INCATools / INCATools/ontology-access-kit

OAK Adapters vs. Invalid URI/CURIEs

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Description

(Possibly related: #499)

It seems that any/many adapter methods are throwing errors/warnings about invalid URI/CURIEs:
```
...
ERROR:root:Skipping statements(subject=MONDO:8000018,predicate=skos:exactMatch,object=,value=None,datatype=None,language=None,); ValueError: is not a valid URI or CURIE
ERROR:root:Skipping statements(subject=MONDO:8000019,predicate=skos:exactMatch,object=,value=None,datatype=None,language=None,); ValueError: is not a valid URI or CURIE
...
WARNING:root:Skipping as it is not a valid CURIE
WARNING:root:Skipping as it is not a valid CURIE
WARNING:root:Skipping as it is not a valid CURIE
...
```

It seems possible the issue is with `phenio.db` itself, but @madanucd informs me this happens with the mondo adapter as well.

The adapter does seem to work regardless, but it is possible that the resulting database adapter is missing information about everything it skipped.

Unsure how to best debug/approach this, thoughts?

Contributor guide

Open the contributing guide

Research direction

Start by reproducing the errors with phenio.db and the mondo adapter, focusing on adapter methods that emit invalid URI/CURIE warnings. Compare skipped statements and properties with the resulting database adapter to determine whether information is missing. Done when the affected identifiers are handled consistently and regression coverage verifies the behavior.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend, databases
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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