Flatten directory structure

[tarleb]

No description provided.

[arfon]

Hey @tarleb – sorry it took me ages to get to this. Is this PR good to merge as far as you're concerned (i.e., flattens all the folders etc.)

[tarleb]

I don't quite remember, but it's possible that the PR doesn't catch all changes that were made to the directory structure, and that it might not update some papers that were added after this PR was created, but before the Inara changes were merged. So it's probably be better to close this and create a new PR. If you prefer to do the changes yourself, here's the script that I used. (at least I *think* that's what I used 😬)

…

---- #!/bin/sh set -e find . -maxdepth 2 -name media -type d | \ while IFS= read -r media; do paper=$(basename ${media%/media*}) printf 'Processing %s...\n' "$paper" find "$media" -type f | while IFS= read -r fullimgpath; do # original path relative to JATS file; remove prefix imgpath=${fullimgpath#*joss.?????/} # image filename img=$(basename "$fullimgpath") # Regex removing folders from image paths printf 'Replacing references to %s\n' "$imgpath" regexp="s#xlink:href=\"$imgpath\"#xlink:href=\"$img\"#g" sed -i'' -e "$regexp" "$paper"/10.21105."$paper".jats # Move image into base dir newpath="${paper}/${img}" printf 'Renaming %s to %s\n' "$fullimgpath" "$newpath" git mv "$fullimgpath" "$newpath" done printf 'Removing media folder %s\n' "$media" rmdir -r "$media" done

[tarleb]

Re-posting the script via the web interface just to get proper syntax highlighting.

#!/bin/sh
set -e
find . -maxdepth 2 -name media -type d | \
while IFS= read -r media; do
    paper=$(basename ${media%/media*})
    printf 'Processing %s...\n' "$paper"
    find "$media" -type f | while IFS= read -r fullimgpath; do
        # original path relative to JATS file; remove prefix
        imgpath=${fullimgpath#*joss.?????/}
        # image filename
        img=$(basename "$fullimgpath")

        # Regex removing folders from image paths
        printf 'Replacing references to %s\n' "$imgpath"
        regexp="s#xlink:href=\"$imgpath\"#xlink:href=\"$img\"#g"
        sed -i'' -e "$regexp" "$paper"/10.21105."$paper".jats

        # Move image into base dir
        newpath="${paper}/${img}"
        printf 'Renaming %s to %s\n' "$fullimgpath" "$newpath"
        git mv "$fullimgpath" "$newpath"
    done

    printf 'Removing media folder %s\n' "$media"
    rmdir -r "$media"
done

[tarleb]

Closing, new PR will follow