From b447ff3fe80b84b1ab7258e4ab554796962d2922 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Fri, 17 Jan 2020 11:30:46 -0500
Subject: [PATCH] Set pandoc-defaults/jats.yaml

---
 build/build.sh                  | 16 +++++-----------
 build/pandoc-defaults/jats.yaml |  7 +++++++
 2 files changed, 12 insertions(+), 11 deletions(-)
 create mode 100644 build/pandoc-defaults/jats.yaml

diff --git a/build/build.sh b/build/build.sh
index 374194f5..2b299e97 100755
--- a/build/build.sh
+++ b/build/build.sh
@@ -82,17 +82,11 @@ if [ "${BUILD_DOCX:-}" = "true" ]; then
     --defaults="$PANDOC_DEFAULTS_DIR/docx.yaml"
 fi
 
-echo "Exporting JATS XML manuscript"
+echo >&2 "Exporting JATS XML manuscript"
+if [ "${BUILD_JATS:-}" != "false" ]; then
 pandoc --verbose \
---from=markdown \
---to=jats \
---filter=pandoc-fignos \
---filter=pandoc-eqnos \
---filter=pandoc-tablenos \
---bibliography=$BIBLIOGRAPHY_PATH \
---csl=$CSL_PATH \
---metadata link-citations=true \
---output=output/manuscript.xml \
-$INPUT_PATH
+    --defaults="$PANDOC_DEFAULTS_DIR/common.yaml" \
+    --defaults="$PANDOC_DEFAULTS_DIR/jats.yaml"
+fi
 
 echo >&2 "Build complete"
diff --git a/build/pandoc-defaults/jats.yaml b/build/pandoc-defaults/jats.yaml
new file mode 100644
index 00000000..efb68e23
--- /dev/null
+++ b/build/pandoc-defaults/jats.yaml
@@ -0,0 +1,7 @@
+# Pandoc --defaults for JATS XML output.
+# Load on top of common defaults.
+to: jats
+output-file: output/manuscript.xml
+resource-path:
+ - '.'
+ - content