diff --git a/main-annotation.plan b/main-annotation.plan
index 32a6015f0b20a9c9d0c85c37762429b77e0baf25..8f2ccc5395dd00395788332ec9c05aaec7d931fa 100644
--- a/main-annotation.plan
+++ b/main-annotation.plan
@@ -13,12 +13,12 @@
<!-- Assign every page with corresponding names of each corpora -->
<load-corpus>
- <bsv class="XMLReader">
- <html/>
+ <bsv class="XMLReader">
+ <html/>
<xslTransform>resources/segmentation/html2alvisnlp.xslt</xslTransform>
<source>resources/corpus/test_d2kab</source>
<constantSectionFeatures>corpus=corpus bsv</constantSectionFeatures>
- </bsv>
+ </bsv>
</load-corpus>
<make-xpath>
@@ -75,6 +75,16 @@
<find-themes href="modules/patterns/find-themes.plan"/>
+<!--
+ ///////////////////////////////////////////////////////////////////////////////////////
+ //
+ // V. Visualize the annotations
+ //
+ ///////////////////////////////////////////////////////////////////////////////////////
+ -->
+ <quick-html href="modules/visualize.plan"/>
+
+
</alvisnlp-plan>
diff --git a/modules/patterns/bbch.plan b/modules/patterns/bbch.plan
index 895204b5ad2a36206a3a39771195be9f8dd40b42..7e815822f6892b32106c7c1b1f33ceab5e64551a 100644
--- a/modules/patterns/bbch.plan
+++ b/modules/patterns/bbch.plan
@@ -5,38 +5,29 @@
<!-- On ne peut pas mettre deux actions, sinon ça crée deux annotations -->
- <!-- ?? BBCH ?? -->
- <!--_bbch_ class="PatternMatcher">
- <pattern>
- [ @form =~ "BBCH" ]
- </pattern>
- <actions>
- <createAnnotation layer = "bbch"/>
- </actions>
- <constantAnnotationFeatures>type=?BBCH?</constantAnnotationFeatures>
- </_bbch_-->
-<!-- BBCH00 -->
- <bbch class="PatternMatcher">
+
+<!-- BBCH9 ou BBCH09 BBCH00 -->
+ <BBCH_GLUED class="PatternMatcher">
<pattern>
- [ @form ^= "BBCH" ]
+ [ @form =~ "^BBCH\\d{1,3}$" ]
</pattern>
<actions>
<createAnnotation layer = "bbch"/>
</actions>
- <constantAnnotationFeatures>type=BBCH</constantAnnotationFeatures>
+ <constantAnnotationFeatures>type=BBCH_GLUED</constantAnnotationFeatures>
<!--constantAnnotationFeatures>uri=http://ontology.inrae.fr/ppdo/ontology/bbch_globalScale</constantAnnotationFeatures-->
- </bbch>
+ </BBCH_GLUED>
- <insert-space class="Action">
- <target>documents.sections.layer:bbch[@type == "BBCH"]</target>
- <action>set:feat:canonical-form(str:replace(@form, "BBCH", "BBCH "))</action>
+ <set-canonical class="Action">
+ <target>documents.sections.layer:bbch[@type == "BBCH_GLUED"]</target>
+ <action>set:feat:canonical-form("BBCH " ^ str:replace(@form, "BBCH", ""))</action>
<setFeatures/>
- </insert-space>
+ </set-canonical>
- <!-- BBCH-00 -->
+ <!-- BBCH-00 ou BBCH 00 ou (BBCH 00 -->
<BBCH_DD class="PatternMatcher">
<pattern>
[ @form =^ "BBCH" ]
@@ -53,28 +44,23 @@
<!-- BBCH-00) -->
<BBCH_DD_PAR class="PatternMatcher">
<pattern>
- [ @form =^ "BBCH" ]
+ [ @form == "BBCH" ]
[ @form == "-"]?
