remove deprecated extid sqlite3 lookup table feature from importers

This was used during initial bulk imports, but is no longer used and
could create serious metadata problems if used accidentially.

In retrospect, it also made metadata provenance less transparent, and
may have done more harm than good overall.

1 files changed, 0 insertions, 52 deletions

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,