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Commit 58460964 authored by Robert Bossy's avatar Robert Bossy
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try to fix everything (defunct method)

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bacdive2alvisnlp.xslt
+ 7
− 0
View file @ 58460964
......@@ -15,7 +15,14 @@
</xsl:template>
<xsl:template match="taxonomy_name/strains/list-item">
<a:section name="subspecies_epithet" xpath-contents="subspecies_epithet"/>
<a:section name="species" xpath-contents="species"/>
<a:section name="genus" xpath-contents="genus"/>
<a:section name="family" xpath-contents="family"/>
<a:section name="ordo" xpath-contents="ordo"/>
<a:section name="class" xpath-contents="class"/>
<a:section name="phylum" xpath-contents="phylum"/>
<a:section name="domain" xpath-contents="domain"/>
<a:section name="full_scientific_name" xpath-contents="normalize-space(full_scientific_name)"/>
<a:section name="designation" xpath-contents="designation"/>
</xsl:template>
......
dsmz-match.plan
+ 258
− 28
View file @ 58460964
......@@ -31,21 +31,153 @@
<createSections/>
</species-and-number>
<match class="FileMapper">
<mark-strains class="Action">
<target>documents.(sections:catalog-number | sections:species-and-number)</target>
<action>set:feat:strain("yes")</action>
<setFeatures/>
</mark-strains>
<mark-candidates class="Action">
<target>documents.(sections[@strain] | sections:species | sections:genus | sections:family | sections:ordo | sections:class | sections:phylum | sections:domain)</target>
<action>set:feat:candidate("yes")</action>
<setFeatures/>
</mark-candidates>
<match class="FileMapper">
<target>documents.sections[@candidate]</target>
<form>contents</form>
<targetFeatures>,taxid,canonical-name,path,pos,rank</targetFeatures>
</match>
<dispatch>
<equivalent class="Action">
<target>documents[(not @dispatch) and sections[@strain and @rank == "no rank"]]</target>
<action>
set:feat:dispatch("equivalent")
| set:feat:taxid(sections[@strain and @rank == "no rank"]{0}.@taxid)
| set:feat:rule(module:id)
</action>
<setFeatures/>
</equivalent>
<separate-subspecies-type-material class="Action">
<target>documents[(not @dispatch) and sections[@strain and @rank == "subspecies"]]</target>
<action>
set:feat:dispatch("new")
| set:feat:taxid(sections[@strain and @rank == "subspecies"]{0}.@taxid)
| set:feat:rule(module:id)
</action>
<setFeatures/>
</separate-subspecies-type-material>
<separate-species-type-material class="Action">
<target>documents[(not @dispatch) and sections[@strain and @rank == "species"]]</target>
<action>
set:feat:dispatch("new")
| set:feat:taxid(sections[@strain and @rank == "species"]{0}.@taxid)
| set:feat:rule(module:id)
</action>
<setFeatures/>
</separate-species-type-material>
<new-strain-for-subspecies class="Action">
<target>documents[(not @dispatch) and sections:species[@rank == "subspecies"]]</target>
<action>
set:feat:dispatch("new")
| set:feat:taxid(sections:species[@rank == "subspecies"].@taxid)
| set:feat:rule(module:id)
</action>
<setFeatures/>
</new-strain-for-subspecies>
<new-strain-for-species class="Action">
<target>documents[(not @dispatch) and sections:species[@rank == "species"]]</target>
<action>
set:feat:dispatch("new")
| set:feat:taxid(sections:species[@rank == "species"].@taxid)
| set:feat:rule(module:id)
</action>
<setFeatures/>
</new-strain-for-species>
<new-strain-for-genus class="Action">
<target>documents[(not @dispatch) and sections:genus[@rank == "genus"]]</target>