- [ @form =~ "[0-9]{2}" and @form =^ ")" ]
+ (num: [ @form =~ "[0-9]{2}\\)"])
</pattern>
<actions>
- <createAnnotation layer="bbch"/>
+ <createAnnotation layer="bbch" features='canonical-form=("BBCH " ^ (group:num =~ "^.."))'/>
<!-- createAnnotation layer="bbch" features='uri=("http://ontology.inrae.fr/ppdo/ontology/bbch_globalScale_secondaryStage_BBCH" ^ str:replace(group:number, ")", ""))'/ -->
</actions>
<constantAnnotationFeatures>type=BBCH-DD-PAR</constantAnnotationFeatures>
</BBCH_DD_PAR>
- <delete-par class="Action">
- <target>documents.sections.layer:bbch[@type == "BBCH-DD-PAR"]</target>
- <action>set:feat:canonical-form(str:replace(@form, ")", " "))</action>
- <setFeatures/>
- </delete-par>
<!-- Stade 00 BBCH -->
<STADE_DD_BBCH class="PatternMatcher">
<pattern>
- [ @form ^= "Stade" ]?
+ [ @lemma == "stade" ]?
(number1:[ @form =~ "[0-9]{2}" ])
[ @form ^= "BBCH" ]
</pattern>
@@ -91,7 +77,7 @@
<pattern>
[ @form ^= "BBCH" ]
[ @form == ":" ]
- [ @form ^= "Stade" ]
+ [ @lemma == "stade" ]
(number2 : [ @form =~ "\\d{2}$" ])
</pattern>
<actions>
@@ -104,20 +90,22 @@
<!-- BBCH 17 Ã 19-->
<!-- BBCH 17 - 19-->
+ <!-- BBCH 17 Ã BBCH 19 -->
<BBCH_RANGE class="PatternMatcher">
<pattern>
[ @form == "BBCH" ]
[ @form == "-"]?
(number3 : [ @form =~ "\\d{2}$" ])
-
[@form == "Ã " or @form == "-"]
+ ([ @form == "BBCH" ]
+ [ @form == "-"]?)?
(number4 : [ @form =~ "\\d{2}$" ])
</pattern>
<actions>
<createAnnotation layer="bbch" features='number=(group:number3 =~ "..$"),canonical-form=("BBCH " ^ (group:number3 =~ "..$"))'/>
<createAnnotation layer="bbch" features='number=(group:number4 =~ "..$"),canonical-form=("BBCH " ^ (group:number4 =~ "..$"))'/>
</actions>
- <constantAnnotationFeatures>type=BBCH_RANGE</constantAnnotationFeatures>
+ <constantAnnotationFeatures>type=BBCH_RANGE,range=True</constantAnnotationFeatures>
</BBCH_RANGE>
@@ -133,7 +121,7 @@
<createAnnotation layer="bbch" features='number=(group:number3bis =~ "^.."),canonical-form=("BBCH " ^ (group:number3bis =~ "^.."))'/>
<createAnnotation layer="bbch" features='number=(group:number3bis =~ "..$"),canonical-form=("BBCH " ^ (group:number3bis =~ "..$"))'/>
</actions>
- <constantAnnotationFeatures>type=BBCH_RANGE</constantAnnotationFeatures>
+ <constantAnnotationFeatures>type=BBCH_RANGE_GLUED,range=True</constantAnnotationFeatures>
</BBCH_RANGE_GLUED>
@@ -204,10 +192,35 @@
<createAnnotation layer="bbch" features='canonical-form=("BBCH " ^ group:number11)'/>
<createAnnotation layer="bbch" features='canonical-form=("BBCH " ^ group:number12)'/>
</actions>
- <constantAnnotationFeatures>type=BBCH_TABLE</constantAnnotationFeatures>
+ <constantAnnotationFeatures>type=BBCH_TABLE_PHYSIO</constantAnnotationFeatures>
</BBCH_TABLE_PHYSIO>
+ <bbch-inverse class="PatternMatcher">
+ <pattern>(num: [ @form =~ "\\d\\d-BBCH"])</pattern>
+ <actions>
+ <createAnnotation layer="bbch" features='canonical-form=("BBCH " ^ group:num =~ "^..")'/>
+ </actions>
+ <constantAnnotationFeatures>type=BBCH_INVERSE</constantAnnotationFeatures>
+ </bbch-inverse>
+
+ <!-- 2-3 feuilles étalées -> BBCH 102 BBCH 103 -->
+ <n-m-feuilles-etalees class="PatternMatcher">
+ <pattern>
+ (num:[@form =~ "^\\d-\\d$"])
+ [@lemma == "feuille"]
+ [@form =~ "étalées?"]
