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.

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,