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License: Apache License 2.0
Additional command inspect
, to inspect the input notebook and attach those info to the file itself, still using nb2rdf. Add those info in a different place to be added to the graph exported initially and insert also the ontology inside this graph
use internals of nb2rdf
it is possible, but quite hard, to make javascript library for fully dynamic exploring
I get this:
"""Error while generating the output graph:
Project version is outdated and a migration is required. Run renku migrate
command to fix the issue.""
and when I migrate, the message does not go away. Could it be made so that in this case auto-reload still works?
through zenodo, olos
add minimal generic python code here to enable jupyter extension
also hover tip should be compatible with the arrow label
plugin can be used to push. but it should be verified
It is pretty deceiving to have a plugin for a renku version of years ago.
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When running the params
command, I get the following error:
"file://~/renku-aqs-test-case/.renku/Mrk 421" does not look like a valid URI, I cannot serialize this as N3/Turtle. Perhaps you wanted to urlencode it?
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Use renku team tools and rdflib tools
not just graph, but also list extracted from graph. to think about
As suggested from the team in UZH
Knowledge Graph Explorer: https://renkulab.io/projects/laura.kinkead/knowledge-graph-dashboard
visNetowrk: https://datastorm-open.github.io/visNetwork/
the library can be used in several places
I suggest to start with 2b and 2a
edit: to be clear 2a and 2b are alternative implementations of 2. 2b is easier (at least for me it's clear how to do, it's mostly python). 2a has a potential to be nicer but it's a bit of a new teritory. But I saw many jupyter lab plugins and the sdk seems simple enough. So we could explore 2a, and if it hard - resort to 2b. and then if we like the use case - put more effort to implement 2a.
if 2a is not too hard - we can do it without 2b.
as suggested in #10 by @vigsterkr
there's a little tool that adds some additional info of a notebook: https://github.com/agoose77/jupyterlab-knowledge-graph
we should also make RTD
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see nbinspect from nb2workflow
From a fresh virtual environment running python 3.10, I installed renku 2.2.0 and then renku_aqs.
After installing the plugin, renku is giving this error that prevents any further use. I have to redo the virtualenv to get rid of the issue.
renku --version
WARNING:nb2workflow.ontology:unable to import odakb.sparql (No module named 'odakb') but proceeding anyway
WARNING:nb2workflow.ontology:unable to import owlready2: No module named 'owlready2'
Traceback (most recent call last):
File "/home/ferrigno/.venv/renkuVE/bin/renku", line 5, in
from renku.ui.cli import cli
File "/home/ferrigno/.venv/renkuVE/lib/python3.10/site-packages/renku/ui/cli/init.py", line 99, in
from renku.ui.cli.dataset import dataset
File "/home/ferrigno/.venv/renkuVE/lib/python3.10/site-packages/renku/ui/cli/dataset.py", line 825, in
@add_provider_options()
File "/home/ferrigno/.venv/renkuVE/lib/python3.10/site-packages/renku/ui/cli/dataset.py", line 808, in add_provider_options
providers = [p for p in ProviderFactory.get_add_providers() if p.get_add_parameters()] # type: ignore
File "/home/ferrigno/.venv/renkuVE/lib/python3.10/site-packages/renku/core/dataset/providers/factory.py", line 49, in get_add_providers
return [p for p in ProviderFactory.get_providers() if issubclass(p, AddProviderInterface)]
File "/home/ferrigno/.venv/renkuVE/lib/python3.10/site-packages/renku/core/dataset/providers/factory.py", line 43, in get_providers
providers = get_supported_dataset_providers()
File "/home/ferrigno/.venv/renkuVE/lib/python3.10/site-packages/renku/core/plugin/dataset_provider.py", line 43, in get_supported_dataset_providers
pm = get_plugin_manager()
File "/home/ferrigno/.venv/renkuVE/lib/python3.10/site-packages/renku/core/plugin/pluginmanager.py", line 41, in get_plugin_manager
pm.load_setuptools_entrypoints("renku")
File "/home/ferrigno/.venv/renkuVE/lib/python3.10/site-packages/pluggy/_manager.py", line 287, in load_setuptools_entrypoints
plugin = ep.load()
File "/usr/lib/python3.10/importlib/metadata/init.py", line 171, in load
module = import_module(match.group('module'))
File "/usr/lib/python3.10/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/home/ferrigno/.venv/renkuVE/lib/python3.10/site-packages/renkuaqs/init.py", line 28, in
import renkuaqs.graph_utils as graph_utils
File "/home/ferrigno/.venv/renkuVE/lib/python3.10/site-packages/renkuaqs/graph_utils.py", line 32, in
from renkuaqs.plugin import AQS
File "/home/ferrigno/.venv/renkuVE/lib/python3.10/site-packages/renkuaqs/plugin.py", line 35, in
from aqsconverters.io import AQS_DIR, COMMON_DIR
ImportError: cannot import name 'AQS_DIR' from 'aqsconverters.io' (/home/ferrigno/.venv/renkuVE/lib/python3.10/site-packages/aqsconverters/io.py)
trying to upgrade aqsconverters did not help
e.g. SkyImage, spectrum
e.g. here https://github.com/oda-hub/renku-graph-vis
astro details can still be in https://github.com/oda-hub/renku-graph-vis just in "example" directory or something, i.e. in a more modular way
also we'll need there a manual how to use and extend for new grphs
also collapsible view of the ttl in the interface
return _bootstrap._gcd_import(name[level:], package, level)
File "/home/savchenk/miniconda-recent/lib/python3.9/site-packages/renkuaqs/plugin.py", line 34, in <module>
from renku.core.management.command_builder import Command, inject
ModuleNotFoundError: No module named 'renku.core.management.command_builder'
try https://pypi.org/project/sqlparse/ to parse adql
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