poetry update currently leads to the inability to validate uriorcurie values about nmdc-schema

[cmungall]

My diagnosis was wrong, sorry!

[cmungall]

EDIT previously misdiagnosed. I should have just listed to @pkalita-lbl. This is something that was recently introduced in genjsonschema. The fix for now is to temporarily pin to not get the latest linkml

[turbomam]

I just did complete make all test in a fresh clone and a fresh poetry environment. I'm not sure what the difference were between my two environments.

[turbomam]

will a poetry update break my local nmdc-schema ?

mark@NUC:~/nmdc-schema$ poetry update

Updating dependencies
Resolving dependencies... (16.1s)

Writing lock file

Package operations: 1 install, 35 updates, 0 removals

Installing overrides (7.3.1)
Updating bioregistry (0.6.99 -> 0.6.108)
Updating certifi (2022.12.7 -> 2023.5.7)
Updating cruft (2.14.0 -> 2.15.0)
Updating curies (0.4.5 -> 0.5.5)
Updating fastjsonschema (2.16.3 -> 2.17.1)
Updating google-api-python-client (2.86.0 -> 2.87.0)
Updating google-auth (2.17.3 -> 2.18.1)
Updating gspread (5.8.0 -> 5.9.0)
Updating ipykernel (6.22.0 -> 6.23.1)
Updating ipython (8.13.0 -> 8.13.2)
Updating jupyter-server (2.5.0 -> 2.6.0)
Updating linkml (1.5.2 -> 1.5.3)
Updating linkml-runtime (1.5.2 -> 1.5.3)
Updating mkdocs (1.4.2 -> 1.4.3)
Updating mkdocs-material (9.1.8 -> 9.1.14)
Updating nbclassic (0.5.5 -> 1.0.0)
Updating nbclient (0.7.4 -> 0.8.0)
Updating nbconvert (7.3.1 -> 7.4.0)
Updating platformdirs (3.3.0 -> 3.5.1)
Updating prometheus-client (0.16.0 -> 0.17.0)
Updating protobuf (4.22.3 -> 4.23.1)
Updating pydantic (1.10.7 -> 1.10.8)
Updating pymdown-extensions (9.11 -> 10.0.1)
Updating qtconsole (5.4.2 -> 5.4.3)
Updating regex (2023.3.23 -> 2023.5.5)
Updating requests (2.29.0 -> 2.31.0)
Updating setuptools (67.7.2 -> 67.8.0)
Updating sphinx-rtd-theme (1.2.0 -> 1.2.1)
Updating sqlalchemy (2.0.10 -> 2.0.15)
Updating tornado (6.3.1 -> 6.3.2)
Updating typer (0.7.0 -> 0.9.0)
Updating typing-extensions (4.5.0 -> 4.6.2)
Updating urllib3 (1.26.15 -> 1.26.16)
Updating virtualenv (20.22.0 -> 20.23.0)
Updating websocket-client (1.5.1 -> 1.5.2)

[turbomam]

Yes! one of those newer versions breaks the testing process.

@pkalita-lbl always told me to be careful about that.

[turbomam]

git restore poetry.lock
poetry install
make all test

restored the local repo that I thought was beyond repair

[turbomam]

back to the nmdc-schema for a moment:

grep -i -R uriorcurie src/schema/*

src/schema/basic_slots.yaml: range: uriorcurie
src/schema/external_identifiers.yaml: typeof: uriorcurie
src/schema/external_identifiers.yaml: range: uriorcurie

[turbomam]

• Show the generated jsonschema with old and new imports
• Also illustrate with a core validation approach

[cmungall]

the problem is here

project/nmdc_materialized_patterns.yaml:
	$(RUN) gen-linkml \
		--format yaml \
		--materialize-patterns \
		--no-materialize-attributes \
		--output $@ $(SOURCE_SCHEMA_PATH)

this loses the import to linkml:types

[turbomam]

Thanks for looking @cmungall but I don't see what you're talking about.

[turbomam]

Even the following canonical validation fails with the same error as the first post in this issue

poetry run linkml-validate --schema src/schema/nmdc.yaml src/data/valid/Database-nmdc-example.yaml

[pkalita-lbl]

linkml/linkml#1465