<action>
set:feat:dispatch("new-species")
| set:feat:taxid(sections:genus[@rank == "genus"].@taxid)
| set:feat:rule(module:id)
</action>
<setFeatures/>
</new-strain-for-genus>
<new-strain-for-family class="Action">
<target>documents[(not @dispatch) and sections:family[@rank == "family"]]</target>
<action>
set:feat:dispatch("new-species")
| set:feat:taxid(sections:family[@rank == "family"].@taxid)
| set:feat:rule(module:id)
</action>
<setFeatures/>
</new-strain-for-family>
<new-strain-for-ordo class="Action">
<target>documents[(not @dispatch) and sections:ordo[@rank == "order"]]</target>
<action>
set:feat:dispatch("new-species")
| set:feat:taxid(sections:ordo[@rank == "order"].@taxid)
| set:feat:rule(module:id)
</action>
<setFeatures/>
</new-strain-for-ordo>
<new-strain-for-class class="Action">
<target>documents[(not @dispatch) and sections:class[@rank == "class"]]</target>
<action>
set:feat:dispatch("new-species")
| set:feat:taxid(sections:class[@rank == "class"].@taxid)
| set:feat:rule(module:id)
</action>
<setFeatures/>
</new-strain-for-class>
<new-strain-for-phylum class="Action">
<target>documents[(not @dispatch) and sections:phylum[@rank == "phylum"]]</target>
<action>
set:feat:dispatch("new-species")
| set:feat:taxid(sections:phylum[@rank == "phylum"].@taxid)
| set:feat:rule(module:id)
</action>
<setFeatures/>
</new-strain-for-phylum>
<new-strain-for-domain class="Action">
<target>documents[(not @dispatch) and sections:domain[@rank == "superkingdom"]]</target>
<action>
set:feat:dispatch("new-species")
| set:feat:taxid(sections:domain[@rank == "superkingdom"].@taxid)
| set:feat:rule(module:id)
</action>
<setFeatures/>
</new-strain-for-domain>
<no-match class="Action">
<target>documents[not @dispatch]</target>
<action>
set:feat:dispatch("no-match")
| set:feat:taxid("")
| set:feat:rule(module:id)
</action>
<setFeatures/>
</no-match>
</dispatch>
<export>
<name-match class="TabularExport">
<full-report class="TabularExport">
<outDir>.</outDir>
<corpusFile>all.txt</corpusFile>
<lines>documents.sections[@taxid]</lines>
<corpusFile>full-report.txt</corpusFile>
<lines>documents.sections[@candidate]</lines>
<columns>
document.@id,
document.sections:species.contents,
document.sections:full_scientific_name.contents,
@name,
contents,
@taxid,
......@@ -53,47 +185,145 @@
@rank
</columns>
<headers>
"ID",
"SPECIES NAME",
"FULL NAME",
"BACDIVE ID",
"FIELD",
"NAME",
"NCBI TAXID",
"NCBI CANONICAL",
"NCBI RANK"
</headers>
</name-match>
</full-report>
<dispatch-report class="TabularExport">
<outDir>.</outDir>
<corpusFile>dispatch-report.txt</corpusFile>
<lines>documents</lines>
<columns>
@id,
@dispatch,
@taxid,
@rule
</columns>
<headers>
"BACDIVE ID",
"DISPATCH",
"NCBI TAXID",
"RULE"
</headers>
</dispatch-report>
<equivalent-strains class="TabularExport">
<outDir>.</outDir>
<corpusFile>equivalent-strains.txt</corpusFile>
<lines>documents[sections[@rank == "no rank"]].sections:catalog-number[contents ?= " "]</lines> <!-- exclude ym20-087 kondo51 etc -->
<lines>documents</lines>
<columns separator=";">
str:replace(str:lower(contents), " ", ":");
document.sections[@rank == "no rank"]{0}.@taxid
(if @dispatch == "equivalent" then @taxid ^ "\t" else "") ^
str:join:'\t'(sections:catalog-number[contents ?= " "], str:replace(str:lower(contents), " ", ":")) <!-- exclude ym20-087 kondo51 etc -->
</columns>
</equivalent-strains>
<new-strains>
<identifier class="Action">
<target>documents[sections[@rank == "species" or @rank == "subspecies"]]</target>
