Use "flat" folder for JATS output

The JATS output file is placed in a folder `paper.jats` together with
all media files. A truly flat structure is ensured, i.e., images are in
the same folder as the resulting `paper.jats` file, and never in
subfolders.

data/defaults/jats.yaml

@@ -1,6 +1,6 @@
 to: jats_publishing+element_citations
 output-file: paper.jats
-extract-media: media
+extract-media: '.'
 
 filters:
   - # Handle `\ref`, `\label`, and `\autoref` commands
@@ -19,6 +19,6 @@ filters:
     type: lua
     path: orcid-uri.lua
 
-# This needs more work before we can really enable it.
-#   - type: lua
-#     path: extract-images.lua
+  - # Ensure that images are placed on the top-level, not in subfolders.
+    type: lua
+    path: unify-image-paths.lua

data/filters/unify-image-paths.lua

@@ -0,0 +1,39 @@
+local mediabag = require 'pandoc.mediabag'
+local path = require 'pandoc.path'
+local sha1 = (require 'pandoc.utils').sha1
+
+--- Map from old image filepaths to new names.
+local updated_filepath = {}
+
+local function unnest (filepath, contents)
+  if updated_filepath[filepath] then
+    return updated_filepath
+  end
+
+  local newpath = path.filename(filepath)
+  if updated_filepath[newpath] then
+    -- the filename is already in use. Prefix with sha1 hash.
+    newpath = sha1(contents) .. '-' .. filepath
+  end
+  updated_filepath[filepath] = newpath
+  return newpath
+end
+
+function Pandoc (doc)
+  -- Ensure that all images have been fetched.
+  doc = mediabag.fill(doc)
+  local newpath
+  for fp, mt, contents in mediabag.items() do
+    -- Delete all mediabag items and re-insert them under their fixed
+    -- name.
+    newpath = unnest(fp, contents)
+    mediabag.delete(fp)
+    mediabag.insert(newpath, mt, contents)
+  end
+  return doc:walk {
+    Image = function (img)
+      img.src = updated_filepath[img.src] or img.src
+      return img
+    end
+  }
+end

example/paper.md

@@ -134,13 +134,13 @@ Images that are larger than the text area are scaled to fit the page. It
 can sometimes be useful to give images an explicit height and/or width,
 e.g. when adding an image as part of a paragraph. The Markdown `![Nyan
 cat](nyan-cat.png){height="9pt"}` includes the image "nyan-cat.png"
-![Nyan cat](nyan-cat.png){height="9pt"} while scaling it to a height of
+![Nyan cat](images/nyan-cat.png){height="9pt"} while scaling it to a height of
 9 pt.
 
 
 ![The "Mandrill" standard test image, sometimes erroneously called
 "Baboon", is a popular sample photo and used in image processing
-research.](mandrill.jpg){#fig:mandrill}
+research.](images/mandrill.jpg){#fig:mandrill}
 
 ### Citations
 
@@ -378,7 +378,7 @@ with `\ref` and `\autoref`.
 
 ![View of coastal dunes in a nature reserve on Sylt, an island in the
 North Sea. Sylt (Danish: *Slid*) is Germany's northernmost
-island.](sylt.jpg){#sylt width="100%"}
+island.](images/sylt.jpg){#sylt width="100%"}
 
 ## Tables and figures
 

scripts/entrypoint.sh

@@ -99,6 +99,15 @@ for format in $(printf "%s" "$outformats" | sed -e 's/,/ /g'); do
     else
         logfile=paper.${format}.log
     fi
+    extra_args=
+    if [ "$format" = "jats" ]; then
+        [ "$verbosity" -gt 0 ] && printf 'Creating folder "paper.jats"'
+        mkdir -p "paper.jats"
+        extra_args="--extract-media=paper.jats --output=paper.jats/paper.jats"
+    fi
+    [ "$verbosity" -gt 0 ] && [ -n "$extra_args" ] && \
+        printf 'Extra pandoc args:%s\n' "${extra_args}"
+
     # Note that the output file must be defined in the format's defaults file.
     /usr/local/bin/pandoc \
 	      --data-dir="$OPENJOURNALS_PATH"/data \
@@ -112,6 +121,7 @@ for format in $(printf "%s" "$outformats" | sed -e 's/,/ /g'); do
         --variable=draft:"$draft" \
         --metadata=draft:"$draft" \
         --log="$logfile" \
+        ${extra_args} \
         "$input_file" \
         "$@" || exit 1
     if [ "$verbosity" -gt 0 ]; then