NCBI,VegCore,Filter,Comments

tax_id,taxonID,,

parent tax_id,parentTaxonID,,

rank,taxonRank,,

embl code,*embl code,,

4,*4,,

5,*5,,

6,*6,,

7,*7,,

8,*8,,

9,*9,,

name_txt,taxonName,,

unique name,*unique name,,

name class,*name class,,

Put template:

<VegBIEN>

    <_simplifyPath id="-1">

        <next>parent_id</next>

        <path>

            <location>

                <locationevent>

                    <taxonoccurrence>

                        <taxondetermination>

                            <taxonverbatim_id>

                                <taxonverbatim>

                                    <taxonlabel_id>

                                        <taxonlabel>

                                            <matched_label_id>

                                                <taxonlabel>

                                                    <creator_id>

                                                        <party>

                                                            <creator_id>0</creator_id>

                                                            <organizationname>TNRS</organizationname>

                                                        </party>

                                                    </creator_id>

                                                    <taxonomicname>$name_txt</taxonomicname>

                                                </taxonlabel>

                                            </matched_label_id>

                                            <_taxonlabel_set_parent_id><parent_id><taxonlabel><sourceaccessioncode>$parent tax_id</sourceaccessioncode></taxonlabel></parent_id></_taxonlabel_set_parent_id>

                                            <rank>$rank</rank>

                                            <sourceaccessioncode>$tax_id</sourceaccessioncode>

                                            <taxonepithet>

                                                <_if name="if is higher taxon">

                                                    <cond><_is_higher_taxon><rank>$rank</rank></_is_higher_taxon></cond>

                                                    <then>$name_txt</then>

                                                </_if>

                                            </taxonepithet>

                                            <taxonomicname>

                                                <_if name="if is higher taxon">

                                                    <cond><_is_higher_taxon><rank>$rank</rank></_is_higher_taxon></cond>

                                                    <else>$name_txt</else>

                                                </_if>

                                            </taxonomicname>

                                        </taxonlabel>

                                    </taxonlabel_id>

                                    <verbatimrank>$rank</verbatimrank>

                                </taxonverbatim>

                            </taxonverbatim_id>

                        </taxondetermination>

                    </taxonoccurrence>

                </locationevent>

            </location>

        </path>

    </_simplifyPath>

</VegBIEN>

Inserted 11 new rows into database

NCBI,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments

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",

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",

parent tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_taxonlabel_set_parent_id/parent_id/taxonlabel/sourceaccessioncode,

parent tax_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/cond/_exists",

rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",

rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/taxonverbatim/verbatimrank",

rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,

tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode,

rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/cond/_is_higher_taxon/rank",

name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if is higher taxon""]/then",

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",

rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/3/_if[@name=""if is higher taxon""]/cond/_is_higher_taxon/rank",

name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/3/_if[@name=""if is higher taxon""]/else",

rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,

4,,** No join mapping for *4 ** 

5,,** No join mapping for *5 ** 

6,,** No join mapping for *6 ** 

7,,** No join mapping for *7 ** 

8,,** No join mapping for *8 ** 

9,,** No join mapping for *9 ** 

embl code,,** No join mapping for *embl code ** 

name class,,** No join mapping for *name class ** 

unique name,,** No join mapping for *unique name ** 

tax_id,taxonID,,

parent tax_id,parentTaxonID,,

rank,taxonRank,,

name_txt,taxonName,,

*embl code

*4

*5

*6

*7

*8

*9

*unique name

*name class

SELECT *

FROM nodes

JOIN names USING (tax_id)

WHERE "name class" = 'scientific name'

;

ALTER TABLE :table ALTER COLUMN tax_id TYPE integer

USING tax_id::integer;

ALTER TABLE :table ALTER COLUMN "parent tax_id" TYPE integer

USING "parent tax_id"::integer;

ALTER TABLE :table ADD PRIMARY KEY (tax_id);

tax_id,parent tax_id,rank,embl code,4,5,6,7,8,9,name_txt,unique name,name class