From d54dfd4c56cda5318c5a3dce26a4162fd0f9c5a9 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Wed, 1 Nov 2017 13:53:35 -0400
Subject: [PATCH 1/3] Preliminary JATS XML output

---
 build/build.sh | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/build/build.sh b/build/build.sh
index 99bba951..374194f5 100755
--- a/build/build.sh
+++ b/build/build.sh
@@ -82,4 +82,17 @@ if [ "${BUILD_DOCX:-}" = "true" ]; then
     --defaults="$PANDOC_DEFAULTS_DIR/docx.yaml"
 fi
 
+echo "Exporting JATS XML manuscript"
+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
+
 echo >&2 "Build complete"

From e341d1ba3bdd7f502a0e97199dde0d931df4b4e1 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 2/3] Set pandoc-defaults/jats.yaml

---
 build/build.sh                  | 18 ++++++------------
 build/pandoc-defaults/jats.yaml |  7 +++++++
 2 files changed, 13 insertions(+), 12 deletions(-)
 create mode 100644 build/pandoc-defaults/jats.yaml

diff --git a/build/build.sh b/build/build.sh
index 374194f5..b097e3e6 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"
-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 \
-$INPUT_PATH
+if [ "${BUILD_JATS:-}" != "false" ]; then
+  echo >&2 "Exporting JATS XML manuscript"
+  pandoc --verbose \
+    --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

From f36146af5d4bae346f3178b202a14140f2a6c79a Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Sun, 1 Nov 2020 18:32:00 -0500
Subject: [PATCH 3/3] update --data-dir

---
 build/build.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/build/build.sh b/build/build.sh
index 9dd0c01a..c7a09fdc 100755
--- a/build/build.sh
+++ b/build/build.sh
@@ -119,8 +119,9 @@ fi
 if [ "${BUILD_JATS:-}" != "false" ]; then
   echo >&2 "Exporting JATS XML manuscript"
   pandoc --verbose \
-    --defaults="$PANDOC_DEFAULTS_DIR/common.yaml" \
-    --defaults="$PANDOC_DEFAULTS_DIR/jats.yaml"
+    --data-dir="$PANDOC_DATA_DIR" \
+    --defaults=common.yaml \
+    --defaults=jats.yaml
 fi
 
 echo >&2 "Build complete"