<action>set:feat:new-taxid(str:replace(str:lower(sections:catalog-number[contents ^= "DSM"].contents), " ", ":"))</action>
<canonical>
<first-dsm class="Action">
<target>documents[@dispatch == "new" or @dispatch == "new-species"].sections:catalog-number[contents ^= "DSM"]{0}</target>
<action>set:feat:canonical("yes")</action>
<setFeatures/>
</first-dsm>
<first-any class="Action">
<target>documents[(@dispatch == "new" or @dispatch == "new-species") and not sections:catalog-number[@canonical]].sections:catalog-number{0}</target>
<action>set:feat:canonical("yes")</action>
<setFeatures/>
</first-any>
<new-taxid class="Action">
<target>documents[@dispatch == "new" or @dispatch == "new-species"].sections:catalog-number[@canonical]</target>
<action>document.set:feat:new-taxid(str:replace(str:lower(target.contents), " ", ":"))</action>
<setFeatures/>
</new-taxid>
<scientific-name class="Action">
<target>documents[@dispatch == "new" or @dispatch == "new-species"].sections:catalog-number[@canonical]</target>
<action>document.sections:species-and-number[contents ?= target.contents]{0}.set:feat:scientific-name("yes")</action>
<setFeatures/>
</scientific-name>
</canonical>
<new-species-id class="Action">
<target>documents[@dispatch == "new-species"]</target>
<action>set:feat:new-species-id("prov:" ^ str:replace(sections:species[contents != "unclassified"].contents, " ", "-"))</action>
<setFeatures/>
</identifier>
</new-species-id>
<export-nodes class="TabularExport">
<outDir>.</outDir>
<corpusFile>dsmz-nodes.dmp</corpusFile>
<lines>documents[@dispatch == "new" or @dispatch == "new-species"]</lines>
<separator trim="false"> | </separator>
<columns>
@new-taxid,
if @dispatch == "new" then @taxid else @new-species-id,
"no rank",
"",
"0",
"1",
"11",
"1",
"0",
"1",
"1",
"0",
""
</columns>
</export-nodes>
<export-species-nodes class="TabularExport">
<outDir>.</outDir>
<corpusFile>dsmz-species-nodes.dmp</corpusFile>
<lines>sort:nsval(documents[@dispatch == "new-species"], @new-species-id ^ "___" ^ @taxid)</lines>
<separator trim="false"> | </separator>
<columns>
@new-species-id,
@taxid,
if sections:subspecies_epithet.contents == "" then "species" else "subspecies",
"",
"0",
"1",
"11",
"1",
"0",
"1",
"1",
"0",
""
</columns>
</export-species-nodes>
<export-names class="TabularExport">
<outDir>.</outDir>
<corpusFile>dsmz-names.dmp</corpusFile>
<lines>documents[@dispatch == "new" or @dispatch == "new-species"].sections[@strain]</lines>
<separator trim="false"> | </separator>
<columns>
document.@new-taxid,
contents,
"",
if @scientific-name then "scientific name" else "equivalent catalog"
</columns>
</export-names>
<export class="TabularExport">
<export-species-names class="TabularExport">
<outDir>.</outDir>
<corpusFile>taxa+id_dsmz.txt</corpusFile>
<lines>documents[@new-taxid].(sections:catalog-number | sections:species-and-number)</lines>
<columns separator=";">
contents;
document.@new-taxid;
document.sections:species-and-number[contents ?= "DSM"].contents;
document.sections[@taxid]{0}.@path ^ "/" ^ document.@new-taxid;
document.sections[@taxid]{0}.@pos;
"no rank"
<corpusFile>dsmz-species-names.dmp</corpusFile>
<lines>documents[@dispatch == "new-species"].sections:species</lines>
<separator trim="false"> | </separator>
<columns>
document.@new-species-id,
contents,
"",
"scientific name"
</columns>
</export>
</export-species-names>
</new-strains>
</export>
</alvisnlp-plan>
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