diff --git a/dsmz-match.plan b/dsmz-match.plan index 0d02a854b87075900269d5602399f47ab7fcd157..9379fae18e5b47a79d83f7ffc63657ce739b5eb1 100644 --- a/dsmz-match.plan +++ b/dsmz-match.plan @@ -11,7 +11,7 @@ <xslTransform>bacdive2alvisnlp.xslt</xslTransform> </read> - <saturate-strain-number> + <saturate-catalog-number> <feature class="Action"> <target>documents.sections:strain_number</target> <action>str:split:',':each(contents)</action> @@ -20,19 +20,19 @@ <section class="Action"> <target>documents.sections:strain_number.nav:features:each</target> - <action>nav:parent.document.new:section:strain-number(str:trim(target.@value))</action> + <action>nav:parent.document.new:section:catalog-number(str:trim(target.@value))</action> <createSections/> </section> - </saturate-strain-number> + </saturate-catalog-number> - <strain-name class="Action"> - <target>documents.sections:strain-number</target> - <action>document.new:section:strain-name(sections:species.contents ^ " " ^ target.contents)</action> + <species-and-number class="Action"> + <target>documents.sections:catalog-number</target> + <action>document.new:section:species-and-number(sections:species.contents ^ " " ^ target.contents)</action> <createSections/> - </strain-name> + </species-and-number> <match class="FileMapper"> - <target>documents.(sections:strain-number | sections:strain-name)</target> + <target>documents.(sections:catalog-number | sections:species-and-number)</target> <form>contents</form> <targetFeatures>,taxid,canonical-name,path,pos,rank</targetFeatures> </match> @@ -67,7 +67,7 @@ <equivalent-strains class="TabularExport"> <outDir>.</outDir> <corpusFile>equivalent-strains.txt</corpusFile> - <lines>documents[sections[@rank == "no rank"]].sections:strain-number[contents ?= " "]</lines> <!-- exclude ym20-087 kondo51 etc --> + <lines>documents[sections[@rank == "no rank"]].sections:catalog-number[contents ?= " "]</lines> <!-- exclude ym20-087 kondo51 etc --> <columns separator=";"> str:replace(str:lower(contents), " ", ":"); document.sections[@rank == "no rank"]{0}.@taxid @@ -77,18 +77,18 @@ <new-strains> <identifier class="Action"> <target>documents[sections[@rank == "species" or @rank == "subspecies"]]</target> - <action>set:feat:new-taxid(str:replace(str:lower(sections:strain-number[contents ^= "DSM"].contents), " ", ":"))</action> + <action>set:feat:new-taxid(str:replace(str:lower(sections:catalog-number[contents ^= "DSM"].contents), " ", ":"))</action> <setFeatures/> </identifier> <export class="TabularExport"> <outDir>.</outDir> <corpusFile>taxa+id_dsmz.txt</corpusFile> - <lines>documents[@new-taxid].(sections:strain-number|sections:strain-name)</lines> + <lines>documents[@new-taxid].(sections:catalog-number | sections:species-and-number)</lines> <columns separator=";"> contents; document.@new-taxid; - document.sections:strain-name[contents ?= "DSM"].contents; + document.sections:species-and-number[contents ?= "DSM"].contents; document.sections[@taxid]{0}.@path ^ "/" ^ document.@new-taxid; document.sections[@taxid]{0}.@pos; "no rank"