make rdflib graph from dandiset metadata
This commit is contained in:
parent
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commit
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3 changed files with 84 additions and 7 deletions
63
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63
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[[package]]
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name = "rdflib"
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version = "7.0.0"
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description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
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[package.dependencies]
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isodate = ">=0.6.0,<0.7.0"
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pyparsing = ">=2.1.0,<4"
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[package.extras]
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berkeleydb = ["berkeleydb (>=18.1.0,<19.0.0)"]
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html = ["html5lib (>=1.0,<2.0)"]
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lxml = ["lxml (>=4.3.0,<5.0.0)"]
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networkx = ["networkx (>=2.0.0,<3.0.0)"]
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[[package]]
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name = "referencing"
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version = "0.30.2"
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|
||||
{file = "ruamel.yaml.clib-0.2.8-cp311-cp311-musllinux_1_1_i686.whl", hash = "sha256:46d378daaac94f454b3a0e3d8d78cafd78a026b1d71443f4966c696b48a6d899"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:09b055c05697b38ecacb7ac50bdab2240bfca1a0c4872b0fd309bb07dc9aa3a9"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp311-cp311-win32.whl", hash = "sha256:53a300ed9cea38cf5a2a9b069058137c2ca1ce658a874b79baceb8f892f915a7"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp311-cp311-win_amd64.whl", hash = "sha256:c2a72e9109ea74e511e29032f3b670835f8a59bbdc9ce692c5b4ed91ccf1eedb"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:ebc06178e8821efc9692ea7544aa5644217358490145629914d8020042c24aa1"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp312-cp312-macosx_13_0_arm64.whl", hash = "sha256:edaef1c1200c4b4cb914583150dcaa3bc30e592e907c01117c08b13a07255ec2"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp312-cp312-manylinux2014_aarch64.whl", hash = "sha256:7048c338b6c86627afb27faecf418768acb6331fc24cfa56c93e8c9780f815fa"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:d176b57452ab5b7028ac47e7b3cf644bcfdc8cacfecf7e71759f7f51a59e5c92"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp312-cp312-manylinux_2_24_aarch64.whl", hash = "sha256:1dc67314e7e1086c9fdf2680b7b6c2be1c0d8e3a8279f2e993ca2a7545fecf62"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp312-cp312-musllinux_1_1_i686.whl", hash = "sha256:3213ece08ea033eb159ac52ae052a4899b56ecc124bb80020d9bbceeb50258e9"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:aab7fd643f71d7946f2ee58cc88c9b7bfc97debd71dcc93e03e2d174628e7e2d"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp312-cp312-win32.whl", hash = "sha256:5c365d91c88390c8d0a8545df0b5857172824b1c604e867161e6b3d59a827eaa"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp312-cp312-win_amd64.whl", hash = "sha256:1758ce7d8e1a29d23de54a16ae867abd370f01b5a69e1a3ba75223eaa3ca1a1b"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:a5aa27bad2bb83670b71683aae140a1f52b0857a2deff56ad3f6c13a017a26ed"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:c58ecd827313af6864893e7af0a3bb85fd529f862b6adbefe14643947cfe2942"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-macosx_12_0_arm64.whl", hash = "sha256:f481f16baec5290e45aebdc2a5168ebc6d35189ae6fea7a58787613a25f6e875"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-manylinux2014_aarch64.whl", hash = "sha256:3fcc54cb0c8b811ff66082de1680b4b14cf8a81dce0d4fbf665c2265a81e07a1"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-manylinux_2_24_aarch64.whl", hash = "sha256:77159f5d5b5c14f7c34073862a6b7d34944075d9f93e681638f6d753606c6ce6"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:7f67a1ee819dc4562d444bbafb135832b0b909f81cc90f7aa00260968c9ca1b3"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-musllinux_1_1_i686.whl", hash = "sha256:4ecbf9c3e19f9562c7fdd462e8d18dd902a47ca046a2e64dba80699f0b6c09b7"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-musllinux_1_1_x86_64.whl", hash = "sha256:87ea5ff66d8064301a154b3933ae406b0863402a799b16e4a1d24d9fbbcbe0d3"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-win32.whl", hash = "sha256:75e1ed13e1f9de23c5607fe6bd1aeaae21e523b32d83bb33918245361e9cc51b"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-win_amd64.whl", hash = "sha256:3f215c5daf6a9d7bbed4a0a4f760f3113b10e82ff4c5c44bec20a68c8014f675"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:1b617618914cb00bf5c34d4357c37aa15183fa229b24767259657746c9077615"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-macosx_12_0_arm64.whl", hash = "sha256:a6a9ffd280b71ad062eae53ac1659ad86a17f59a0fdc7699fd9be40525153337"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-manylinux2014_aarch64.whl", hash = "sha256:665f58bfd29b167039f714c6998178d27ccd83984084c286110ef26b230f259f"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-manylinux_2_24_aarch64.whl", hash = "sha256:305889baa4043a09e5b76f8e2a51d4ffba44259f6b4c72dec8ca56207d9c6fe1"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:700e4ebb569e59e16a976857c8798aee258dceac7c7d6b50cab63e080058df91"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-musllinux_1_1_i686.whl", hash = "sha256:e2b4c44b60eadec492926a7270abb100ef9f72798e18743939bdbf037aab8c28"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:e79e5db08739731b0ce4850bed599235d601701d5694c36570a99a0c5ca41a9d"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-win32.whl", hash = "sha256:955eae71ac26c1ab35924203fda6220f84dce57d6d7884f189743e2abe3a9fbe"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-win_amd64.whl", hash = "sha256:56f4252222c067b4ce51ae12cbac231bce32aee1d33fbfc9d17e5b8d6966c312"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:03d1162b6d1df1caa3a4bd27aa51ce17c9afc2046c31b0ad60a0a96ec22f8001"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:bba64af9fa9cebe325a62fa398760f5c7206b215201b0ec825005f1b18b9bccf"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-manylinux2014_aarch64.whl", hash = "sha256:9eb5dee2772b0f704ca2e45b1713e4e5198c18f515b52743576d196348f374d3"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-manylinux_2_24_aarch64.whl", hash = "sha256:a1a45e0bb052edf6a1d3a93baef85319733a888363938e1fc9924cb00c8df24c"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:da09ad1c359a728e112d60116f626cc9f29730ff3e0e7db72b9a2dbc2e4beed5"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:184565012b60405d93838167f425713180b949e9d8dd0bbc7b49f074407c5a8b"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:a75879bacf2c987c003368cf14bed0ffe99e8e85acfa6c0bfffc21a090f16880"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-win32.whl", hash = "sha256:84b554931e932c46f94ab306913ad7e11bba988104c5cff26d90d03f68258cd5"},
|
||||
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-win_amd64.whl", hash = "sha256:25ac8c08322002b06fa1d49d1646181f0b2c72f5cbc15a85e80b4c30a544bb15"},
|
||||
{file = "ruamel.yaml.clib-0.2.8.tar.gz", hash = "sha256:beb2e0404003de9a4cab9753a8805a8fe9320ee6673136ed7f04255fe60bb512"},
|
||||
|
|
@ -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"
|
||||
|
|
|
|||
|
|
@ -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
26
scrape_dandi/summary.py
Normal 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
|
||||
Loading…
Reference in a new issue