#!/usr/bin/env python3 import os import sys import json import magic import urllib import hashlib import mimetypes import subprocess import fatcat_openapi_client from fatcat_openapi_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_openapi_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]))