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-rwxr-xr-xextra/extid_map/load_core.py42
1 files changed, 42 insertions, 0 deletions
diff --git a/extra/extid_map/load_core.py b/extra/extid_map/load_core.py
new file mode 100755
index 00000000..a6a09e8a
--- /dev/null
+++ b/extra/extid_map/load_core.py
@@ -0,0 +1,42 @@
+#!/usr/bin/env python3
+"""
+Run like:
+
+ zcat CORE_FILE | ./load_core.py release_ids.db
+"""
+
+import sys
+import csv
+import sqlite3
+
+def run(db_path):
+ #db = sqlite3.connect("file:{}?mode=ro".format(db_path)
+ db = sqlite3.connect(db_path)
+ c = db.cursor()
+ count = 0
+ inserted = 0
+ for row in sys.stdin:
+ row = row.strip().split("\t")
+ if len(row) != 2:
+ continue
+ (doi, coreid) = row[:2]
+ if count % 1000 == 0:
+ print("read {}, wrote {}".format(count, inserted))
+ db.commit()
+ count = count + 1
+ coreid = int(coreid)
+ doi = doi.lower()
+ # UPSERTS were only added to sqlite3 in summer 2018 (not in xenial version)
+ try:
+ c.execute("""INSERT INTO ids (doi, core) VALUES (?, ?)""", (doi, coreid))
+ except sqlite3.IntegrityError:
+ c.execute("""UPDATE ids SET core = ? WHERE doi = ?""", (coreid, doi))
+ inserted = inserted + 1
+ db.commit()
+ db.close()
+
+if __name__=="__main__":
+ if len(sys.argv) != 2:
+ print("Need single argument: db_path")
+ sys.exit(-1)
+ run(sys.argv[1])