+ </pattern>
+ <actions>
+ <createAnnotation layer="bbch" features='canonical-form=("BBCH 10" ^ group:num =~ "^.")'/>
+ <createAnnotation layer="bbch" features='canonical-form=("BBCH 10" ^ group:num =~ ".$")'/>
+ </actions>
+ <constantAnnotationFeatures>type=N-M-FEUILLES-ETALEES</constantAnnotationFeatures>
+ </n-m-feuilles-etalees>
+
+
+<bbch-context>
+<active>false</active>
<bbch_in_context50 class="PatternMatcher">
<pattern>
@@ -419,5 +432,6 @@
<constantAnnotationFeatures>type=BBCH_in_context500</constantAnnotationFeatures>
</bbch_in_context500>
+</bbch-context>
</alvisnlp-plan>
diff --git a/modules/patterns/find-themes.plan b/modules/patterns/find-themes.plan
index bda31471bd94115fa48c70da368ab488bb270d56..dc2fd01420e2f665bbeb4309b2b05019a35c29ab 100644
--- a/modules/patterns/find-themes.plan
+++ b/modules/patterns/find-themes.plan
@@ -2,6 +2,38 @@
<alvisnlp-plan id="themes">
+ <fcu>
+ <numeric-themes>
+ <most-prominent-words>
+ <active>false</active>
+ <!-- calculate tf-idf score with standard parameters -->
+ <tfidf-score class="KeywordsSelector">
+ <!-- input terms -->
+ <keywords>sections.layer:fcu-baseline</keywords>
+ <keywordForm>@skos-prefLabel</keywordForm>
+ <!-- parameters -->
+ <scoreFunction>tfidf</scoreFunction>
+ <scoreThreshold>-1000</scoreThreshold>
+ <!-- save -->
+ <outFile>output/annotations/fcu-baseline-tfidf.csv</outFile>
+ </tfidf-score>
+
+ <!-- calculate bm25 score with standard parameters -->
+ <bm25-score class="KeywordsSelector">
+ <!-- input terms -->
+ <keywords>sections.layer:fcu-baseline</keywords>
+ <keywordForm>@skos-prefLabel</keywordForm>
+ <documentId>document.@id</documentId>
+ <!-- parameters -->
+ <scoreFunction type="bm25" k1="1.2" b="0.75"/>
+ <scoreThreshold>-1000</scoreThreshold>
+ <!-- save -->
+ <outFile>output/annotations/fcu-baseline-bm25.csv</outFile>
+ </bm25-score>
+ </most-prominent-words>
+ </numeric-themes>
+ </fcu>
+
<patterns>
diff --git a/modules/projectors.plan b/modules/projectors.plan
index 66544a2c8bfbcfadbc17fc4d8b7177d86829e7d5..217df5aff10f9701b455313360869dc74a57b023 100644
--- a/modules/projectors.plan
+++ b/modules/projectors.plan
@@ -14,11 +14,10 @@
<baseline>
<fcu>
- <!-- Project concepts on text -->
- <project class="RDFProjector">
- <!-- project concepts on the lemmas from the corpus -->
+ <!-- project concepts on the text -->
+ <project class="RDFProjector">
<source>resources/thesaurus/fcu/frenchCropUsage_20210817.rdf</source>
- <subject layer="words" feature="lemma"/>
+ <subject layer="words" feature="form"/>
<!-- save only owl:individuals with their iri and french labels-->
<resourceTypeURIs>owl:NamedIndividual</resourceTypeURIs>
<language>fr</language>
@@ -26,81 +25,17 @@
<!-- parameters of mapping -->
<allowJoined>true</allowJoined>
<joinDash>true</joinDash>
+ <ignoreDiacritics/>
<caseInsensitive>true</caseInsensitive>
<!-- place annotations to a layer -->
<targetLayer>fcu-baseline</targetLayer>
- <constantAnnotationFeatures>type=RDFProjector</constantAnnotationFeatures>
- </project>
-
- <filter>
- <!-- filter some of ambiguous words -->
- <ambiguous-words class="Action">
- <target>documents.sections.layer:fcu-baseline[
- @lemma == "orange"
- or @lemma== "marron"
- or @lemma == "fruit"
- or @lemma == "semence"
- or @lemma == "côte"
- or @lemma == "soleil"
- or @lemma == "gel"
- or @lemma == "fleur"]</target>
- <action>remove:fcu-baseline</action>
- <removeFromLayer/>
- </ambiguous-words>
-
