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[Bug]: `graphify export svg` writes a graph.svg that is not well-formed XML when a label contains a control character

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#4,241 1 comment 0 reactions 0 assignees View on GitHub

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  • #4244 by @Yyunozor — closed without merging

Assessment

Difficulty
2/5
Estimated time
1-3 hours
Newbie friendliness
72/100
Issue type
Bug
Clarity
Clearly specified
Activity status
Active
Tech stack
python
Domain
data-visualization

Research direction

In graphify/export.py, inspect to_svg and the existing _strip_xml_illegal usage in to_graphml. Add or extend a regression test alongside the tests for #2897, covering control characters in node labels and the legend. Run the focused export tests; done means SVG output is well-formed XML and the control characters are dropped from the drawn text.

Written by the indexing model from the issue text.

Description

Pre-flight checks
  • I have checked the Troubleshooting section in the README
What happened?

A node or community label that contains a C0 control character (an ANSI escape from a pasted terminal capture, a form feed used as a section separator, a NUL) ends up in graph.svg. XML 1.0 forbids those characters, so the file is not well-formed. graphify export svg still prints graph.svg written and exits 0.

The same graph exports a well-formed graph.graphml. #2897 made to_graphml strip these characters and left to_svg out, for a reason given in #2899: to_svg does not crash, matplotlib only warns about a missing glyph and draws a box. That holds for a label without a pair of $ (between two of them, a control character can make matplotlib read invalid mathtext and to_svg raise ValueError), but the file it writes is not valid XML, and the command reports success.

Expected: a well-formed graph.svg, with the control character dropped from the drawn text, as to_graphml does.

Cause, in graphify/export.py: to_svg hands the raw node labels to nx.draw_networkx_labels and the raw community label to mpatches.Patch. With the default svg.fonttype, matplotlib's SVG backend writes each drawn string into a comment (<!-- text -->). Its comment escaping handles &, <, > and --, not control characters. _strip_xml_illegal is only called from to_graphml.

Steps to reproduce
mkdir svg-repro && cd svg-repro
printf '# Notes\n\n## Build \033[31mlog capture\033[0m\n\nSome text.\n\n## Deploy\n\nSee [[Notes]].\n' > notes.md
printf 'def helper():\n    return 1\n\ndef main():\n    return helper()\n' > app.py
graphify update .
graphify export svg
xmllint --noout graphify-out/graph.svg
graphify export graphml
xmllint --noout graphify-out/graph.graphml

The legend takes the same path. On a project with no control character in any heading, graphify export svg --labels labels.json with {"0": "Core \u001b[0mmodule", "1": "Other\u000cgroup"} gives the same xmllint error (<!-- Core [0mmodule (4) -->).

Error output or graph output
.../graphify/export.py:1409: UserWarning: Glyph 27 () missing from font(s) DejaVu Sans.
  plt.savefig(output_path, format="svg", bbox_inches="tight",
graph.svg written - embeds in Obsidian, Notion, GitHub READMEs
graphify-out/graph.svg:513: parser error : xmlParseComment: invalid xmlChar value 27
     <!-- Build [31mlog capture[0m -->

The parentheses of the warning hold the ESC character. xmllint exits 1 on graph.svg and 0 on graph.graphml. The heading becomes the node Build \x1b[31mlog capture\x1b[0m in graph.json.

Graphify version

0.9.80 (v8 @ 6478eb7)

Operating System

macOS

Python Version

3.12

Installation Method

built from source (git clone)

Additional Environment Details

uv sync --all-extras --frozen, matplotlib 3.10.9 (the uv.lock version); the same file is malformed with matplotlib 3.11.2. AST-only path (graphify update), no API key involved. Reproduced on a clean checkout of v8 at 6478eb7 (no local change).

Additional context

I have a small fix and can open a PR: pass the node labels and the legend text through _strip_xml_illegal in to_svg, with a regression test next to the #2897 tests.

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