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-rwxr-xr-xextra/extid_map/load_pmc.py47
1 files changed, 47 insertions, 0 deletions
diff --git a/extra/extid_map/load_pmc.py b/extra/extid_map/load_pmc.py
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+++ b/extra/extid_map/load_pmc.py
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+#!/usr/bin/env python3
+"""
+Run like:
+
+ zcat PMID_PMCID_DOI.csv.gz | ./load_pmc.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)
+ reader = csv.reader(sys.stdin)
+ c = db.cursor()
+ count = 0
+ inserted = 0
+ for row in reader:
+ (pmid, pmcid, doi) = row
+ if count % 1000 == 0:
+ print("read {}, wrote {}".format(count, inserted))
+ db.commit()
+ count = count + 1
+ if not doi.startswith("http"):
+ continue
+ doi = doi.replace("https://doi.org/", "").lower()
+ if pmcid == '':
+ pmcid = None
+ if pmid == '':
+ pmid = None
+ else:
+ pmid = int(pmid)
+ # UPSERTS were only added to sqlite3 in summer 2018 (not in xenial version)
+ try:
+ c.execute("""INSERT INTO ids (doi, pmid, pmcid) VALUES (?, ?, ?)""", (doi, pmid, pmcid))
+ except sqlite3.IntegrityError:
+ c.execute("""UPDATE ids SET pmid = ?, pmcid = ? WHERE doi = ?""", (pmid, pmcid, 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])