extid map generation scripts+README

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diff --git a/extra/extid_map/README.md b/extra/extid_map/README.md
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+
+Process for generating a sqlite3 database file mapping between:
+
+- DOI
+- Wikidata QID
+- CORE database id
+- PubMed Central id
+- PubMed id
+
+This fast/indexed local database file, which is about a gigabyte compressed, is
+useful for optimizing some fatcat 'release' entity imports and operations.
+
+There is an example database at <https://archive.org/details/ia_journal_pid_map_munge_20180908>
+
+## Data Sources
+
+EuropePMC mapping (more works than the USA PubMedCentral mapping)
+- <ftp://ftp.ebi.ac.uk/pub/databases/pmc/DOI/PMID_PMCID_DOI.csv.gz>
+- <https://archive.org/details/europepmc-id-map-2018-08-31>
+
+Wikicite data snapshot
+- <https://archive.org/details/wikicite-biblio-data-20180903>
+
+CORE dataset
+- <https://core.ac.uk/services#api>
+- <https://archive.org/download/core_oa_metadata_20180301>
+
+## Wikidata Extract
+
+Early query:
+
+    zcat wikidata-20180806-publications.ndjson.gz.crdownload | rg '"P356"' | jq '{qid: .id, doi: .claims.P356[0]}' -c | pv -l | head
+
+Polished:
+
+    zcat wikidata-20180903-publications.ndjson.gz | rg '"P356"' | jq '[(.claims.P356[0] | ascii_downcase), .id] | @tsv' -cr | pv -l > doi_wikidata.20180903.tsv
+
+    # 13.6M 0:26:13 [8.65k/s]
+
+Hrm, got this but seemed to continue:
+
+    jq: error (at <stdin>:455616): explode input must be a string
+
+## CORE Extract
+
+    xzcat core_json/*.json.xz | jq -rc 'select(.doi != null) | [(.doi | ascii_downcase), .coreId] | @tsv' | pv -l > doi_core.20180301.tsv
+
+    # bnewbold@bnewbold-dev$ wc -l doi_core.20180301.tsv
+    # 28210779 doi_core.20180301.tsv
+
+## PMCID/PMID
+
+In a nice CSV format, no extract needed.
+
+    bnewbold@bnewbold-dev$ zcat PMID_PMCID_DOI.csv.gz | rg doi.org | wc -l
+    19441168
+
+## sqlite schema
+
+    CREATE TABLE ids (doi text not null, core int, pmid int, pmcid text, wikidata text);
+    CREATE UNIQUE INDEX ids_doi on ids (doi);
+
+Run CORE import first (largest mapping, thus fewest exception/update paths),
+then pubmed, then wikidata.
+
+## Run import
+
+    cat doi_core.20180301.tsv | ./load_core.py release_ids.db
+    => read 28210000, wrote 28210000
+    => overnight? but seemed to run fast
+
+    zcat doi_wikidata.20180903.tsv.gz | ./load_wikidata.py release_ids.db
+    => uhoh, seems very slow. lots of IOWAIT. switching to host with SSD
+    => wow, like 5-10x faster at least. sigh.
+    => ran in a few hours
+
+    zcat PMID_PMCID_DOI.csv.gz | ./load_pmc.py release_ids.db
+    => read 29692000, wrote 19441136
+
+
+    sqlite> select count(*) from ids;
+    24831337
+
+    # only 2.3 million works have all IDs
+    sqlite> select count(*) from ids where wikidata not null and core not null and pmid not null;
+    2314700
+
+    # almost (but not all) PubMedCentral items are PubMed items
+    sqlite> select count(*) from ids where pmid not null;
+    19328761
+    sqlite> select count(*) from ids where pmcid not null;
+    3739951
+    sqlite> select count(*) from ids where pmcid not null and pmid not null;
+    3682486
+
+    # wikidata DOIs seem to mostly come from pmid mapping
+    sqlite> select count(*) from ids where wikidata not null;
+    13608497
+    sqlite> select count(*) from ids where pmid not null and wikidata not null;
+    13179156
+
+    # core IDs are more independent (?)
+    sqlite> select count(*) from ids where core not null;
+    7903910
+    sqlite> select count(*) from ids where core not null and wikidata not null;
+    2372369
+    sqlite> select count(*) from ids where core not null and pmid not null;
+    2783344
+
diff --git a/extra/extid_map/load_core.py b/extra/extid_map/load_core.py
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+#!/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])
diff --git a/extra/extid_map/load_pmc.py 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])
diff --git a/extra/extid_map/load_wikidata.py b/extra/extid_map/load_wikidata.py
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+++ b/extra/extid_map/load_wikidata.py
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+#!/usr/bin/env python3
+"""
+Run like:
+
+    zcat doi_wikidata.20180903.tsv.gz | ./load_wikidata.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, qid) = row[:2]
+        if count % 1000 == 0:
+            print("read {}, wrote {}".format(count, inserted))
+            db.commit()
+        count = count + 1
+        if not doi.startswith("10.") or not qid.startswith('Q'):
+            continue
+        doi = doi.lower()
+        # UPSERTS were only added to sqlite3 in summer 2018 (not in xenial version)
+        try:
+            c.execute("""INSERT INTO ids (doi, wikidata) VALUES (?, ?)""", (doi, qid))
+        except sqlite3.IntegrityError:
+            c.execute("""UPDATE ids SET wikidata = ? WHERE doi = ?""", (qid, 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])