- <!-- filter overlapping annotations -->
- <overlaps class="RemoveOverlaps">
- <layer>fcu-baseline</layer>
- <removeEqual/>
- <removeIncluded>true</removeIncluded>
- <removeOverlapping>true</removeOverlapping>
- </overlaps>
- </filter>
-
- <export>
- <annotations href="modules/export.plan">
- <!-- focus on the annotations made by rdf-projector -->
- <outLayer>documents.sections.(layer:fcu-baseline)</outLayer>
- <!-- save to a tabular file-->
- <outFile>fcu-baseline-annotations.csv</outFile>
- </annotations>
-
- <most-prominent-words>
- <!-- calculate tf-idf score with standard parameters -->
- <tfidf-score class="KeywordsSelector">
- <!-- input terms -->
- <keywords>sections.layer:fcu-baseline</keywords>
- <keywordForm>@skos-prefLabel</keywordForm>
- <!-- parameters -->
- <scoreFunction>tfidf</scoreFunction>
- <scoreThreshold>-1000</scoreThreshold>
- <!-- save -->
- <outFile>output/annotations/fcu-baseline-tfidf.csv</outFile>
- </tfidf-score>
+ <constantAnnotationFeatures>type=RDFProjector,projectedOn=form</constantAnnotationFeatures>
+ </project>
- <!-- calculate bm25 score with standard parameters -->
- <bm25-score class="KeywordsSelector">
- <!-- input terms -->
- <keywords>sections.layer:fcu-baseline</keywords>
- <keywordForm>@skos-prefLabel</keywordForm>
- <documentId>document.@id</documentId>
- <!-- parameters -->
- <scoreFunction type="bm25" k1="1.2" b="0.75"/>
- <scoreThreshold>-1000</scoreThreshold>
- <!-- save -->
- <outFile>output/annotations/fcu-baseline-bm25.csv</outFile>
- </bm25-score>
- </most-prominent-words>
- </export>
- </fcu>
-
-
-
- <ppdo>
- <!-- Project concepts on text -->
- <project class="RDFProjector">
+ <!-- Project concepts on lemmatized text -->
+ <project-lemma class="RDFProjector">
<!-- project concepts on the lemmas from the corpus -->
- <source>resources/thesaurus/ppdo/ppdo_20210726.rdf</source>
+ <source>resources/thesaurus/fcu/frenchCropUsage_20210817.rdf</source>
<subject layer="words" feature="lemma"/>
<!-- save only owl:individuals with their iri and french labels-->
<resourceTypeURIs>owl:NamedIndividual</resourceTypeURIs>
@@ -110,15 +45,166 @@
<allowJoined>true</allowJoined>
<joinDash>true</joinDash>
<caseInsensitive>true</caseInsensitive>
+ <ignoreDiacritics/>
<!-- place annotations to a layer -->
- <targetLayer>ppdo-baseline</targetLayer>
- <constantAnnotationFeatures>type=RDFProjector</constantAnnotationFeatures>
- </project>
+ <targetLayer>fcu-baseline</targetLayer>
+ <constantAnnotationFeatures>type=RDFProjector,projectedOn=lemma</constantAnnotationFeatures>
+ </project-lemma>
+ <dedup-double-projection>
+ <!-- Removing included mentions ex betterave if we also have betterave sucrière -->
+ <rm-included class="RemoveOverlaps">
+ <layer>fcu-baseline</layer>
+ <removeEqual>false</removeEqual>
+ <removeIncluded>true</removeIncluded>
+ <removeOverlapping>false</removeOverlapping>
+ </rm-included>
+
+ <!-- Removing equal mentions (same span), except if they have different uris (which can happen for example with jardin
+ which is linked to both zone non agricole and jardin) -->
+ <!-- This is needed because of the double projection of fcu on form and lemma -->
+ <dedup class="Action">
+ <target>documents.sections.sort:nsval(layer:fcu-baseline, start ^ "---" ^ end ^ "---" ^ @uri)</target>
+ <action>set:feat:keep("yes")</action>
+ <setFeatures/>
+ </dedup>
+
+ <remove class="Action">
+ <target>documents.sections.layer:fcu-baseline[@keep != "yes"]</target>
