Add SemanticArtefactCatalog for the mod-api implementation

[imadbourouche]

Context

We need to implement a model to define the SemanticArtefactCatalog that will represent the catalog and the portal configurations.

Requirements

• This model will be the main model for the / route.
• The attributes should be as defined in the MOD3.0.
• The model should be persisted in the triple store and we should be able to update it
• The attributes should had default values that we define them in a yaml file
• Ability to edit the attributes and save the new values in the triple store (not the computed one)
• Remove the config file that we are using now
• Ability to edit the portal configurations from a dedicated interface in the admin page

References

• MOD3.0 working document: https://docs.google.com/spreadsheets/d/1APdKgSCFKlM8Wxi4WCl_weaiU7x3I-xW6cgg-RS3_zw/edit?gid=1127055612#gid=1127055612
• Mod ttl file: https://github.com/FAIR-IMPACT/MOD/blob/main/mod.ttl

[jonquet]

Maybe also mention the elements discussed related to :

• default values (via YAML)
• replacement of the config file(s)
• automatic population of some of those values
• edition page in the admin page with some fields (the one computed) not editable

[syphax-bouazzouni]

This need to be done before merging, #183 (comment)

[imadbourouche]

This need to be done before merging, #183 (comment)

done here: e7a0e8f

[syphax-bouazzouni]

This need to be done before merging, #183 (comment)

done here: e7a0e8f

@imadbourouche ,the code you added, do the sum of all the metrics, not only the latest submission of each ontology metrics.
And do a PR not a commit.

[imadbourouche]

This need to be done before merging, #183 (comment)

done here: e7a0e8f

@imadbourouche ,the code you added, do the sum of all the metrics, not only the latest submission of each ontology metrics. And do a PR not a commit.

@syphax-bouazzouni , but this will give wrong metrics no ? for example numberOfClasses will be more even the number of classes is the same in all submissions, so if submissions in ontology has number of classes is 30 and we have 3 submissions, if we do the sum of all submissions we will have 90 classes which are in fact just 30 or i'm wrong ?

[syphax-bouazzouni]

This need to be done before merging, #183 (comment)

done here: e7a0e8f

@imadbourouche ,the code you added, do the sum of all the metrics, not only the latest submission of each ontology metrics. And do a PR not a commit.

@syphax-bouazzouni , but this will give wrong metrics no ? for example numberOfClasses will be more even the number of classes is the same in all submissions, so if submissions in ontology has number of classes is 30 and we have 3 submissions, if we do the sum of all submissions we will have 90 classes which are in fact just 30 or i'm wrong ?

@imadbourouche exactly, but your code is doing the inverse,

When you do LinkedData::Models::Metric.where.include(:classes).all,
you will get the full list of all metrics, see example bellow, the ontology AFEO appears more then one time. You need to filter it to have only one record of metric for AFEO in the list,

[...
#<LinkedData::Models::Metric:0x00007f304ac9a690
  @aggregates=nil,
  @classes=37,
  @id=#<RDF::URI:0x852a0 URI:http://data.bioontology.org/ontologies/AFEO/submissions/1/metrics>,
  @loaded_attributes=#<Set: {:classes}>,
  @modified_attributes=#<Set: {}>,
  @persistent=true,
  @previous_values=nil,
  @unmapped=nil>,
 #<LinkedData::Models::Metric:0x00007f304abbc700
  @aggregates=nil,
  @classes=68,
  @id=#<RDF::URI:0x852b4 URI:http://data.bioontology.org/ontologies/AFEO/submissions/11/metrics>,
  @loaded_attributes=#<Set: {:classes}>,
  @modified_attributes=#<Set: {}>,
  @persistent=true,
  @previous_values=nil,
  @unmapped=nil>,
 #<LinkedData::Models::Metric:0x00007f304ad780f8
  @aggregates=nil,
  @classes=145,
  @id=#<RDF::URI:0x852c8 URI:http://data.bioontology.org/ontologies/AFEO/submissions/12/metrics>,
  @loaded_attributes=#<Set: {:classes}>,
  @modified_attributes=#<Set: {}>,
  @persistent=true,
  @previous_values=nil, 
...]