From 030ff98a90b4f01984bd496751f0a172b7b3eff4 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Fri, 25 Mar 2022 10:37:51 +0100
Subject: [PATCH 1/2] parametrize taxa.plan
---
plans/entities.plan | 9 +++++----
plans/taxa.plan | 18 ++++++++++++++++--
2 files changed, 21 insertions(+), 6 deletions(-)
diff --git a/plans/entities.plan b/plans/entities.plan
index 8523ddb1..b54e298c 100644
--- a/plans/entities.plan
+++ b/plans/entities.plan
@@ -131,12 +131,12 @@
</param-->
<param name="taxid_microorganisms">
- <alias module="taxa.microorganisms.taxids" param="mappingFile"/>
+ <alias module="taxa" param="taxid_microorganisms"/>
<alias module="microorganisms-after-strains.taxids" param="mappingFile"/>
</param>
<param name="taxa+id_full">
- <alias module="taxa.dict" param="dictFile"/>
+ <alias module="taxa" param="taxaDict"/>
</param>
@@ -236,8 +236,9 @@
<setFeatures/>
</set-year>
- <taxa file="plans/taxa.plan"/>
-
+ <taxa file="plans/taxa.plan">
+ <sectionFilter>@name == "title" or @name == "abstract" or @name == "text"</sectionFilter>
+ </taxa>
<!-- Project stopwords -->
<stopwordsprojector class="TabularProjector">
diff --git a/plans/taxa.plan b/plans/taxa.plan
index df5d51b3..a250a16d 100644
--- a/plans/taxa.plan
+++ b/plans/taxa.plan
@@ -1,9 +1,23 @@
<alvisnlp-plan id="taxa">
+ <param name="taxaDict">
+ <alias module="dict" param="dictFile"/>
+ </param>
+
+ <param name="compiledDict">
+ <alias module="dict" param="trieSource"/>
+ </param>
+
+ <param name="sectionFilter">
+ <alias module="dict" param="sectionFilter"/>
+ </param>
+
+ <param name="taxid_microorganisms">
+ <alias module="microorganisms.taxids" param="mappingFile"/>
+ </param>
<dict class="TabularProjector">
- <sectionFilter>@name == "title" or @name == "abstract" or @name == "text"</sectionFilter>
<targetLayerName>taxa</targetLayerName>
- <dictFile>ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt</dictFile>
+ <!--<dictFile>ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt</dictFile>-->
<!--<trieSource>ancillaries/extended-microorganisms-taxonomy/taxa+id_full.trie</trieSource>-->
<matchStartCaseInsensitive/>
<valueFeatures>,taxid,canonical-name,path,pos,rank,species-taxid,species-name</valueFeatures>
--
GitLab
From 8a1b552577ab89a0b42bd5c035cd8c210cf51aca Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Fri, 25 Mar 2022 11:59:32 +0100
Subject: [PATCH 2/2] all plans reference taxa.plan. removed taxa_generic.plan
---
plans/map_microorganisms.plan | 12 ++---
plans/taxa_generic.plan | 85 -----------------------------------
2 files changed, 4 insertions(+), 93 deletions(-)
delete mode 100644 plans/taxa_generic.plan
diff --git a/plans/map_microorganisms.plan b/plans/map_microorganisms.plan
index 06d8a3c4..c4d29456 100644
--- a/plans/map_microorganisms.plan
+++ b/plans/map_microorganisms.plan
@@ -8,19 +8,15 @@
<alias module="print-mapping" param="corpusFile"/>
</param>
- <param name="taxid_microorganisms">
+ <param name="taxid_microorganisms">
<alias module="microorganisms-after-strains.taxids" param="mappingFile"/>
- <alias module="taxa.microorganisms.taxids" param="mappingFile"/>
+ <alias module="taxa" param="taxid_microorganisms"/>
</param>
<param name="taxa+id_full">
- <alias module="taxa.dict" param="dictFile"/>
+ <alias module="taxa.dict" param="taxaDict"/>
</param>
- <param name="NCBI_taxa_ontobiotope">
- <alias module="taxa.dict" param="dictFile"/>
