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Fix RStudio treating .wdl files as binary via libmagic override (PHP-130724) #332

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Merged
emmarogge merged 7 commits into from
Mar 6, 2026
Merged

Fix RStudio treating .wdl files as binary via libmagic override (PHP-130724) #332

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d3c737b
Register .wdl as text MIME type for RStudio (PHP-130724)
emmarogge Mar 3, 2026
8ff3347
Move .wdl MIME fix to Dockerfiles for reliability (PHP-130724)
emmarogge Mar 5, 2026
a2e02f3
Revert Dockerfile approach; place MIME fix early in post-startup.sh (…
emmarogge Mar 5, 2026
8aeffe9
Remove unintended files from commit
emmarogge Mar 5, 2026
6f174c9
Use libmagic override instead of MIME database for WDL detection (PHP…
emmarogge Mar 5, 2026
bdb15af
Also override libmagic for WDL files starting with import (PHP-130724)
emmarogge Mar 6, 2026
45f5bcd
Remove mkdir for /etc/magic — it already exists as a file (PHP-130724)
emmarogge Mar 6, 2026
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23 changes: 23 additions & 0 deletions startupscript/post-startup.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -218,6 +218,29 @@ sed -i '/user_allow_other/s/^#//g' /etc/fuse.conf

source "${CLOUD_SCRIPT_DIR}/resource-mount.sh"

###############################
# RStudio file type configuration
###############################
# Register additional file types as text to prevent RStudio from
# misidentifying them as binary (PHP-130724).
if command -v rstudio-server &> /dev/null; then
emit "Registering additional MIME types for RStudio..."
# Add WDL (Workflow Description Language) MIME type so RStudio
# recognizes .wdl files as text instead of binary.
cat > /usr/share/mime/packages/wdl.xml << 'MIME_EOF'
<?xml version="1.0" encoding="UTF-8"?>
<mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info">
<mime-type type="text/x-wdl">
<comment>Workflow Description Language</comment>
<glob pattern="*.wdl"/>
</mime-type>
</mime-info>
MIME_EOF
if command -v update-mime-database &> /dev/null; then
update-mime-database /usr/share/mime
fi
fi

###############################
# cloud platform specific setup
###############################
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