Update docs and code

lexica/cell/README.md

@@ -0,0 +1,45 @@
+# Cell and Cell Line Lexicon
+
+This directory contains a coherent, merged lexical index for the following resources:
+
+1. Medical Subject Headings (MeSH) (children of `mesh:D002477`)
+2. Experimental Factor Ontology (EFO) (children of `efo:0000324`)
+3. Cellosaurus
+4. Cancer Cell Line Encyclopedia (CCLE)
+5. DepMap
+6. BRENDA Tissue Ontology (BTO)
+7. Cell Ontology (CL)
+8. Cell Line Ontology (CLO)
+
+
+## Using in Python
+
+Use in Python like in the following:
+
+```python
+import biolexica
+import gilda
+
+URL = "https://github.com/biopragmatics/biolexica/raw/main/lexica/cell/terms.tsv.gz"
+
+grounder: gilda.Grounder = biolexica.load_grounder(URL)
+scored_matches = grounder.ground("HeLA")
+```
+
+## Running an API
+
+If you've cloned the repository, you can run:
+
+```shell
+python web.py
+```
+
+If you have `biolexica[web]` installed, you can do:
+
+```python
+from biolexica.web import run_app
+
+URL = "https://github.com/biopragmatics/biolexica/raw/main/lexica/cell/terms.tsv.gz"
+
+run_app(URL)
+```

setup.cfg

@@ -81,6 +81,10 @@ docs =
     sphinx-click
     sphinx_automodapi
     autodoc_pydantic
+web =
+    uvicorn
+    fastapi
+
 
 [options.entry_points]
 console_scripts =

src/biolexica/api.py

@@ -1,8 +1,10 @@
 """API for assembling biomedial lexica."""
 
 import logging
+import tempfile
 from pathlib import Path
 from typing import TYPE_CHECKING, Iterable, List, Literal, Optional, Union
+from urllib.request import urlretrieve
 
 import bioregistry
 import biosynonyms
@@ -21,13 +23,16 @@
     "Input",
     "assemble_terms",
     "iter_terms_by_prefix",
+    "load_grounder",
 ]
 
 logger = logging.getLogger(__name__)
 
 HERE = Path(__file__).parent.resolve()
 Processor = Literal["pyobo", "bioontologies", "biosynonyms", "gilda"]
 
+GrounderHint = Union[gilda.Grounder, str, Path]
+
 
 class Input(BaseModel):
     """An input towards lexicon assembly."""
@@ -43,6 +48,18 @@ class TermsInput(BaseModel):
     terms: List[gilda.Term]
 
 
+def load_grounder(grounder: GrounderHint) -> gilda.Grounder:
+    """Load a gilda grounder, potentially from a remote location."""
+    if isinstance(grounder, str) and grounder.startswith("http"):
+        with tempfile.TemporaryDirectory() as directory:
+            path = Path(directory).joinpath("terms.tsv.gz")
+            urlretrieve(grounder, path)  # noqa:S310
+            return gilda.Grounder(path)
+    if isinstance(grounder, (str, Path)):
+        return gilda.Grounder(grounder)
+    return grounder
+
+
 def assemble_grounder(
     inputs: List[Union[Input, TermsInput]],
     mappings: Optional[List["semra.Mapping"]] = None,

src/biolexica/web.py

@@ -1,14 +1,15 @@
 """A FastAPI wrapper for Gilda."""
 
-import pathlib
-from typing import List, Union
+from typing import List
 
 import fastapi
 import gilda
 from curies import Reference
 from fastapi import FastAPI, Request
 from pydantic import BaseModel
 
+from biolexica.api import GrounderHint, load_grounder
+
 __all__ = [
     "run_app",
     "get_app",
@@ -25,20 +26,17 @@ class Match(BaseModel):
     score: float
 
 
-def run_app(grounder: Union[gilda.Grounder, str, pathlib.Path]):
+def run_app(grounder: GrounderHint):
     """Costruct a FastAPI app from a Gilda grounder and run with :mod:`uvicorn`."""
     import uvicorn
 
-    if isinstance(grounder, (str, pathlib.Path)):
-        grounder = gilda.Grounder(grounder)
-
     uvicorn.run(get_app(grounder))
 
 
-def get_app(grounder: gilda.Grounder) -> FastAPI:
+def get_app(grounder: GrounderHint) -> FastAPI:
     """Construct a FastAPI app from a Gilda grounder."""
     app = FastAPI(title="Biolexica Grounder")
-    app.state = grounder
+    app.state = load_grounder(grounder)
     app.include_router(api_router, prefix="/api")
     return app
 

tox.ini

@@ -111,7 +111,9 @@ commands = pyroma --min=10 .
 description = Run the pyroma tool to check the package friendliness of the project.
 
 [testenv:mypy]
-deps = mypy
+deps =
+    mypy
+    pydantic
 skip_install = true
 commands = mypy --install-types --non-interactive --ignore-missing-imports src/
 description = Run the mypy tool to check static typing on the project.