- </param>
-
<read class="TextFileReader">
@@ -28,7 +24,7 @@
<linesLimit>1</linesLimit>
</read>
- <taxa file="plans/taxa_generic.plan"/>
+ <taxa file="plans/taxa.plan"/>
<syntax file="plans/syntax.plan"/>
diff --git a/plans/taxa_generic.plan b/plans/taxa_generic.plan
deleted file mode 100644
index c7b8d74c..00000000
--- a/plans/taxa_generic.plan
+++ /dev/null
@@ -1,85 +0,0 @@
-<alvisnlp-plan id="taxa">
- <dict class="TabularProjector">
- <targetLayerName>taxa</targetLayerName>
- <matchStartCaseInsensitive/>
- <valueFeatures>,taxid,canonical-name,path,pos,rank,species-taxid,species-name</valueFeatures>
- <constantAnnotationFeatures>source=NCBI</constantAnnotationFeatures>
- </dict>
-
- <disambiguate>
- <not-ambiguous class="Action">
- <target>documents.sections.layer:taxa[not span:taxa]</target>
- <action>set:feat:not-ambiguous("yes")</action>
- <setFeatures/>
- </not-ambiguous>
-
- <disambiguate-coreferences class="Action">
- <target>documents.sections.layer:taxa[@not-ambiguous != "yes" and $ as x.(section.nav:sections-before.layer:taxa|before:taxa)[@not-ambiguous == "yes" and @taxid == x.@taxid]]</target>
- <action>set:feat:not-ambiguous("yes")</action>
- <setFeatures/>
- </disambiguate-coreferences>
-
- <disambiguate-coreferences-more-specific class="Action">
- <target>documents.sections.layer:taxa[@not-ambiguous != "yes" and $ as x.(section.nav:sections-before.layer:taxa|before:taxa)[@not-ambiguous == "yes" and x.@path ^= @path]]</target>
- <action>set:feat:not-ambiguous("yes")</action>
- <setFeatures/>
- </disambiguate-coreferences-more-specific>
-
- <disambiguate-coreference-more-general class="Action">
- <target>documents.sections.layer:taxa[@not-ambiguous != "yes" and $ as x.(section.nav:sections-before.layer:taxa|before:taxa)[@not-ambiguous == "yes" and @path ^= x.@path]]</target>
- <action>set:feat:not-ambiguous("yes")</action>
- <setFeatures/>
- </disambiguate-coreference-more-general>
-
- <remove-alternative-to-not-ambiguous class="Action">
- <target>documents.sections.layer:taxa[@not-ambiguous == "yes"].span:taxa[@not-ambiguous != "yes"]</target>
- <action>remove:taxa</action>
- <removeFromLayer/>
- </remove-alternative-to-not-ambiguous>
- </disambiguate>
-
- <!--
- -->
-
- <!-- tag microorganisms -->
- <microorganisms>
- <taxids class="FileMapper">
- <target>documents.sections.layer:taxa</target>
- <form>@taxid</form>
- <targetFeatures>microorganism</targetFeatures>
- </taxids>
-
- <layer class="Action">
- <target>documents.sections.layer:taxa[@microorganism]</target>
- <action>add:microorganism</action>
- <addToLayer/>
- </layer>
-
- <overlaps class="RemoveOverlaps">
- <layerName>microorganism</layerName>
- </overlaps>
- </microorganisms>
-
- <!-- tag bacteria -->
- <bacteria>
- <tag class="Action">
- <target>documents.sections.layer:taxa[@microorganism and @path ^= "/ncbi:1/ncbi:131567/ncbi:2/"]</target>
- <action>set:feat:bacteria("true")|add:bacteria</action>
- <setFeatures/>
- <addToLayer/>
- </tag>
-
- <check class="Assert">
- <target>$</target>
- <assertion>documents.sections.layer:bacteria</assertion>
- <message>"no bacteria, maybe the Eubacteria path is wrong"</message>
- <severe>false</severe>
- </check>
-
- <overlaps class="RemoveOverlaps">
- <layerName>bacteria</layerName>
- </overlaps>
- </bacteria>
-
- <strains file="plans/strains-1.plan"/>
-</alvisnlp-plan>
--
GitLab