INCATools / INCATools/ontology-access-kit
JSONDecodeError when initializing OboGraphImplementation
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- Python
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Description
## Overview
I wasn't sure which implementation to use for to load an Obograph, but `OboGraphImplementation` seemed aptly named for this, so I gave it a go. However I got an error when trying to initialize an `OboGraphImplementation` object.
## Code
```py
from oaklib.resource import OntologyResource
from oaklib.implementations.obograph.obograph_implementation import OboGraphImplementation
resource = OntologyResource(slug='path/to/mondo-example.owl', local=True)
oi = OboGraphImplementation(resource)
```
## Error
```
/Users/joeflack4/projects/ontology-access-kit/src/oaklib/converters/../../../tests/input/mondo-example.owl
Traceback (most recent call last):
File "/usr/local/Cellar/python@3.9/3.9.12/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
Process finished with exit code 1
```
## Additional information
It doesn't appear to be a problem with my `mondo-example.owl`, as I was able to successfully load an Obograph using `ProntoImplementation`.
Contributor guide
Research direction
Start with the OboGraphImplementation initialization shown in the issue and trace how the OntologyResource for mondo-example.owl is loaded. Compare that path with ProntoImplementation, using the provided example to reproduce the JSONDecodeError. Done means the intended ontology input is handled correctly or the supported input expectations are made explicit.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100