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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, clean_isbn13, clean_pmid
from .common import SANE_MAX_RELEASES, SANE_MAX_URLS, EntityImporter, make_rel_url
class ShadowLibraryImporter(EntityImporter):
"""
Importer for shadow library files (matched to releases)
Input format is JSON with keys:
- shadow
- shadow_corpus (string slug)
- shadow_id (string)
- doi
- pmid
- isbn13
- file_meta
- sha1hex
- sha256hex
- md5hex
- size_bytes
- mimetype
- cdx (may be null)
- url
- datetime
"""
def __init__(self, api: DefaultApi, **kwargs) -> None:
eg_desc = (
kwargs.pop("editgroup_description", None)
or "Import of 'Shadow Library' file/release matches"
)
eg_extra = kwargs.pop("editgroup_extra", dict())
eg_extra["agent"] = eg_extra.get("agent", "fatcat_tools.ShadowLibraryImporter")
super().__init__(api, editgroup_description=eg_desc, editgroup_extra=eg_extra, **kwargs)
self.default_link_rel = kwargs.get("default_link_rel", "web")
def want(self, raw_record: Any) -> bool:
"""
Only want to import records with complete file-level metadata
"""
fm = raw_record["file_meta"]
if not (fm["mimetype"] and fm["md5hex"] and fm["sha256hex"] and fm["size_bytes"]):
self.counts["skip-file-meta-incomplete"] += 1
return False
if fm["mimetype"] != "application/pdf":
self.counts["skip-not-pdf"] += 1
return False
return True
def parse_record(self, obj: Dict[str, Any]) -> Optional[FileEntity]:
"""
We do the release lookup in this method. Try DOI, then PMID, last ISBN13.
"""
shadow_corpus = obj["shadow"]["shadow_corpus"]
assert shadow_corpus == shadow_corpus.strip().lower()
doi = clean_doi(obj["shadow"].get("doi"))
pmid = clean_pmid(obj["shadow"].get("pmid"))
isbn13 = clean_isbn13(obj["shadow"].get("isbn13"))
shadow_id = obj["shadow"].get("shadow_id").strip()
assert shadow_id
extra = {"{}_id".format(shadow_corpus): shadow_id}
for (ext_type, ext_id) in [("doi", doi), ("pmid", pmid), ("isbn13", isbn13)]:
if not ext_id:
continue
extra["{}_{}".format(shadow_corpus, ext_type)] = ext_id
# lookup release via several idents
re = None
for (ext_type, ext_id) in [("doi", doi), ("pmid", pmid), ("isbn13", isbn13)]:
if not ext_id:
continue
try:
re = self.api.lookup_release(**{ext_type: ext_id})
except fatcat_openapi_client.rest.ApiException as err:
if err.status not in (404, 400):
raise err
re = None
if re:
break
if not re:
self.counts["skip-release-not-found"] += 1
return None
release_ids = [
re.ident,
]
# parse single CDX into URLs (if exists)
urls = []
if obj.get("cdx"):
url = make_rel_url(obj["cdx"]["url"], default_link_rel=self.default_link_rel)
if url is not None:
urls.append(url)
wayback = "https://web.archive.org/web/{}/{}".format(
obj["cdx"]["datetime"], obj["cdx"]["url"]
)
urls.append(("webarchive", wayback))
urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
fe = FileEntity(
md5=obj["file_meta"]["md5hex"],
sha1=obj["file_meta"]["sha1hex"],
sha256=obj["file_meta"]["sha256hex"],
size=int(obj["file_meta"]["size_bytes"]),
mimetype=obj["file_meta"]["mimetype"] or None,
release_ids=release_ids,
urls=urls,
extra=dict(shadows=extra),
)
return fe
def try_update(self, fe: FileEntity) -> Optional[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
if not existing.extra:
existing.extra = {}
if (
existing.extra.get("shadows")
and list(fe.extra["shadows"].keys())[0] in existing.extra["shadows"]
):
# already imported from this shadow library; skip
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
if fe.sha1 in [e.sha1 for e in self._edits_inflight]:
raise Exception("Inflight insert; shouldn't happen")
# 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"
if u.rel == "social":
u.rel = "academicsocial"
# merge the existing into this one and update
merged_urls = {}
for u in fe.urls + existing.urls:
merged_urls[u.url] = u
existing.urls = list(merged_urls.values())
if not existing.extra.get("shadows"):
existing.extra["shadows"] = fe.extra["shadows"]
else:
existing.extra["shadows"].update(fe.extra["shadows"])
# do these "plus ones" because we really want to do these updates when possible
if len(existing.urls) > SANE_MAX_URLS + 1:
self.counts["skip-update-too-many-url"] += 1
return None
existing.release_ids = list(set(fe.release_ids + existing.release_ids))
if len(existing.release_ids) > SANE_MAX_RELEASES + 1:
self.counts["skip-update-too-many-releases"] += 1
return None
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)
# add sha1 to non-entity edit row, so we can do more aggressive
# group-level de-dupe
edit.sha1 = existing.sha1
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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