linkml
Module failures when running examples notebook
When running the examples.ipynb notebook, it failed to successfully load the as_json_obj and the yamlmagic would not work correctly. Specifically:
import jsonasobj.as_json_obj ## ERROR: I'm getting error No module named 'jsonasobj.as_json_obj'
and
%%yaml --loader DupCheckYamlLoader yaml
## ERROR: running this cell produces 2 errors:
## 1. Javascript Error: require is not defined
## 2. File "<ipython-input-3-f6f890ca4330>", line 4
## id: http://example.org/sample/example1
^
## SyntaxError: invalid syntax
I order to work around these errors I had to make a number of changes. I am attaching my notebook exapmple-debug.ipynb (in a zip file)
to show how I did this. Comment marked ## ERROR: show where I had issues.
Steps:
- install a venv:
python -m venv .env - activate the venv
- install
requirement.txt - run jupyter lab
- within jupyter lab, open and run
examples.ipynb
This results in the error:
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-2-f82244ba019b> in <module>
2 from types import ModuleType
3 from json import loads, dumps
----> 4 from jsonasobj import JsonObj, as_json_object
5 from rdflib import Graph
6
ImportError: cannot import name 'as_json_object' from 'jsonasobj' (/Users/wdduncan/opt/anaconda3/lib/python3.7/site-packages/jsonasobj/__init__.py)
To fix (locally) I changed import JsonObj, as_json_object to import JsonObj, as_json_obj.
And I had to changes call to as_json_object to as_json_obj
However, this now causes and error with rdflib.graph() because the variable jsonld is a dict:
TypeError: a bytes-like object is required, not 'dict'
To fix this, I used json.dumps() to convert the jsonld dict into a json string:
Another error ....
Cell magic %%yaml --loader DupCheckYamlLoader yaml to work I had to remove the --loader DupCheckYamlLoader yaml
I also get this strange error Javascript Error: require is not defined:
I don't know. Do the errors occur when running the new linkml? I'd have to run the notebook to find out ...
Cataloging errors as I attempt to run examples.ipynb.
Setup before running:
- created a virtual environment:
python -m venv .env - installed both the
requirements.txtand requirements-dev.txtfiles usingpip`.
I get the error: ModuleNotFoundError: No module named 'linkml.dumpers'
dumpers have moved to linkml-runtime. I'd forgotten that we'd turned off the notebooks test case, so apologies for missing this. Will turn it back on (for some reason I can't get it to work in the github actions...) and update and submit the changes.
Thanks for catching this!
no, the notebook needs fixed, and more broadly we need a strategy for notebooks. Either get rid of them or commit to keeping them complete and informative, use papermill + CI to check