aboutsummaryrefslogtreecommitdiffstats
path: root/python/fatcat_tools/importers
diff options
context:
space:
mode:
Diffstat (limited to 'python/fatcat_tools/importers')
-rw-r--r--python/fatcat_tools/importers/crossref.py54
-rw-r--r--python/fatcat_tools/importers/datacite.py54
-rw-r--r--python/fatcat_tools/importers/jalc.py52
3 files changed, 0 insertions, 160 deletions
diff --git a/python/fatcat_tools/importers/crossref.py b/python/fatcat_tools/importers/crossref.py
index a41e2bf5..9c69fee3 100644
--- a/python/fatcat_tools/importers/crossref.py
+++ b/python/fatcat_tools/importers/crossref.py
@@ -1,5 +1,4 @@
import datetime
-import sqlite3
from typing import Any, Dict, List, Optional, Sequence
import fatcat_openapi_client
@@ -128,8 +127,6 @@ class CrossrefImporter(EntityImporter):
"""
Importer for Crossref metadata.
- Can use a local sqlite3 file for faster "external identifier" lookups
-
See https://github.com/CrossRef/rest-api-doc for JSON schema notes
"""
@@ -150,50 +147,8 @@ class CrossrefImporter(EntityImporter):
)
self.create_containers: bool = kwargs.get("create_containers", True)
- extid_map_file = kwargs.get("extid_map_file")
- self.extid_map_db: Optional[Any] = None
- if extid_map_file:
- db_uri = "file:{}?mode=ro".format(extid_map_file)
- print("Using external ID map: {}".format(db_uri))
- self.extid_map_db = sqlite3.connect(db_uri, uri=True)
- else:
- print("Not using external ID map")
-
self.read_issn_map_file(issn_map_file)
- def lookup_ext_ids(self, doi: str) -> Optional[Any]:
- if self.extid_map_db is None:
- return dict(
- core_id=None,
- pmid=None,
- pmcid=None,
- wikidata_qid=None,
- arxiv_id=None,
- jstor_id=None,
- )
- row = self.extid_map_db.execute(
- "SELECT core, pmid, pmcid, wikidata FROM ids WHERE doi=? LIMIT 1", [doi.lower()]
- ).fetchone()
- if row is None:
- return dict(
- core_id=None,
- pmid=None,
- pmcid=None,
- wikidata_qid=None,
- arxiv_id=None,
- jstor_id=None,
- )
- row = [str(cell or "") or None for cell in row]
- return dict(
- core_id=row[0],
- pmid=row[1],
- pmcid=row[2],
- wikidata_qid=row[3],
- # TODO:
- arxiv_id=None,
- jstor_id=None,
- )
-
def map_release_type(self, crossref_type: str) -> Optional[str]:
return CROSSREF_TYPE_MAP.get(crossref_type)
@@ -473,9 +428,6 @@ class CrossrefImporter(EntityImporter):
# unknown
release_stage = None
- # external identifiers
- extids: Dict[str, Any] = self.lookup_ext_ids(doi=obj["DOI"].lower()) or {}
-
# filter out unreasonably huge releases
if len(abstracts) > 100:
self.counts["skip-huge-abstracts"] += 1
@@ -538,13 +490,7 @@ class CrossrefImporter(EntityImporter):
publisher=publisher,
ext_ids=fatcat_openapi_client.ReleaseExtIds(
doi=obj["DOI"].lower(),
- pmid=extids["pmid"],
- pmcid=extids["pmcid"],
- wikidata_qid=extids["wikidata_qid"],
isbn13=isbn13,
- core=extids["core_id"],
- arxiv=extids["arxiv_id"],
- jstor=extids["jstor_id"],
),
volume=clean(obj.get("volume")),
issue=clean(obj.get("issue")),
diff --git a/python/fatcat_tools/importers/datacite.py b/python/fatcat_tools/importers/datacite.py
index d5622960..d4d7a9f5 100644
--- a/python/fatcat_tools/importers/datacite.py
+++ b/python/fatcat_tools/importers/datacite.py
@@ -12,7 +12,6 @@ import collections
import datetime
import json
import re
-import sqlite3
import sys
from typing import Any, Dict, List, Optional, Sequence, Set, Tuple
@@ -248,15 +247,6 @@ class DataciteImporter(EntityImporter):
)
self.create_containers = kwargs.get("create_containers", True)
- extid_map_file = kwargs.get("extid_map_file")
- self.extid_map_db = None
- if extid_map_file:
- db_uri = "file:{}?mode=ro".format(extid_map_file)
- print("Using external ID map: {}".format(db_uri), file=sys.stderr)
- self.extid_map_db = sqlite3.connect(db_uri, uri=True)
- else:
- print("Not using external ID map", file=sys.stderr)
-
self.read_issn_map_file(issn_map_file)
self.debug = debug
self.insert_log_file = insert_log_file
@@ -264,42 +254,6 @@ class DataciteImporter(EntityImporter):
print("datacite with debug={}".format(self.debug), file=sys.stderr)
- def lookup_ext_ids(self, doi: str) -> Dict[str, Any]:
- """
- Return dictionary of identifiers referring to the same things as the given DOI.
