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from typing import Any, Dict, List, Optional
import fatcat_openapi_client
from fatcat_openapi_client import DefaultApi, FileEntity
from fatcat_tools.normal import clean_doi
from .common import SANE_MAX_RELEASES, SANE_MAX_URLS, EntityImporter, make_rel_url
class MatchedImporter(EntityImporter):
"""
Importer for "file to crossref DOI" matches.
These matches are currently generated by Internet Archive hadoop jobs
written in scala (part of the 'sandcrawler' repo/project), but could be
generated by other parties as well.
Input format is JSON with keys:
- dois (list)
- sha1 (hex)
- md5 (hex)
- sha256 (hex)
- size (int)
- cdx (list of objects)
- dt (optional; if included creates wayback link)
- url
- mimetype
- urls (list of strings... or objects?)
Future handlings/extensions:
- core_id, wikidata_id, pmcid, pmid: not as lists
"""
def __init__(self, api: DefaultApi, **kwargs) -> None:
eg_desc = (
kwargs.pop("editgroup_description", None)
or "Import of large-scale file-to-release match results. Source of metadata varies."
)
eg_extra = kwargs.pop("editgroup_extra", dict())
eg_extra["agent"] = eg_extra.get("agent", "fatcat_tools.MatchedImporter")
super().__init__(api, editgroup_description=eg_desc, editgroup_extra=eg_extra, **kwargs)
self.default_link_rel = kwargs.get("default_link_rel", "web")
self.default_mimetype = kwargs.get("default_mimetype", None)
def want(self, raw_record: Any) -> bool:
return True
def parse_record(self, obj: Dict[str, Any]) -> Optional[FileEntity]:
dois = [d.lower() for d in obj.get("dois", [])]
# lookup dois
re_list = set()
for doi in dois:
doi = clean_doi(doi)
if not doi:
self.counts["skip-bad-doi"] += 1
return None
try:
re = self.api.lookup_release(doi=doi)
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
re = None
if re is None:
# print("DOI not found: {}".format(doi))
pass
else:
re_list.add(re.ident)
# look up other external ids
for extid_type in (
"arxiv",
"pmid",
"pmcid",
"jstor",
"wikidata_qid",
"core",
"isbn13",
"ark",
):
extid = obj.get(extid_type)
if extid:
try:
re = self.api.lookup_release(**{extid_type: extid})
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
re = None
if re is None:
pass
else:
re_list.add(re.ident)
release_ids = list(re_list)
if len(release_ids) == 0:
self.counts["skip-no-releases"] += 1
return None
if len(release_ids) > SANE_MAX_RELEASES:
self.counts["skip-too-many-releases"] += 1
return None
# parse URLs and CDX
urls_set = set()
for url in obj.get("urls", []):
url = make_rel_url(url, default_link_rel=self.default_link_rel)
if url is not None:
urls_set.add(url)
for cdx in obj.get("cdx", []):
original = cdx["url"]
if cdx.get("dt"):
wayback = "https://web.archive.org/web/{}/{}".format(cdx["dt"], original)
urls_set.add(("webarchive", wayback))
url = make_rel_url(original, default_link_rel=self.default_link_rel)
if url is not None:
urls_set.add(url)
urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls_set]
if len(urls) == 0:
self.counts["skip-no-urls"] += 1
return None
if len(urls) > SANE_MAX_URLS:
self.counts["skip-too-many-urls"] += 1
return None
size = obj.get("size")
if size:
size = int(size)
mimetype = obj.get("mimetype", self.default_mimetype)
if not mimetype and urls:
if urls[0].url.endswith(".pdf"):
mimetype = "application/pdf"
fe = FileEntity(
md5=obj.get("md5"),
sha1=obj["sha1"],
sha256=obj.get("sha256"),
size=size,
mimetype=mimetype,
release_ids=release_ids,
urls=urls,
)
return fe
def try_update(self, fe: FileEntity) -> bool:
# lookup sha1, or create new entity
existing = None
try:
existing = self.api.lookup_file(sha1=fe.sha1)
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
if not existing:
return True
combined_release_ids = list(set(fe.release_ids + existing.release_ids))
if set(combined_release_ids) == set(existing.release_ids) and len(existing.urls) > 0:
# no new release matches *and* there are already existing URLs
self.counts["exists"] += 1
return False
# check for edit conflicts
if existing.ident in [e.ident for e in self._edits_inflight]:
self.counts["skip-update-inflight"] += 1
return False
# minimum viable "existing" URL cleanup to fix dupes and broken links:
# remove 'None' wayback URLs, and set archive.org rel 'archive'
existing.urls = [
u for u in existing.urls if not ("://web.archive.org/web/None/" in u.url)
]
for i in range(len(existing.urls)):
u = existing.urls[i]
if u.rel == "repository" and "://archive.org/download/" in u.url:
existing.urls[i].rel = "archive"
# special case: if importing *new* from archive.org arxiv collections,
# blow away any existing release_id mappings; this is a direct arxiv_id
# map. This *should* be safe to run in all matched imports.
is_arxiv = False
for u in fe.urls:
if "archive.org/download/arxiv" in u.url.lower():
is_arxiv = True
break
if is_arxiv and fe.release_ids:
existing.release_ids = fe.release_ids
# merge the existing into this one and update
existing.urls = list(set([(u.rel, u.url) for u in fe.urls + existing.urls]))
existing.urls = [
fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in existing.urls
]
if len(existing.urls) > SANE_MAX_URLS:
self.counts["skip-update-too-many-url"] += 1
return False
existing.release_ids = list(set(fe.release_ids + existing.release_ids))
if len(existing.release_ids) > SANE_MAX_RELEASES:
self.counts["skip-update-too-many-releases"] += 1
return False
existing.mimetype = existing.mimetype or fe.mimetype
existing.size = existing.size or fe.size
existing.md5 = existing.md5 or fe.md5
existing.sha1 = existing.sha1 or fe.sha1
existing.sha256 = existing.sha256 or fe.sha256
edit = self.api.update_file(self.get_editgroup_id(), existing.ident, existing)
self._edits_inflight.append(edit)
self.counts["update"] += 1
return False
def insert_batch(self, batch: List[FileEntity]) -> None:
self.api.create_file_auto_batch(
fatcat_openapi_client.FileAutoBatch(
editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description, extra=self.editgroup_extra
),
entity_list=batch,
)
)
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