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#!/usr/bin/env python3
import os
import sys
import json
import magic
import urllib
import hashlib
import mimetypes
import subprocess
import fatcat_client
from fatcat_client import *
from .common import clean
from .crossref import lookup_license_slug
def single_file(prefix, path):
full = prefix + path
size_bytes = os.stat(full).st_size
hashes = [
hashlib.md5(),
hashlib.sha1(),
hashlib.sha256(),
]
with open(full, 'rb') as fp:
while True:
data = fp.read(2**20)
if not data:
break
for h in hashes:
h.update(data)
mime = magic.Magic(mime=True).from_file(full)
if mime == 'application/octet-stream':
# magic apparently isn't that great; try using filename as well
guess = mimetypes.guess_type(full)[0]
if guess:
mime = guess
fsf = FilesetFile(
path=path,
size=size_bytes,
md5=hashes[0].hexdigest(),
sha1=hashes[1].hexdigest(),
sha256=hashes[2].hexdigest(),
extra=dict(mimetype=mime))
return fsf
def make_manifest(base_dir):
manifest = []
for root, dirs, files in os.walk(base_dir):
for f in files:
manifest.append(single_file(root, f))
return manifest
def cdl_dash_release(meta, extra=None):
if not extra:
extra = dict()
assert meta['identifier']['type'] == 'DOI'
doi = meta['identifier']['value'].lower()
assert doi.startswith('10.')
ark_id = None
for extid in meta.get('alternativeIdentifiers', []):
if extid['value'].startswith('ark:'):
ark_id = extid['value']
assert ark_id
license_slug = lookup_license_slug(meta['rights']['uri'])
abstracts = []
for desc in meta['descriptions']:
if desc['type'] == "abstract":
abstracts.append(ReleaseAbstract(
mimetype="text/html",
content=clean(desc['value'])))
#print(abstracts)
if not abstracts:
abstracts = None
contribs = []
for creator in meta['creator']:
contribs.append(ReleaseContrib(
given_name=creator['given'],
surname=creator['family'],
# sorry everybody
raw_name="{} {}".format(creator['given'], creator['family']),
raw_affiliation=creator.get('affiliation'),
role="author", # presumably, for these datasets?
))
r = ReleaseEntity(
ext_ids=ReleaseExtIds(
doi=doi,
ark=ark_id,
),
title=clean(meta['title'], force_xml=True),
publisher=clean(meta['publisher']),
release_year=int(meta['publicationYear']),
release_type="dataset",
license_slug=license_slug,
contribs=contribs,
abstracts=abstracts,
extra=extra,
)
return r
def make_release_fileset(dat_path):
if dat_path.endswith('/'):
dat_path = dat_path[:-1]
dat_discovery = dat_path
extra = dict()
assert len(dat_discovery) == 64
with open(dat_path + "/cdl_dash_metadata.json", 'r') as fp:
meta_dict = json.loads(fp.read())
release = cdl_dash_release(meta_dict)
ark_id = release.extra['ark_id']
dash_version = None
# really crude XML parse-out
with open(dat_path + "/stash-wrapper.xml", 'r') as fp:
for line in fp:
line = line.strip()
if line.startswith("<st:version_number>"):
dash_version = int(line[19:].split('<')[0])
assert dash_version is not None
extra['cdl_dash'] = dict(version=dash_version)
release.extra['cdl_dash'] = dict(version=dash_version)
manifest = make_manifest(dat_path + "/files/")
bundle_url = dict(
url="https://merritt.cdlib.org/u/{}/{}".format(
urllib.parse.quote(ark_id, safe=''),
dash_version),
rel="repo-bundle")
repo_url = dict(
url="https://merritt.cdlib.org/d/{}/{}/".format(
urllib.parse.quote(ark_id, safe=''),
dash_version),
rel="repo")
dat_url = dict(
url="dat://{}/files/".format(dat_discovery),
rel="dweb")
fs = FilesetEntity(
urls=[bundle_url, repo_url, dat_url],
release_ids=None,
manifest=manifest,
extra=extra)
return (release, fs)
def auto_cdl_dash_dat(api, dat_path, release_id=None, editgroup_id=None):
git_rev = subprocess.check_output(
["git", "describe", "--always"]).strip().decode('utf-8')
(release, fileset) = make_release_fileset(dat_path)
if not editgroup_id:
eg = api.create_editgroup(Editgroup(
description="One-off import of dataset(s) from CDL/DASH repository (via IA, Dat dweb pilot project)",
extra=dict(
git_rev=git_rev,
agent="fatcat_tools.auto_cdl_dash_dat")))
editgroup_id = eg.editgroup_id
if not release_id and release.ext_ids.doi:
try:
r = api.lookup_release(doi=release.ext_ids.doi)
release_id = r.ident
except fatcat_client.rest.ApiException:
pass
if not release_id:
edit = api.create_release(eg.editgroup_id, release)
release_id = edit.ident
release = api.get_release(release_id, expand="filesets")
if len(release.filesets):
print("A fileset already exists for release {}".format(release.ident))
return (None, None, None)
fileset.release_ids = [release.ident]
edit = api.create_fileset(eg.editgroup_id, fileset)
fileset = api.get_fileset(edit.ident)
return (editgroup_id, release, fileset)
if __name__=='__main__':
# pass this a discovery key that has been cloned to the local directory
print(make_release_fileset(sys.argv[1]))
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