From 7c6afa0a21883dc8037f3d021246db24eef39b41 Mon Sep 17 00:00:00 2001
From: Bryan Newbold <bnewbold@robocracy.org>
Date: Mon, 29 Nov 2021 15:02:27 -0800
Subject: clean up extra/ folder a bit

---
 extra/cleanups/check_extid.sh | 49 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100755 extra/cleanups/check_extid.sh

(limited to 'extra/cleanups/check_extid.sh')

diff --git a/extra/cleanups/check_extid.sh b/extra/cleanups/check_extid.sh
new file mode 100755
index 00000000..f74f50b6
--- /dev/null
+++ b/extra/cleanups/check_extid.sh
@@ -0,0 +1,49 @@
+#!/usr/bin/env bash
+
+set -e -u -o pipefail
+
+export LC_ALL=C
+
+EXTID_FILE=$1
+
+zcat $EXTID_FILE \
+    | awk '{print $3 "\t" $1}' \
+    | rg -v '^\t' \
+    | sort -S 4G \
+    > doi_ident.tsv
+zcat $EXTID_FILE \
+    | awk '{print $4 "\t" $1}' \
+    | rg -v '^\t' \
+    | sort -S 4G \
+    > pmid_ident.tsv
+zcat $EXTID_FILE \
+    | awk '{print $5 "\t" $1}' \
+    | rg -v '^\t' \
+    | sort -S 4G \
+    > pmcid_ident.tsv
+zcat $EXTID_FILE \
+    | awk '{print $6 "\t" $1}' \
+    | rg -v '^\t' \
+    | sort -S 4G \
+    > wikidata_ident.tsv
+
+# these identifiers aren't fixed-width, so we need to join (sigh)
+cut -f1 doi_ident.tsv \
+    | uniq -d \
+    | join -t$'\t' - doi_ident.tsv \
+    > doi_ident.dupes.tsv
+cut -f1 pmid_ident.tsv \
+    | uniq -d \
+    | join -t$'\t' - pmid_ident.tsv \
+    > pmid_ident.dupes.tsv
+cut -f1 pmcid_ident.tsv \
+    | uniq -d \
+    | join -t$'\t' - pmcid_ident.tsv \
+    > pmcid_ident.dupes.tsv
+cut -f1 wikidata_ident.tsv \
+    | uniq -d \
+    | join -t$'\t' - wikidata_ident.tsv \
+    > wikidata_ident.dupes.tsv
+
+wc -l doi_ident.dupes.tsv pmid_ident.dupes.tsv pmcid_ident.dupes.tsv wikidata_ident.dupes.tsv >> counts.txt
+
-- 
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