Exception in thread "main" es.weso.wdsub.UnsupportedShape

[andrawaag]

when running wdsub I ran into the following error message:

Exception in thread "main" es.weso.wdsub.UnsupportedShape
        at es.weso.wdsub.ShEx2WShEx$.convertShape(ShEx2WShEx.scala:46)
        at es.weso.wdsub.ShEx2WShEx$.convertShapeExpr(ShEx2WShEx.scala:24)
        at es.weso.wdsub.ShEx2WShEx$.$anonfun$convertSchema$2(ShEx2WShEx.scala:19)
        at scala.collection.immutable.List.map(List.scala:293)
        at es.weso.wdsub.ShEx2WShEx$.convertSchema(ShEx2WShEx.scala:19)
        at es.weso.wdsub.DumpProcessor$.$anonfun$acquireShEx$2(DumpProcessor.scala:27)
        at cats.effect.IOFiber.flatMapK(IOFiber.scala:1213)
        at cats.effect.IOFiber.succeeded(IOFiber.scala:1013)
        at cats.effect.IOFiber.mapK(IOFiber.scala:1205)
        at cats.effect.IOFiber.succeeded(IOFiber.scala:1012)
        at cats.effect.IOFiber.mapK(IOFiber.scala:1205)
        at cats.effect.IOFiber.succeeded(IOFiber.scala:1012)
        at cats.effect.IOFiber.runLoop(IOFiber.scala:259)
        at cats.effect.IOFiber.afterBlockingSuccessfulR(IOFiber.scala:1162)
        at cats.effect.IOFiber.run(IOFiber.scala:129)
        at cats.effect.unsafe.WorkerThread.run(WorkerThread.scala:359)

I got here by running the following bash script:

# -----------------------------------------------------------------------
# CONFIGURATION VARIABLES
shex_files_path='/home/andra/projects/genewikisub/shex/small_example';
shex_file_names=(do);
results_files_path='/home/andra/projects/genewikisub/small_results';
data_files_path='/home/andra/projects/genewikisub/data';
# -----------------------------------------------------------------------
# DO NOT MODIFY ANYTHING BELOW THIS LINE!!!

echo 'Welcome to WDSub GenWiki!';
echo 'This script will create a subset for each defined shape.';

echo 'Pulling wdsub docker image...';
docker pull wesogroup/wdsub:0.0.23;


for shex_file_name in "${shex_file_names[@]}"
do
    echo "Creating subset for ${shex_files_path}/${shex_file_name}.shex";
    dockerID=`docker run -d -v $data_files_path:/data \
        -v $shex_files_path:/shex \
        -v $results_files_path:/dumps \
        wesogroup/wdsub:0.0.11 dump \
        -o /dumps/result_$shex_file_name.json.gz \
        -s /shex/$shex_file_name.shex \
        --processor WDTK \
        /data/latest-all.json.gz;`
    echo "Subsetting is being created  for ${shex_files_path}/${shex_file_name}.shex";
    echo "Check ${dockerID} for progres" 
done

Running this script leads to the error message.

The shex file used here is:

PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX p: <http://www.wikidata.org/prop/>
PREFIX ps: <http://www.wikidata.org/prop/statement/>
PREFIX obo: <http://purl.obolibrary.org/obo/> 
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX pr: <http://www.wikidata.org/prop/reference/>
PREFIX identorg: <http://identifiers.org/doid/>
PREFIX orphanet: <http://www.orpha.net/ORDO/Orphanet>
PREFIX icd: <https://icd.who.int/>
PREFIX umls: <http://linkedlifedata.com/resource/umls>
PREFIX : <http://www.wikidata.org/entity/>


:do
   {
    p:P279 @<#P279_subclassof>+ ;
    p:P279 . * ;
    p:P2888 @<#P2888_exactmatch>+ ;
    p:P780 @<#P780_symptoms>* ;
  
    # Identifiers
    p:P699       @<#P699_disease_ontology> ;
    p:P492      @<#P492_omim_id>* ;
   p:P1550     @<#P1550_orphanet_id>* ;
   p:P1748     @<#P1748_nci_theraurus_id>* ;
    p:P4229     @<#P4229_icd10-cm>* ;
    p:P5806		@<#P5806-snomed-ct>* ;
} 

## Shapes describing statements in detail.
<#P279_subclassof> {
   ps:P279 [wd:~] ;
       prov:wasDerivedFrom 	@<#disease-ontology-reference> OR 
                            @<#mondo-disease-reference> OR @<#reference> + ;
}
    
<#P492_omim_id> {
   ps:P492 xsd:string ;    
}

<#P699_disease_ontology> {
   ps:P699 xsd:string ;
   prov:wasDerivedFrom @<#disease-ontology-reference> 
                       OR @<#mondo-disease-reference> OR @<#reference>  + ;   
}
      
<#P780_symptoms>  {
   ps:P780 {} ; # TODO create and import EntitySchema for the Symptom Ontology  
}

<#P1550_orphanet_id> {
   ps:P1550 xsd:string ;  
}

<#P1748_nci_theraurus_id> {
   ps:P1748 xsd:string ;
}
            
<#P2888_exactmatch>   {
  ps:P2888 [obo:~ identorg:~ orphanet:~ icd:~ umls:~ ]  ;
}

<#P4229_icd10-cm>  {
  ps:P4229 xsd:string ; 
  prov:wasDerivedFrom 	@<#disease-ontology-reference>
  			OR @<#mondo-disease-reference> OR @<#reference> + ;
}

<#P5270_mondo_id> {
   ps:P5270 xsd:string ;
   prov:wasDerivedFrom @<#disease-ontology-reference> 
                       OR @<#mondo-disease-reference> OR @<#reference> + ;   
}

<#P5806-snomed-ct> {
   ps:P5806 xsd:string ;
   prov:wasDerivedFrom @<#disease-ontology-reference> 
                       OR @<#mondo-disease-reference> OR @<#reference> + ;
}

## References
<#reference> {}

<#disease-ontology-reference> { # reference to a term from the disease ontology term
  pr:P248   [ wd:Q5282129 ] ; # stated in [P248] Disease ontology
  pr:P699   xsd:string ; # Disease Ontology ID
  pr:P813    xsd:dateTime ; # Date of retrieval
}


<#identifiers-org-reference> { # reference to a identifiers.org
  pr:P248   [ wd:Q16335166 ] ; # stated in [P248] identifiers.org [Q16335166] ;
  pr:P854   [<https://registry.identifiers.org/registry/doid>] ;
}

<#mondo-disease-reference> { # reference to a term from the MonDo ontology
  pr:P248   [ wd:Q27468140 wd:Q55345445 ] ; # stated in [P248] Mondo disease ontology [Q27468140]
  pr:P5270  xsd:string ; # Mondo ID
  pr:P813    xsd:dateTime ; # Date of retrieval
}

<#symptom-ontology-reference> { # reference to a term from the Symptom Ontology
  pr:P248   [ wd:Q5282129 ] ; # stated in [P248] Symptom ontology [Q27468140]
  pr:P8656   xsd:string ; # Symptom Ontology ID
  pr:P813    xsd:dateTime ; # Date of retrieval
}