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from typing import Any, Dict, List, Optional
import fatcat_openapi_client
from fatcat_openapi_client import ApiClient, ContainerEntity
from fatcat_tools.normal import clean_str
from .common import EntityImporter
class ChoculaImporter(EntityImporter):
"""
Creates or updates container entities based on output of "chocula" script,
which munges/processes journal metadata from several sources, including
fatcat itself.
See guide for details on the many 'extra' fields used here.
"""
def __init__(self, api: ApiClient, **kwargs) -> None:
eg_desc = kwargs.get(
"editgroup_description",
"Automated import of container-level metadata from Chocula tool.",
)
eg_extra = kwargs.get("editgroup_extra", dict())
eg_extra["agent"] = eg_extra.get("agent", "fatcat_tools.ChoculaImporter")
super().__init__(api, editgroup_description=eg_desc, editgroup_extra=eg_extra, **kwargs)
def want(self, raw_record: Any) -> bool:
if not raw_record.get("ident") and not raw_record.get("_known_issnl"):
self.counts["skip-unknown-new-issnl"] += 1
return False
if raw_record.get("issnl") and raw_record.get("name"):
return True
else:
self.counts["skip-partial-metadata"] += 1
return False
def parse_record(self, row: Dict[str, Any]) -> Optional[ContainerEntity]:
"""
row is a python dict (parsed from JSON).
returns a ContainerEntity (or None if invalid or couldn't parse)
"""
name = clean_str(row.get("name"))
if name and name.endswith("."):
name = name[:-1]
if not name:
# Name is required (by schema)
return None
extra = dict()
for k in (
"urls",
"webarchive_urls",
"country",
"sherpa_romeo",
"ezb",
"szczepanski",
"doaj",
"languages",
"ia",
"scielo",
"kbart",
"publisher_type",
"platform",
):
if row["extra"].get(k):
extra[k] = row["extra"][k]
container_type = None
if "proceedings" in name.lower():
container_type = "proceedings"
elif "journal " in name.lower():
container_type = "journal"
if row["extra"].get("issnp"):
row["extra"]["issnp"] = row["extra"]["issnp"].upper()
if row["extra"].get("issne"):
row["extra"]["issne"] = row["extra"]["issne"].upper()
ce = ContainerEntity(
issnl=row["issnl"],
issnp=row["extra"].get("issnp"),
issne=row["extra"].get("issne"),
ident=row["ident"],
name=name,
container_type=container_type,
publisher=clean_str(row.get("publisher")),
wikidata_qid=row.get("wikidata_qid"),
extra=extra,
)
return ce
def try_update(self, ce: ContainerEntity) -> bool:
existing = None
if ce.ident:
try:
existing = self.api.get_container(ce.ident)
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
self.counts["exists"] += 1
self.counts["exists-not-found"] += 1
return False
if existing.state != "active":
self.counts["exists"] += 1
self.counts["exists-inactive"] += 1
return False
if not existing:
# check if existing by ISSN-L
try:
existing = self.api.lookup_container(issnl=ce.issnl)
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
if existing:
self.counts["exists"] += 1
self.counts["exists-by-issnl"] += 1
return False
# doesn't exist, always create
return True
# decide whether to update
do_update = False
if not self.do_updates:
self.counts["exists"] += 1
return False
if not existing.extra:
existing.extra = dict()
if ce.extra.get("urls") and not ce.extra.get("urls", []):
do_update = True
if ce.extra.get("webarchive_urls") and not ce.extra.get("webarchive_urls", []):
do_update = True
for k in ("kbart", "ia", "doaj"):
# always update these fields if not equal (chocula override)
if ce.extra.get(k) and ce.extra[k] != existing.extra.get(k):
do_update = True
if ce.wikidata_qid and not existing.wikidata_qid:
do_update = True
if do_update:
existing.wikidata_qid = existing.wikidata_qid or ce.wikidata_qid
existing.publisher = existing.publisher or ce.publisher
existing.container_type = existing.container_type or ce.container_type
existing.publication_status = existing.publication_status or ce.publication_status
# move issne/issnp from "extra" to top-level fields (new schema)
if not existing.issne:
tmp_issn = existing.extra.pop("issne", None)
# clean up bad ISSNs in extra metadata
if tmp_issn and len(tmp_issn) == 9:
existing.issne = tmp_issn.upper()
if not existing.issnp:
tmp_issn = existing.extra.pop("issnp", None)
if tmp_issn and len(tmp_issn) == 9:
existing.issnp = tmp_issn.upper()
existing.issne = existing.issne or ce.issne
existing.issnp = existing.issnp or ce.issnp
for k in ("urls", "webarchive_urls"):
# be conservative about URL updates; don't clobber existing URL lists
# may want to make this behavior more sophisticated in the
# future, or at least a config flag
if ce.extra.get(k) and not existing.extra.get(k):
existing.extra[k] = ce.extra.get(k, [])
for k in (
"sherpa_romeo",
"ezb",
"szczepanski",
"doaj",
"ia",
"scielo",
"kbart",
):
# always update (chocula over-rides)
if ce.extra.get(k):
existing.extra[k] = ce.extra[k]
for k in ("country", "publisher_type", "platform"):
# only include if not set (don't clobber human edits)
if ce.extra.get(k) and not existing.extra.get(k):
existing.extra[k] = ce.extra[k]
if ce.extra.get("languages"):
if not existing.extra.get("languages"):
existing.extra["languages"] = ce.extra["languages"]
elif not ce.extra["languages"][0] in existing.extra["languages"]:
existing.extra["languages"].append(ce.extra["languages"][0])
self.api.update_container(self.get_editgroup_id(), existing.ident, existing)
self.counts["update"] += 1
return False
else:
self.counts["exists"] += 1
self.counts["exists-skip-update"] += 1
return False
# if we got this far, it's a bug
raise NotImplementedError
def insert_batch(self, batch: List[ContainerEntity]) -> None:
self.api.create_container_auto_batch(
fatcat_openapi_client.ContainerAutoBatch(
editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description, extra=self.editgroup_extra
),
entity_list=batch,
)
)
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