Fix: optimize the way we do our calls to the API

[syphax-bouazzouni]

Context

This repository is responsible for translating our front Ruby code to the corresponding HTTP call to the API, e.g Ontology.all we will be translated to /ontologies and Ontology.get(id) to /ontologies/{id}

Issue

Some important optimization can be easily done, below is a list of the issues that this PR is resolving:

• Fetching top-level links on each request For any request done to the API we do at list 2, e.g Ontology.all

  Getting: https://data.agroportal.lirmm.fr 
  Getting: https://data.agroportal.lirmm.fr/ontologies 

  Instead of just https://data.agroportal.lirmm.fr/ontologies, we do the first call to get the links part of https://data.agroportal.lirmm.fr and to know the endpoint of the resource, for example for Ontology it would be https://data.agroportal.lirmm.fr/ontologies. The fix here was to save the response returned by https://data.agroportal.lirmm.fr the first in a variable so that we do call each time.

In the future, we can remove this call.

• Using .find() instead systematicity .get() This one is the one really demanding in response time, which when we do Ontology.find(id) to go to /ontologies/{id} and return the JSON-LD of an ontology. In reality, was doing /ontologies, fetching all ontologies, and then filtering the result by the id provided.

The fix here is to deprecate .find() method (and remove it in the future), and replace it with .get() which does the direct call Ontology.find(id) => https://data.agroportal.lirmm.fr/ontologies/{id}

• Refresh caching on each update

Each time we do a save or an update we refresh the cache, of the current resource updated/saved, all its brothers and all the ontologies, and all the submissions and all the users.

So for example if update/save an Ontology 1, I refresh its cache (which is good), but also all the ontologies, and all the ontologies a second time, and all the submissions and all the users caches. Resulting in these calls on each update/save

Getting: https://data.agroportal.lirmm.fr/ontologies/WHEATPHENOTYPE (0.2069408730021678s)
Update (Put): https://data.agroportal.lirmm.fr/ontologies/WHEATPHENOTYPE

Getting: https://data.agroportal.lirmm.fr/ontologies/WHEATPHENOTYPE with invalidate cache header (0.2069408730021678s)
Getting: https://data.agroportal.lirmm.fr/ontologies with invalidate cache header  (1.135303320013918s)
Getting: https://data.agroportal.lirmm.fr/submissions with invalidate cache header   (1.0787174180150032s)
Getting: https://data.agroportal.lirmm.fr/users  with invalidate cache header (0.3540415579918772s)

Changes

• use $DEBUG_API_CLIENT instead of $DEBUG for debugging request (https://github.com/ontoportal-lirmm/ontologies_api_ruby_client/pull/14/commits/169afb7c1002f9db2b3276af36d552575cc80ba2)
• add $API_CLIENT_INVALIDATE_CACHE option to disable cache (https://github.com/ontoportal-lirmm/ontologies_api_ruby_client/pull/14/commits/38e4299d8cad25aef71779704d9eff1aabbca1ce)
• save and re-use the top_level_links http response as the result do not change (https://github.com/ontoportal-lirmm/ontologies_api_ruby_client/pull/14/commits/fe41668785affb77cc6d8a133da800819529447f)
• deprecate the find method in favor of get method for better performance (https://github.com/ontoportal-lirmm/ontologies_api_ruby_client/pull/14/commits/ab9048ec0dd2b4b5ef1aef9d40fa0df61282b5ef)
• disable the refresh_cache on each update call (https://github.com/ontoportal-lirmm/ontologies_api_ruby_client/pull/14/commits/cb62d5cb6ff91310ca2f4310e6b50758a22578cd)