From 5600712d326f77e73cb5c887fe6eb4006e008abb Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 17 Feb 2021 12:33:24 +0100
Subject: [PATCH] renamed strain form fields
---
dsmz-match.plan | 24 ++++++++++++------------
1 file changed, 12 insertions(+), 12 deletions(-)
diff --git a/dsmz-match.plan b/dsmz-match.plan
index 0d02a85..9379fae 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"
--
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