientific name' |
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; |
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|
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ALTER TABLE :table ALTER COLUMN tax_id TYPE integer |
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USING tax_id::integer; |
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ALTER TABLE :table ALTER COLUMN "parent tax_id" TYPE integer |
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USING "parent tax_id"::integer; |
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ALTER TABLE :table ADD PRIMARY KEY (tax_id); |
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| inputs/.NCBI/higher_taxa/header.csv | ||
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tax_id,parent tax_id,rank,embl code,4,5,6,7,8,9,name_txt,unique name,name class |
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| inputs/.NCBI/higher_taxa/map.csv | ||
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NCBI,VegCore,Filter,Comments |
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tax_id,taxonID,, |
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parent tax_id,parentTaxonID,, |
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rank,taxonRank,, |
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embl code,*embl code,, |
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4,*4,, |
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5,*5,, |
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6,*6,, |
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7,*7,, |
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8,*8,, |
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9,*9,, |
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name_txt,taxonName,, |
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unique name,*unique name,, |
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name class,*name class,, |
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| inputs/.NCBI/higher_taxa/test.xml.ref | ||
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| 1 |
Put template: |
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<VegBIEN> |
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<_simplifyPath id="-1"> |
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<next>parent_id</next> |
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<path> |
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<location> |
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<locationevent> |
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<taxonoccurrence> |
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<taxondetermination> |
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<taxonverbatim_id> |
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<taxonverbatim> |
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<taxonlabel_id> |
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<taxonlabel> |
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<matched_label_id> |
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<taxonlabel> |
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<creator_id> |
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<party> |
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<creator_id>0</creator_id> |
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<organizationname>TNRS</organizationname> |
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</party> |
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</creator_id> |
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<taxonomicname>$name_txt</taxonomicname> |
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</taxonlabel> |
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</matched_label_id> |
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<_taxonlabel_set_parent_id><parent_id><taxonlabel><sourceaccessioncode>$parent tax_id</sourceaccessioncode></taxonlabel></parent_id></_taxonlabel_set_parent_id> |
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<rank>$rank</rank> |
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<sourceaccessioncode>$tax_id</sourceaccessioncode> |
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<taxonepithet> |
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<_if name="if is higher taxon"> |
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<cond><_is_higher_taxon><rank>$rank</rank></_is_higher_taxon></cond> |
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<then>$name_txt</then> |
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</_if> |
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</taxonepithet> |
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<taxonomicname> |
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<_if name="if is higher taxon"> |
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<cond><_is_higher_taxon><rank>$rank</rank></_is_higher_taxon></cond> |
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<else>$name_txt</else> |
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</_if> |
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</taxonomicname> |
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</taxonlabel> |
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</taxonlabel_id> |
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<verbatimrank>$rank</verbatimrank> |
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</taxonverbatim> |
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</taxonverbatim_id> |
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</taxondetermination> |
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</taxonoccurrence> |
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</locationevent> |
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</location> |
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</path> |
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</_simplifyPath> |
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</VegBIEN> |
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Inserted 11 new rows into database |
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| inputs/.NCBI/higher_taxa/VegBIEN.csv | ||
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| 1 |
NCBI,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments |
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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/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
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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/_alt/2/_join_words/1/_alt/2/_join_words/6", |
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parent tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_taxonlabel_set_parent_id/parent_id/taxonlabel/sourceaccessioncode, |
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parent tax_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/cond/_exists", |
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rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
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rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/taxonverbatim/verbatimrank", |
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rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
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tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
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rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/cond/_is_higher_taxon/rank", |
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name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/then", |
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rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
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rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/3/_if[@name=""if is higher taxon""]/cond/_is_higher_taxon/rank", |
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name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/3/_if[@name=""if is higher taxon""]/else", |
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rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
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4,,** No join mapping for *4 ** |
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5,,** No join mapping for *5 ** |
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6,,** No join mapping for *6 ** |
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7,,** No join mapping for *7 ** |
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8,,** No join mapping for *8 ** |
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9,,** No join mapping for *9 ** |
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embl code,,** No join mapping for *embl code ** |
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name class,,** No join mapping for *name class ** |
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unique name,,** No join mapping for *unique name ** |
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| inputs/.NCBI/higher_taxa/new_terms.csv | ||
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tax_id,taxonID,, |
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parent tax_id,parentTaxonID,, |
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rank,taxonRank,, |
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name_txt,taxonName,, |
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| inputs/.NCBI/higher_taxa/unmapped_terms.csv | ||
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*embl code |
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*4 |
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*5 |
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*6 |
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*7 |
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*8 |
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*9 |
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*unique name |
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*name class |
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| inputs/.NCBI/nodes/VegBIEN.csv | ||