+ <action>delete</action>
+ <deleteElements/>
+ </remove>
+ </dedup-double-projection>
+
+ <!-- Because of the ignoreDiacritics maïs is projected on mais, which we don't wan't -->
+ <mais-filter class="Action">
+ <target>documents.sections.layer:fcu-baseline[ str:lower(@form) == "mais"]</target>
+ <action>remove:fcu-baseline</action>
+ <removeFromLayer/>
+ </mais-filter>
+
+ <!-- same for côte -> http://ontology.inrae.fr/frenchcropusage/Poirees -->
+ <cote-filter class="Action">
+ <target>documents.sections.layer:fcu-baseline[ str:lower(@form) == "côté"]</target>
+ <action>remove:fcu-baseline</action>
+ <removeFromLayer/>
+ </cote-filter>
- <find-patterns>
+
+ <filter>
+ <!-- filter some of ambiguous words -->
+ <!-- annotations in fcu-baseline do not have lemma features, we have to go in the words layer to use this feature -->
+ <!-- previous filter tried to target: orange/marron/fruit/semence/côte/soleil/gel/fleur -->
+ <!-- côte -> peut référer à la bette mais presque jamais utilisé pour ça -->
+ <ambiguous-words class="Action">
+ <target>documents.sections.layer:fcu-baseline[ outside:words[
+ @lemma == "fruit"
+ or @lemma == "semence"
+ or @lemma == "côte"
+ or @lemma == "soleil"
+ or @lemma == "gel"
+ or @lemma == "fleur"]]</target>
+ <action>remove:fcu-baseline</action>
+ <removeFromLayer/>
+ </ambiguous-words>
+ </filter>
+
+ <export-fcu href="modules/export.plan">
+ <!-- focus on the annotations made by rdf-projector -->
+ <outLayer>documents.sections.(layer:fcu-baseline)</outLayer>
+ <!-- save to a tabular file-->
+ <outFile>fcu-baseline-annotations.csv</outFile>
+ </export-fcu>
+
+
+ </fcu>
+
+ <phenological-stages>
+ <ppdo>
+ <project class="RDFProjector">
+ <!-- project concepts on the text -->
+ <!-- updated rdf with no beginning and ending whitespaces in the labels -->
+ <source>resources/thesaurus/ppdo/ppdo_20230127.rdf</source>
+ <subject layer="words" feature="form"/>
+ <!-- save only owl:individuals with their iri and french labels-->
+ <resourceTypeURIs>owl:NamedIndividual</resourceTypeURIs>
+ <!-- <labelURIs>skos:prefLabel</labelURIs> -->
+ <language>fr</language>
+ <uriFeature>uri</uriFeature>
+ <!-- parameters of mapping -->
+ <allowJoined>true</allowJoined>
+ <joinDash>true</joinDash>
+ <caseInsensitive>true</caseInsensitive>
+ <!-- place annotations to a layer -->
+ <targetLayer>ppdo-baseline</targetLayer>
+ <constantAnnotationFeatures>type=RDFProjector, projectedOn=form</constantAnnotationFeatures>
+ </project>
+ <project-lemma class="RDFProjector">
+ <!-- project concepts on the lemmas -->
+ <!-- updated rdf with no beginning and ending whitespaces in the labels -->
+ <source>resources/thesaurus/ppdo/ppdo_20230127.rdf</source>
+ <subject layer="words" feature="lemma"/>
+ <!-- save only owl:individuals with their iri and french labels-->
+ <resourceTypeURIs>owl:NamedIndividual</resourceTypeURIs>
+ <language>fr</language>
+ <uriFeature>uri</uriFeature>
+ <!-- parameters of mapping -->
+ <allowJoined>true</allowJoined>
+ <joinDash>true</joinDash>
+ <caseInsensitive>true</caseInsensitive>
+ <!-- place annotations to a layer -->
+ <targetLayer>ppdo-baseline</targetLayer>
+ <constantAnnotationFeatures>type=RDFProjector,projectedOn=lemma</constantAnnotationFeatures>
+ </project-lemma>
+
+ <dedup-double-projection>
+ <rm-included class="RemoveOverlaps">
+ <layer>ppdo-baseline</layer>
+ <removeEqual>false</removeEqual>
+ <removeIncluded>true</removeIncluded>
