get concept tree to root issue

[syphax-bouazzouni]

In the stageportal going to this URL: http://stageportal.lirmm.fr/ontologies/INRAETHES/?p=classes&conceptid=http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_405ccee4

Don't show the full tree until the concept amygdale (cerveau) instead just stop in the roots, as shown in the screenshot below

It is not a UI issue because we can find the same issue in the API endpoint http://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_405ccee4/tree

[syphax-bouazzouni]

It seems that the issue is the same with the NCBO code.

Path to the issue

1. When trying to get the child "05. BIOLOGY" here https://github.com/ontoportal-lirmm/ontologies_linked_data/blob/master/lib/ontologies_linked_data/models/class.rb#L325 it return an empty array for its children

  self.in(submission).models(single_load).include(ld << {children: [:prefLabel]}).all

2. The SPARQL request that is sent the following

SELECT DISTINCT ?id ?prefLabel ?definition ?synonym ?children 
FROM  <http://data.bioontology.org/ontologies/INRAETHES/submissions/1>
FROM <http://www.w3.org/2004/02/skos/core#Concept> 
WHERE { 
?id a <http://www.w3.org/2004/02/skos/core#Concept> . 
OPTIONAL { 
         ?id ?rewrite0 ?prefLabel .
          FILTER(?rewrite0 = <http://data.bioontology.org/metadata/def/prefLabel> || ?rewrite0 =
          <http://www.w3.org/2004/02/skos/core#prefLabel>)
 } 
OPTIONAL { 
         ?id ?rewrite1 ?definition . 
         FILTER(?rewrite1 = <http://www.w3.org/2000/01/rdf-schema#comment> || ?rewrite1 = 
         <http://www.w3.org/2004/02/skos/core#definition>) 
} 
OPTIONAL { 
         ?id <http://www.w3.org/2004/02/skos/core#altLabel> ?synonym . 
 } 
OPTIONAL { 
        ?children ?rewrite2 ?id . 
       FILTER(?rewrite2 = <http://www.w3.org/2004/02/skos/core#broadMatch> || ?rewrite2 = 
       <http://www.w3.org/2004/02/skos/core#broader>) 
} 
FILTER(?id = <http://opendata.inrae.fr/thesaurusINRAE/c_405ccee4> || ?id = 
<http://opendata.inrae.fr/thesaurusINRAE/d_5>) }

3. This works fine in an external Triple store (Jena) and returns the children, but it does not work for 4store.

[syphax-bouazzouni]

Updating the submission didn't change nothing

[syphax-bouazzouni]

Resolved by ontoportal-lirmm/ontologies_linked_data@843696a

It seems that doing, the following works :

self.in(submission).models(single_load).include({children: [:prefLabel]}).all

But above not :

self.in(submission).models(single_load).include([:prefLabel, :definition, :synonym, {children: [:prefLabel]}]).all

which is not relevant

[syphax-bouazzouni]

Seems to be fixed, 5 months after (with #262)