make rdflib graph from dandiset metadata

This commit is contained in:
sneakers-the-rat 2023-11-22 19:29:54 -08:00
parent 6be5c5aeb8
commit 30ac5351f1
3 changed files with 84 additions and 7 deletions

63
poetry.lock generated
View file

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@ -2811,4 +2860,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
[metadata]
lock-version = "2.0"
python-versions = "^3.11"
content-hash = "0b2410046c8281d17cfe2c2d93fe3fa2f52aa6213755d5b33c6054ebf59576fe"
content-hash = "9c6f8341a24044d4bb5e61f3e8c1f2dbd5c37e1b53d7573138d36753a49deacc"

View file

@ -15,6 +15,8 @@ scrape-dandi = "scrape_dandi:main"
python = "^3.11"
dandi = "^0.56.2"
matplotlib = "^3.8.0"
dandischema = "^0.8.4"
rdflib = "^7.0.0"
[build-system]

26
scrape_dandi/summary.py Normal file
View file

@ -0,0 +1,26 @@
import json
import yaml
from pathlib import Path
from rdflib import Graph
from tqdm import tqdm
def gather_metadata(path:Path, output:Path = Path('.')):
"""
Convert all ``dandiset.yaml`` files to JSON-LD,
renaming to the dandiset ID, and putting all in output directory
"""
for input in tqdm(path.glob('**/dandiset.yaml')):
with open(input, 'r') as in_yaml:
data = yaml.safe_load(in_yaml)
out_fn = output / (data['identifier'] + '.json')
with open(out_fn, 'w') as ofile:
json.dump(data, ofile)
def build_graph(path:Path = Path('.')) -> Graph:
"""
Load all the JSON-LD into a graph!
"""
g = Graph()
for input in tqdm(path.glob('*.json')):
g.parse(str(input))
return g