extid map generation scripts+README

1 files changed, 47 insertions, 0 deletions

diff --git a/extra/extid_map/load_pmc.py b/extra/extid_map/load_pmc.py
new file mode 100755
index 00000000..5454541e
--- /dev/null
+++ b/extra/extid_map/load_pmc.py
@@ -0,0 +1,47 @@
+#!/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])