Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add data integrity tests #15

Merged
merged 13 commits into from
Oct 25, 2022
+194 −105
Merged

Add data integrity tests #15

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
13 commits
Select commit Hold shift + click to select a range
f31018f
Add data integrity tests
cthoyt Oct 20, 2022
af5dee6
Lint
cthoyt Oct 20, 2022
e29c159
Curate bioportal until passing
cthoyt Oct 20, 2022
7a91e22
Skip merged
cthoyt Oct 20, 2022
6e7ec1b
Update poetry dependencies so curies >0.3.0
caufieldjh Oct 24, 2022
5b4c9f0
Merge branch 'bioportal' into add-guarantees
cthoyt Oct 24, 2022
f872c8c
Update test_integrity.py
cthoyt Oct 25, 2022
3e2e3b0
Update test_integrity.py
cthoyt Oct 25, 2022
d94dc1c
Update tests
cthoyt Oct 25, 2022
bb2b4c3
Update BP maps for namespace integrity
caufieldjh Oct 25, 2022
627da40
Update .gitignore
caufieldjh Oct 25, 2022
dc08bf8
Lil' poetry update to get most recent bioregistry version
caufieldjh Oct 25, 2022
1a57104
Merge remote-tracking branch 'upstream/main' into add-guarantees
cthoyt Oct 25, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 1 addition & 2 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
.idea
.vscode
__pycache__
.pyc
.ipynb_checkpoints/
docs/_build/
tests/output/
Expand All @@ -11,8 +12,6 @@ db/
notebooks/output/*json
notebooks/output/*tsv
notebooks/input/go.db


notebooks/api-key.txt

.template.db
Expand Down
144 changes: 67 additions & 77 deletions poetry.lock
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ importlib-metadata = "^4.12.0"
pytest = "^5.2"
bioregistry = "^0.5.54"
linkml = "^1.3.1"
curies = "^0.2.0"
curies = "^0.3.0"
coverage = "^6.4.4"

[tool.poetry.extras]
Expand Down
9 changes: 9 additions & 0 deletions src/prefixmaps/data/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,12 @@
from pathlib import Path
from typing import Mapping

__all__ = [
"data_path",
"context_paths",
]

data_path = Path(__file__).parent

#: A mapping from contexts to their paths
context_paths: Mapping[str, Path] = {path.stem: path for path in data_path.glob("*.csv")}
Loading