Register .wdl as text MIME type for RStudio (PHP-130724)

[emmarogge]

Problem

RStudio misidentifies .wdl files containing import statements as binary/JavaScript, preventing users from opening them in the editor. This only affects RStudio — VS Code handles them fine.

Root cause: When .wdl isn't registered as a known MIME type, GIO/libmagic falls back to content-based detection, sees the import keyword, infers JavaScript, and RStudio treats it as non-text.

Fix

Register .wdl as text/x-wdl via the freedesktop shared-mime-info system during post-startup.sh. This ensures extension-based MIME resolution takes priority over content-based detection.

• Creates /usr/share/mime/packages/wdl.xml with a glob pattern for *.wdl
• Runs update-mime-database to rebuild the MIME database
• Only runs when rstudio-server is present, so non-RStudio apps are unaffected

Both r-analysis and r-analysis-aou apps benefit since they both invoke post-startup.sh. Verified that the MIME XML is well-formed and the guard condition correctly scopes to RStudio environments.

Validation Plan

Validation Plan: PHP-130724 — Register .wdl as text MIME type for RStudio

1. CI smoke test (automatic)

• PR triggers the test-pr.yaml workflow
• r-analysis smoke test passes
• r-analysis-aou smoke test passes
• Non-RStudio app smoke tests (e.g., vscode) still pass

2. Local devcontainer build

• Build and start the R app locally:

  cd src/r-analysis
  devcontainer up --workspace-folder .

• Confirm /usr/share/mime/packages/wdl.xml exists in the container:

  devcontainer exec --workspace-folder . /bin/bash -c "cat /usr/share/mime/packages/wdl.xml"

3. MIME resolution check

• Create a test .wdl file with an import statement inside the container:

  cat > /tmp/main.wdl << 'EOF'
  import "tasks/align.wdl" as align
  workflow main {
    call align.bwa_mem
  }
  EOF

• Verify xdg-mime query filetype /tmp/main.wdl returns text/x-wdl (not application/javascript)
• Verify file --mime-type /tmp/main.wdl returns a text/* type

4. RStudio Server UI test

• Open RStudio Server at localhost:8787
• Clone the reproducer repo or create a .wdl file with import statements
• Click on workflows/main.wdl in the RStudio file browser
• Confirm the file opens in the editor as text (no "binary file" error)
• Confirm other .wdl files (without import) also still open normally

5. Workbench deployment test

• Deploy a test r-analysis app in a Workbench workspace using the branch image
• Open the app and clone a repo with .wdl files
• Click on main.wdl (the file containing import statements) in the RStudio file browser
• Verify it opens as text, not as binary

6. Negative testing

• Confirm post-startup.sh does not create /usr/share/mime/packages/wdl.xml on a VS Code or Jupyter app (the command -v rstudio-server guard should skip it)
• Verify a VS Code app still starts and functions normally

PHP-130724