+ <removeOverlapping>false</removeOverlapping>
+ </rm-included>
+
+ <!-- Removing equal mentions (same span), except if they have different uris (which can happen for example with levée
+ which is linked to both bbch_generalScale_secondaryStage_BBCH09 andbbch_globalScale_secondaryStage_BBCH009) -->
+ <!-- This is needed because of the double projection of ppdo on form and lemma -->
+ <dedup class="Action">
+ <target>documents.sections.sort:nsval(layer:ppdo-baseline, start ^ "---" ^ end ^ "---" ^ @uri)</target>
+ <action>set:feat:keep("yes")</action>
+ <setFeatures/>
+ </dedup>
+
+ <remove class="Action">
+ <target>documents.sections.layer:ppdo-baseline[@keep != "yes"]</target>
+ <action>delete</action>
+ <deleteElements/>
+ </remove>
+ </dedup-double-projection>
+
+ </ppdo>
+ <pattern-based>
<bbch>
- <patterns href="modules/patterns/bbch.plan"/>
+ <find-patterns href="modules/patterns/bbch.plan"/>
+
+ <rm-included class="RemoveOverlaps">
+ <layer>bbch</layer>
+ <removeEqual>false</removeEqual>
+ <removeIncluded>true</removeIncluded>
+ <removeOverlapping>false</removeOverlapping>
+ </rm-included>
+ <!-- Removing equal mentions (same span), except if they have different canonical forms (@uris aren't available at this stage) -->
+ <find-duplicates class="Action">
+ <target>documents.sections.sort:nsval(layer:bbch, start ^ "---" ^ end ^ "---" ^ @canonical-form)</target>
+ <action>set:feat:keep("yes")</action>
+ <setFeatures/>
+ </find-duplicates>
+
+ <remove class="Action">
+ <target>documents.sections.layer:bbch[@keep != "yes"]</target>
+ <action>delete</action>
+ <deleteElements/>
+ </remove>
+
<export href="modules/export.plan">
<!-- focus on the matches made with patterns-->
<outLayer>documents.sections.(layer:bbch)</outLayer>
@@ -126,22 +212,23 @@
<outFile>ppdo-baseline-bbch.csv</outFile>
</export>
<align class="RDFProjector">
- <!-- create a correspondance between matches and real concepts from ppdo-->
- <source>resources/thesaurus/ppdo/ppdo_20210726.rdf</source>
- <subject layer="bbch" feature="canonical-form"/>
- <targetLayer>ppdo-baseline</targetLayer>
- <!-- information that has to be saved and added to the baseline layer-->
- <resourceTypeURIs>owl:NamedIndividual</resourceTypeURIs>
- <language>fr</language>
- <uriFeature>uri</uriFeature>
- <!-- parameters -->
- <wordStartCaseInsensitive/>
- <allowJoined/>
- <constantAnnotationFeatures>type=PATTERN_BBCH
- </constantAnnotationFeatures>
+ <!-- create a correspondance between matches and real concepts from ppdo-->
+ <source>resources/thesaurus/ppdo/ppdo_20230127.rdf</source>
+ <subject layer="bbch" feature="canonical-form"/>
+ <targetLayer>ppdo-combined</targetLayer>
+ <!-- information that has to be saved and added to the baseline layer-->
+ <resourceTypeURIs>owl:NamedIndividual</resourceTypeURIs>
+ <language>fr</language>
+ <uriFeature>uri</uriFeature>
+ <!-- parameters -->
+ <wordStartCaseInsensitive/>
+ <allowJoined/>
+ <constantAnnotationFeatures>type=PATTERN_BBCH
+ </constantAnnotationFeatures>
</align>
+
+
</bbch>
-
<baggiolini>
<active>false</active>
<patterns href="modules/patterns/baggiolini.plan"/>
@@ -153,7 +240,7 @@
</export>
<align class="RDFProjector">
<!-- create a correspondance between matches and real concepts from ppdo-->
- <source>resources/thesaurus/ppdo/ppdo_20210726.rdf</source>
+ <source>resources/thesaurus/ppdo/ppdo_20230127.rdf</source>
<subject layer="baggiolini" feature="canonical-form"/>
