From 7f537e9195a4c6edcffefc823646615006a7f034 Mon Sep 17 00:00:00 2001
From: Albert Krewinkel <albert@zeitkraut.de>
Date: Sat, 11 May 2024 01:36:34 +0200
Subject: [PATCH] Fix image paths in JATS

---
 data/{filters/unify-image-paths.lua => custom/jats.lua} | 8 ++++++--
 data/defaults/jats.yaml                                 | 8 ++------
 2 files changed, 8 insertions(+), 8 deletions(-)
 rename data/{filters/unify-image-paths.lua => custom/jats.lua} (83%)

diff --git a/data/filters/unify-image-paths.lua b/data/custom/jats.lua
similarity index 83%
rename from data/filters/unify-image-paths.lua
rename to data/custom/jats.lua
index a6887be..53e3ebc 100644
--- a/data/filters/unify-image-paths.lua
+++ b/data/custom/jats.lua
@@ -19,7 +19,7 @@ local function unnest (filepath, contents)
   return newpath
 end
 
-function Pandoc (doc)
+function Writer (doc, opts)
   -- Ensure that all images have been fetched.
   doc = mediabag.fill(doc)
   local newpath
@@ -30,10 +30,14 @@ function Pandoc (doc)
     mediabag.delete(fp)
     mediabag.insert(newpath, mt, contents)
   end
-  return doc:walk {
+  doc = doc:walk {
     Image = function (img)
       img.src = updated_filepath[img.src] or img.src
       return img
     end
   }
+  pandoc.mediabag.write('paper.jats')
+  return pandoc.write(doc, 'jats_publishing+element_citations', opts)
 end
+
+Template = pandoc.template.default 'jats'
diff --git a/data/defaults/jats.yaml b/data/defaults/jats.yaml
index f8e846f..c490360 100644
--- a/data/defaults/jats.yaml
+++ b/data/defaults/jats.yaml
@@ -1,6 +1,6 @@
-to: jats_publishing+element_citations
+to: jats.lua
 output-file: paper.jats/paper.jats
-extract-media: paper.jats
+
 
 filters:
   - # Handle `\ref`, `\label`, and `\autoref` commands
@@ -18,7 +18,3 @@ filters:
     # do it here for that reason.
     type: lua
     path: orcid-uri.lua
-
-  - # Ensure that images are placed on the top-level, not in subfolders.
-    type: lua
-    path: unify-image-paths.lua