Multi Shot Ingestion gives wrong importsFrom, exportsTo, definedBy and appearsIn values for entities

[giraygi]

Describe the bug
Multi Shot Ingestion does not create accurate "numAppearsIn", "linkedEntities", "importsFrom", "exportsTo", "definedBy", "appearsIn", "isDefiningOntology", "hasLocalDefinition" fields since these fields can only be calculated with the whole set of ontologies.

To Reproduce
The problem can be seen in the metadata of all types of entities. (i.e. it can be seen in the ontology main page and /api/v2/ontologies/{ont} call )

Expected behavior
"numAppearsIn", "linkedEntities", "importsFrom", "exportsTo", "definedBy", "appearsIn", "isDefiningOntology", "hasLocalDefinition" links should be updated and accurate in each ingestion.

[giraygi]

Proposed solution: adding the earlier version rdf2json outputs along with the latest rdf2json to the linker module as parameters. Then the logic of merging all rdf2json outputs will be performed in the linker. If the same ontology are present in multiple versions, the most recent one will be given priority.

[giraygi]

afo, aeon, bau ontologies are used as examples

[giraygi]

common.csv

onlyinthefirst.csv

afo, aeon, bau ontologies are used as examples

AEON_0000158 and AEON_0000001 has AEON_0000223 in linkedEntities but linkerfromservice doesn't put it in their linked entities.

The files are extracted from the csv files to be ingested to ols4 after json2neo and the linkedEntities fields of AEON_0000001 entity has been compared between both versions of aeon_classes.csv files.