Obsolete-and-replace DrOn ingredients with non-obsolete labels in ChEBI

src/scripts/obsolete-dron-ingredients.sh

@@ -0,0 +1,29 @@
+#!/bin/sh
+#
+# Add DRON ingredients to obsolete.tsv
+# if they match ChEBI labels.
+
+fail() {
+  echo "ERROR: " "$@"
+  exit 1
+}
+
+ROOT=$(git rev-parse --show-toplevel) || fail "Not a git repository"
+DIR="${ROOT}/src/ontology"
+SCRIPTSDIR="${ROOT}/src/scripts"
+TEMPLATEDIR="${ROOT}/src/templates"
+DB="${DIR}/tmp/dron.db"
+
+# Load template TSVs into SQLite.
+cd "${DIR}" || fail "Could not cd to ${DIR}"
+make tmp/dron.db || fail "Could not make tmp/dron.db"
+make tmp/chebi.db || fail "Could not make tmp/chebi.db"
+
+# Find DRON ingredients matching ChEBI labels.
+sqlite3 "${DB}" < "${SCRIPTSDIR}/obsolete-dron-ingredients.sql" \
+|| fail "Could not run query for ingredients"
+
+# Save obsolete.tsv.
+cd "${TEMPLATEDIR}" \
+&& sqlite3 "${DB}" < "${SCRIPTSDIR}/save-dron-tables.sql" \
+|| fail "Could not save updated obsolete.tsv"

src/scripts/obsolete-dron-ingredients.sql

@@ -0,0 +1,23 @@
+ATTACH 'tmp/dron.db' AS dron;
+ATTACH 'tmp/chebi.db' AS chebi;
+
+CREATE INDEX IF NOT EXISTS dron.idx_ingredient_label ON ingredient(label);
+WITH labels AS (
+    SELECT subject, object AS label
+    FROM chebi.chebi
+    WHERE predicate = 'rdfs:label'
+      AND subject NOT IN (
+        SELECT subject
+        FROM chebi.chebi
+        WHERE predicate = 'owl:deprecated'
+      )
+)
+INSERT OR IGNORE INTO dron.obsolete
+SELECT
+    i.curie AS curie,
+    'obsolete ' || i.label AS label,
+    'owl:Class' AS type,
+    l.subject AS replaced_by
+FROM dron.ingredient AS i
+JOIN labels AS l ON l.label = i.label
+WHERE i.curie LIKE 'DRON:%';

src/scripts/report-problems.sql

@@ -62,6 +62,11 @@ WITH labels AS (
     SELECT subject, object AS label
     FROM chebi.chebi
     WHERE predicate = 'rdfs:label'
+      AND subject NOT IN (
+        SELECT subject
+        FROM chebi.chebi
+        WHERE predicate = 'owl:deprecated'
+      )
 )
 INSERT INTO problem
 SELECT