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Add data integrity tests #15

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merged 13 commits into from
Oct 25, 2022
Merged

Add data integrity tests #15

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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
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3 changes: 1 addition & 2 deletions .gitignore
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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
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144 changes: 67 additions & 77 deletions poetry.lock
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2 changes: 1 addition & 1 deletion pyproject.toml
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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]
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9 changes: 9 additions & 0 deletions src/prefixmaps/data/__init__.py
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@@ -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")}
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