- """
- if self.extid_map_db is None:
- return dict(
- core_id=None,
- pmid=None,
- pmcid=None,
- wikidata_qid=None,
- arxiv_id=None,
- jstor_id=None,
- )
- row = self.extid_map_db.execute(
- "SELECT core, pmid, pmcid, wikidata FROM ids WHERE doi=? LIMIT 1", [doi.lower()]
- ).fetchone()
- if row is None:
- return dict(
- core_id=None,
- pmid=None,
- pmcid=None,
- wikidata_qid=None,
- arxiv_id=None,
- jstor_id=None,
- )
- row = [str(cell or "") or None for cell in row]
- return dict(
- core_id=row[0],
- pmid=row[1],
- pmcid=row[2],
- wikidata_qid=row[3],
- # TODO:
- arxiv_id=None,
- jstor_id=None,
- )
-
def parse_record(self, obj: Dict[str, Any]) -> Optional[ReleaseEntity]:
"""
Mapping datacite JSON to ReleaseEntity.
@@ -706,8 +660,6 @@ class DataciteImporter(EntityImporter):
if release_month:
extra["release_month"] = release_month
- extids = self.lookup_ext_ids(doi=doi)
-
# Assemble release.
re = fatcat_openapi_client.ReleaseEntity(
work_id=None,
@@ -722,12 +674,6 @@ class DataciteImporter(EntityImporter):
publisher=publisher,
ext_ids=fatcat_openapi_client.ReleaseExtIds(
doi=doi,
- pmid=extids["pmid"],
- pmcid=extids["pmcid"],
- wikidata_qid=extids["wikidata_qid"],
- core=extids["core_id"],
- arxiv=extids["arxiv_id"],
- jstor=extids["jstor_id"],
),
contribs=contribs,
volume=volume,
diff --git a/python/fatcat_tools/importers/jalc.py b/python/fatcat_tools/importers/jalc.py
index 2f10e533..a737ac9f 100644
--- a/python/fatcat_tools/importers/jalc.py
+++ b/python/fatcat_tools/importers/jalc.py
@@ -1,5 +1,4 @@
import datetime
-import sqlite3
import sys
from typing import Any, Dict, List, Optional, Sequence
@@ -117,50 +116,8 @@ class JalcImporter(EntityImporter):
)
self.create_containers = kwargs.get("create_containers", True)
- extid_map_file = kwargs.get("extid_map_file")
- self.extid_map_db = None
- if extid_map_file:
- db_uri = "file:{}?mode=ro".format(extid_map_file)
- print("Using external ID map: {}".format(db_uri))
- self.extid_map_db = sqlite3.connect(db_uri, uri=True)
- else:
- print("Not using external ID map")
-
self.read_issn_map_file(issn_map_file)
- def lookup_ext_ids(self, doi: str) -> Dict[str, Any]:
- if self.extid_map_db is None:
- return dict(
- core_id=None,
- pmid=None,
- pmcid=None,
- wikidata_qid=None,
- arxiv_id=None,
- jstor_id=None,
- )
- row = self.extid_map_db.execute(
- "SELECT core, pmid, pmcid, wikidata FROM ids WHERE doi=? LIMIT 1", [doi.lower()]
- ).fetchone()
- if row is None:
- return dict(
- core_id=None,
- pmid=None,
- pmcid=None,
- wikidata_qid=None,
- arxiv_id=None,
- jstor_id=None,
- )
- row = [str(cell or "") or None for cell in row]
- return dict(
- core_id=row[0],
- pmid=row[1],
- pmcid=row[2],
- wikidata_qid=row[3],
- # TODO:
- arxiv_id=None,
- jstor_id=None,
- )
-
def want(self, raw_record: Any) -> bool:
return True
@@ -330,9 +287,6 @@ class JalcImporter(EntityImporter):
# reasonable default for this collection
release_type = "article-journal"
- # external identifiers
- extids = self.lookup_ext_ids(doi=doi)
-
# extra:
# translation_of
# aliases
@@ -356,12 +310,6 @@ class JalcImporter(EntityImporter):
release_year=release_year,
ext_ids=fatcat_openapi_client.ReleaseExtIds(
doi=doi,
- pmid=extids["pmid"],
- pmcid=extids["pmcid"],
- wikidata_qid=extids["wikidata_qid"],
- core=extids["core_id"],
- arxiv=extids["arxiv_id"],
- jstor=extids["jstor_id"],
),
volume=volume,
issue=issue,
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-07 18:06:51 +0000