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from typing import Any, Dict, List, Optional
import fatcat_openapi_client
from fatcat_openapi_client import ApiClient, FileEntity
from .common import SANE_MAX_RELEASES, SANE_MAX_URLS, EntityImporter, b32_hex, make_rel_url
ARABESQUE_MATCH_WHERE_CLAUSE = "WHERE hit = 1 AND identifier IS NOT NULL"
class ArabesqueMatchImporter(EntityImporter):
"""
Importer for arabesque crawl report .sqlite files, which contain
file/identifier matches based on URL/identifier seedlists.
Uses a SQL query to iterate through table looking for rows with:
- GROBID status 200
- known SHA-1 (base32 format)
- known timestamp
Looks up release (by identifier) and file (by SHA-1). If no release exists,
bail.
If no file exists, create one from metadata (using both direct and wayback
URLs), link to release, and insert.
If file exists, optionally update it:
- if no release match, match to the release
- if new URL not included, add it (and wayback)
Config options:
- default URL rel
- crawl id (for editgroup metadata)
- identifier type
TODO:
- a mode to insert bare files even if identifier not known?
"""
def __init__(
self, api: ApiClient, extid_type: str, require_grobid: bool = True, **kwargs
) -> None:
eg_desc = (
kwargs.get("editgroup_description", None)
or "Match web crawl files to releases based on identifier/URL seedlist"
)
eg_extra = kwargs.get("editgroup_extra", dict())
eg_extra["agent"] = eg_extra.get("agent", "fatcat_tools.ArabesqueMatchImporter")
if kwargs.get("crawl_id"):
eg_extra["crawl_id"] = kwargs.get("crawl_id")
kwargs["do_updates"] = kwargs.get("do_updates", False)
super().__init__(api, editgroup_description=eg_desc, editgroup_extra=eg_extra, **kwargs)
assert extid_type in ("doi", "pmcid", "pmid")
self.extid_type = extid_type
self.default_link_rel = kwargs.get("default_link_rel", "web")
assert self.default_link_rel
self.default_mimetype = kwargs.get("default_mimetype", None)
self.require_grobid = require_grobid
if self.require_grobid:
print("Requiring GROBID status == 200")
else:
print("NOT checking GROBID status column")
def want(self, row: Any) -> bool:
if self.require_grobid and not row["postproc_status"] == "200":
return False
if (
bool(row["hit"]) is True
and row["final_sha1"]
and row["final_timestamp"]
and row["final_timestamp"] != "-"
and len(row["final_timestamp"]) == 14
and row["final_mimetype"]
and bool(row["hit"]) is True
and row["identifier"]
):
return True
else:
return False
def parse_record(self, row: Dict[str, Any]) -> Optional[FileEntity]:
extid = row["identifier"].strip()
# check/cleanup DOI
if self.extid_type == "doi":
extid = extid.lower()
extid.replace("http://doi.org/", "")
extid.replace("https://doi.org/", "")
if extid.startswith("doi:"):
extid = extid[4:]
if not extid.startswith("10."):
self.counts["skip-extid-invalid"]
return None
# lookup extid
try:
re = self.api.lookup_release(**{self.extid_type: extid})
except fatcat_openapi_client.rest.ApiException as err:
if err.status == 404:
# bail on 404 (release not in DB)
self.counts["skip-extid-not-found"] += 1
return None
elif err.status == 400:
self.counts["skip-extid-invalid"] += 1
return None
else:
raise err
url = make_rel_url(row["final_url"], self.default_link_rel)
if not url:
self.counts["skip-url"] += 1
return None
if not row["final_timestamp"]:
self.counts["skip-missing-timestamp"] += 1
return None
wayback = "https://web.archive.org/web/{}/{}".format(
row["final_timestamp"], row["final_url"]
)
urls = [url, ("webarchive", wayback)]
urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
if len(urls) > SANE_MAX_URLS:
self.counts["skip-too-many-url"] += 1
return None
fe = fatcat_openapi_client.FileEntity(
sha1=b32_hex(row["final_sha1"]),
mimetype=row["final_mimetype"] or self.default_mimetype,
release_ids=[re.ident],
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
if (fe.release_ids[0] in existing.release_ids) and existing.urls:
# TODO: could still, in theory update with the new URL?
self.counts["exists"] += 1
return False
if not self.do_updates:
self.counts["skip-update-disabled"] += 1
return False
if existing.ident in [e.ident for e in self._edits_inflight]:
self.counts["skip-update-inflight"] += 1
return False
# TODO: this code path never gets hit because of the check above
if set(fe.release_ids) == set(existing.release_ids):
existing_urls = set([u.url for u in existing.urls])
new_urls = set([u.url for u in fe.urls])
if existing_urls.issuperset(new_urls):
self.counts["skip-update-nothing-new"] += 1
return False
# 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-url"] += 1
return False
existing.mimetype = existing.mimetype or fe.mimetype
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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