161 Add ontological modules generation

[trojczak]

Signed-off-by: Rafał Trójczak rafal@trojczak.pl

[dasawanaka]

If I took the pizza ontology and used it in the viewer would it generate the modules by itself? Or test it in another way?

[trojczak]

If I took the pizza ontology and used it in the viewer would it generate the modules by itself? Or test it in another way?

Yes, indeed. It should display all loaded ontologies as a flat list of modules. The only requirement is that this ontology should have a defined ontology label.

[mereolog]

I am testing this PR using docker and IDMP set of ontologies (in /docker/runtime/server/ontologies) folder
There seems to be a problem with the tree of ontologies displayed in the left-hand site.

I was not able to find ISO11240-IdentificationAndExchangeOfUnitsOfMeasure ontology although the ontology is loaded.
Also the tree structure seems to include only FIBO domain, modules, and ontologies.

[mereolog]

onto-viewer seems to ignore all files with the ttl extension - it loads only .rdf files.
For example, I was not able to find SubstanceIdentifier resource, although it is defined in iso11238.ttl file

[mereolog]

See my comments above.

[trojczak]

@mereolog Yes, indeed Turtle files are ignored but this was always the case. If we want to support other types of serialization I propose to create a separate issue for that matter.

[mereolog]

@mereolog Yes, indeed Turtle files are ignored but this was always the case. If we want to support other types of serialization I propose to create a separate issue for that matter.

See: #168.

[patrycjamia]

For the GAO ontology, a module is created that contains the ontology and an empty module named "owl".
I checked several ontologies such as urbanOnto, ontoghis, bdotk10k, pizzaOntology and ontologies from https://bioportal.bioontology.org/ontologies.
The pizza and urbanoOnto ontologies do not load. In the others only the owl module is created with nothing in it.

[trojczak]

I am testing this PR using docker and IDMP set of ontologies (in /docker/runtime/server/ontologies) folder There seems to be a problem with the tree of ontologies displayed in the left-hand site. I was not able to find ISO11240-IdentificationAndExchangeOfUnitsOfMeasure ontology although the ontology is loaded. Also the tree structure seems to include only FIBO domain, modules, and ontologies.

With the same setup I have this:

[trojczak]

@patrycjamia Ontologies have to have .rdf or .owl extensions for now. That's why the OntoUrban ontologies do not load. I don't know why the Pizza ontology doesn't load but it doesn't have anything to do with the new generation of modules.

[trojczak]

Details of some ontologies can't be displayed because the IRIs of these ontologies don't end with / which is the OV requirement...

[trojczak]

@mereolog I propose to create a new issue to change the way how ontologies are looked for within the application. For now, the logic is as follows: there is one endpoint for obtaining both ontologies and different types of entities; it is assumed that an ontology has an IRI ending with /. This, obviously, is not correct for many ontologies. I think we should create two separate endpoints: one for ontologies and one for other types of entities.

[mereolog]

Different icons are displayed for "modularized ontologies":

Perhaps this one is for @dasawanaka or @patrycjamia

[mereolog]

There is a difference between the current prod and this PR - here is an example.
https://www.omg.org/spec/LCC/Countries/CountryRepresentation/ displayed in prod:

https://www.omg.org/spec/LCC/Countries/CountryRepresentation/ displayed in PR-166:

First, the LCC ontologies should not be displayed at all because they are imported and not stored in FIBO.
Secondly, an ontology without maturity level should not be assumed to be provisional - we should assume fibo-fnd-utl-av:Informative for them.

[trojczak]

@mereolog, @patrycjamia, @dasawanaka I've updated PR.

[dasawanaka]

When load pizza ontology, viewer generate one module 'pizza', but when i try to click it, it shows info Not found element in ontology with IRI. For pizza doesn't work any graph...

@mereolog, If it is for new issue i will accept pr.

[patrycjamia]

Modules are generated but are empty. When clicked, all the ontology resources should appear. classes etc. Ontology in general is loaded, through 'search' you can search for resources.

[trojczak]

@dasawanaka @patrycjamia Your problems are related to the fact that in the current form the OV can only find an ontology when its IRI ends with /. We already have a task for this: #171