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| 1 |
NCBI,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments |
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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/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
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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/_alt/2/_join_words/1/_alt/2/_join_words/6", |
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parent tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_taxonlabel_set_parent_id/parent_id/taxonlabel/sourceaccessioncode, |
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parent tax_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/cond/_exists", |
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rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
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rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/taxonverbatim/verbatimrank", |
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rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
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tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
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rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/cond/_is_higher_taxon/rank", |
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name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/then", |
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rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
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rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/3/_if[@name=""if is higher taxon""]/cond/_is_higher_taxon/rank", |
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name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/3/_if[@name=""if is higher taxon""]/else", |
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rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
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4,,** No join mapping for *4 ** |
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5,,** No join mapping for *5 ** |
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6,,** No join mapping for *6 ** |
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7,,** No join mapping for *7 ** |
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8,,** No join mapping for *8 ** |
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9,,** No join mapping for *9 ** |
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embl code,,** No join mapping for *embl code ** |
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name class,,** No join mapping for *name class ** |
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unique name,,** No join mapping for *unique name ** |
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| inputs/.NCBI/nodes/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
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<VegBIEN> |
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<_simplifyPath id="-1"> |
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<next>parent_id</next> |
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<path> |
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<location> |
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<locationevent> |
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<taxonoccurrence> |
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<taxondetermination> |
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<taxonverbatim_id> |
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<taxonverbatim> |
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<taxonlabel_id> |
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<taxonlabel> |
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<matched_label_id> |
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<taxonlabel> |
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<creator_id> |
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<party> |
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<creator_id>0</creator_id> |
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<organizationname>TNRS</organizationname> |
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</party> |
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</creator_id> |
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<taxonomicname>$name_txt</taxonomicname> |
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</taxonlabel> |
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</matched_label_id> |
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<_taxonlabel_set_parent_id><parent_id><taxonlabel><sourceaccessioncode>$parent tax_id</sourceaccessioncode></taxonlabel></parent_id></_taxonlabel_set_parent_id> |
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<rank>$rank</rank> |
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<sourceaccessioncode>$tax_id</sourceaccessioncode> |
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<taxonepithet> |
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<_if name="if is higher taxon"> |
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<cond><_is_higher_taxon><rank>$rank</rank></_is_higher_taxon></cond> |
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<then>$name_txt</then> |
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</_if> |
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</taxonepithet> |
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<taxonomicname> |
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<_if name="if is higher taxon"> |
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<cond><_is_higher_taxon><rank>$rank</rank></_is_higher_taxon></cond> |
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<else>$name_txt</else> |
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</_if> |
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</taxonomicname> |
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</taxonlabel> |
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</taxonlabel_id> |
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<verbatimrank>$rank</verbatimrank> |
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</taxonverbatim> |
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</taxonverbatim_id> |
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</taxondetermination> |
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</taxonoccurrence> |
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</locationevent> |
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</location> |
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</path> |
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</_simplifyPath> |
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</VegBIEN> |
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Inserted 11 new rows into database |
|
| inputs/.NCBI/nodes/create.sql | ||
|---|---|---|
| 1 |
SELECT * |
|
| 2 |
FROM nodes |
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JOIN names USING (tax_id) |
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WHERE "name class" = 'scientific name' |
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; |
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|
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ALTER TABLE :table ALTER COLUMN tax_id TYPE integer |
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USING tax_id::integer; |
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ALTER TABLE :table ALTER COLUMN "parent tax_id" TYPE integer |
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USING "parent tax_id"::integer; |
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| 11 |
|
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ALTER TABLE :table ADD PRIMARY KEY (tax_id); |
|
| inputs/.NCBI/nodes/header.csv | ||
|---|---|---|
| 1 |
tax_id,parent tax_id,rank,embl code,4,5,6,7,8,9,name_txt,unique name,name class |
|
| inputs/.NCBI/nodes/map.csv | ||
|---|---|---|
| 1 |
NCBI,VegCore,Filter,Comments |
|
| 2 |
tax_id,taxonID,, |
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| 3 |
parent tax_id,parentTaxonID,, |
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| 4 |
rank,taxonRank,, |
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| 5 |
embl code,*embl code,, |
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| 6 |
4,*4,, |
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5,*5,, |
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| 8 |
6,*6,, |
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| 9 |
7,*7,, |
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| 10 |
8,*8,, |
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| 11 |
9,*9,, |
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| 12 |
name_txt,taxonName,, |
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| 13 |
unique name,*unique name,, |
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| 14 |
name class,*name class,, |
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| inputs/.NCBI/nodes/new_terms.csv | ||
|---|---|---|
| 1 |
tax_id,taxonID,, |
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| 2 |
parent tax_id,parentTaxonID,, |
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| 3 |
rank,taxonRank,, |
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| 4 |
name_txt,taxonName,, |
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| inputs/.NCBI/nodes/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*embl code |
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| 2 |
*4 |
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| 3 |
*5 |
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| 4 |
*6 |
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| 5 |
*7 |
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| 6 |
*8 |
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| 7 |
*9 |
|
| 8 |
*unique name |
|
| 9 |
*name class |
|
Also available in: Unified diff
inputs/.NCBI/: Renamed higher_taxa to nodes because it currently doesn't just contain the higher taxa