<targetLayer>ppdo-baseline</targetLayer>
<!-- information that has to be saved and added to the baseline layer-->
@@ -175,7 +262,7 @@
</export>
<align class="RDFProjector">
<!-- create a correspondance between matches and real concepts from ppdo-->
- <source>resources/thesaurus/ppdo/ppdo_20210726.rdf</source>
+ <source>resources/thesaurus/ppdo/ppdo_20230127.rdf</source>
<subject layer="eicchorn-lorenz" feature="canonical-form"/>
<targetLayer>ppdo-baseline</targetLayer>
<!-- information that has to be saved and added to the baseline layer-->
@@ -187,24 +274,37 @@
</constantAnnotationFeatures>
</align>
</eicchorn-lorenz>
- </find-patterns>
+ </pattern-based>
+
+ <merging-ppdo-bbch>
+ <merge class="MergeLayers">
+ <sourceLayers>ppdo-baseline,ppdo-combined</sourceLayers>
+ <targetLayer>ppdo-combined</targetLayer>
+ </merge>
+ <dedup class="Action">
+ <target>documents.sections.sort:nsval(layer:ppdo-combined, start ^ "---" ^ end ^ "---" ^ @uri)</target>
+ <action>set:feat:keep("yes")</action>
+ <setFeatures/>
+ </dedup>
+
+ <remove class="Action">
+ <target>documents.sections.layer:ppdo-combined[@keep != "yes"]</target>
+ <action>delete</action>
+ <deleteElements/>
+ </remove>
+ <export href="modules/export.plan">
+ <!-- export both the matches from ppdo and the bbch patterns that have been aligned-->
+ <outLayer>documents.sections.(layer:ppdo-combined)</outLayer>
+ <!-- save to a tabular file-->
+ <outFile>ppdo-baseline-annotations.csv</outFile>
+ </export>
+ </merging-ppdo-bbch>
+
+ </phenological-stages>
+
+
- <!-- filter overlapping annotations form baseline layer -->
- <filter>
- <overlaps class="RemoveOverlaps">
- <layer>ppdo-baseline</layer>
- <removeEqual>false</removeEqual>
- <removeIncluded>false</removeIncluded>
- <removeOverlapping>true</removeOverlapping>
- </overlaps>
- </filter>
- <!-- save ppdo stages to a tabular file -->
- <export href="modules/export.plan">
- <outLayer>documents.sections.(layer:ppdo-baseline)</outLayer>
- <outFile>ppdo-baseline-annotations.csv</outFile>
- </export>
- </ppdo>
<others>
<wine-bioagressors class="TabularProjector">
@@ -233,7 +333,7 @@
<!-- parameters of mapping -->
<valueFeatures>$</valueFeatures>
<allowJoined/>
- <caseInsensitive/>
+ <allUpperCaseInsensitive>true</allUpperCaseInsensitive>
<ignoreDiacritics/>
<skipWhitespace/>
<!-- place annotations to a layer -->
diff --git a/modules/visualize.plan b/modules/visualize.plan
new file mode 100644
index 0000000000000000000000000000000000000000..357ea535bbaf4e8ebdeaa731a14ef153e45f6acc
--- /dev/null
+++ b/modules/visualize.plan
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<alvisnlp-plan id="visualize">
+
+ <!-- Adding a feature by layer so we can target them with quickhtml -->
+ <add-crops-feat class="Action">
+ <target>documents.sections.layer:fcu-baseline</target>
+ <action>set:feat:layer("crops")</action>
+ <setFeatures/>
+ </add-crops-feat>
+ <add-ppdo-feat class="Action">
+ <target>documents.sections.layer:ppdo-baseline</target>
+ <action>set:feat:layer("ppdo")</action>
+ <setFeatures/>
+ </add-ppdo-feat>
+ <add-bbch-pattern-feat class="Action">
+ <target>documents.sections.layer:bbch</target>
+ <action>set:feat:layer("bbch-pattern")</action>
+ <setFeatures/>
+ </add-bbch-pattern-feat>
+
+
+ <html class="QuickHTML">
+ <outDir>html</outDir>
+ <classFeature>layer</classFeature>
+ <layers>fcu-baseline,ppdo-baseline,bbch</layers>
+ </html>
+
+</alvisnlp-plan>
\ No newline at end of file