Graph Colorize — Color-code the Obsidian Graph View

You are rewriting $OBSIDIAN_VAULT_PATH/.obsidian/graph.json so Obsidian's graph view tints nodes by tag, folder, or visibility.

Obsidian stores graph settings in <vault>/.obsidian/graph.json. The colorGroups array is a list of {query, color} pairs; the first matching query wins per node. Queries use Obsidian's search syntax: tag:#foo, path:"concepts", file:foo, and frontmatter property search ["category":"concept"] (for flat vaults), etc. Color is {"a": 1, "rgb": <packed-int>} where the int is (R << 16) | (G << 8) | B.

Before You Start

1. Resolve the vault path (precedence, highest first): the OBSIDIAN_VAULT_PATH environment variable if set, else a .env in the current working directory (vault-scoped), else ~/.obsidian-wiki/config (global default).
2. Confirm $OBSIDIAN_VAULT_PATH/.obsidian/ exists. If it doesn't, the vault has never been opened in Obsidian — tell the user to open the vault once in Obsidian, then re-run.

3. Obsidian must be fully quit before you write — this is the single most common failure. Obsidian holds graph settings in memory and rewrites graph.json from memory on close and periodically while running, so a write made while it is open gets silently clobbered within seconds (Cmd/Ctrl+R does not reliably save you). The correct sequence is:

   1. Ask the user to fully quit Obsidian (Cmd+Q / Ctrl+Q), not just close the window.
   2. Verify it is not running (e.g. pgrep -x Obsidian) before writing.
   3. Write colorGroups, then have the user re-open Obsidian.

   If you cannot get the user to quit, warn them the change will likely not stick.

Step 1: Pick a Mode

Infer the mode from the user's phrasing. If ambiguous, default to by-tag.

Step 2: Build the colorGroups Array

Palette (10 distinct, colorblind-friendly colors)

Use in order. If more groups than colors, cycle and add a lightness shift by dividing brightness ~20% via a second pass — or just cap at 10 and tell the user the remaining tags share the "other" color.

Every color is wrapped as {"a": 1, "rgb": <int>}.

Mode: by-tag

1. Glob $VAULT_PATH/**/*.md excluding _archives/, _raw/, .obsidian/, node_modules/, index.md, log.md, _insights.md.
2. Parse frontmatter tags from each page. Count usage per tag.
3. Drop visibility/* tags from the frequency list — they are reserved system tags, handled only in by-visibility or combined mode.
4. Take the top 10 tags by usage. If there are fewer than 10 unique tags, use all of them.
5. For each tag T at index i: emit {"query": "tag:#T", "color": palette[i]}.
6. Optionally, append a final catch-all entry for untagged pages at the end: {"query": "-[\"tag\":]", "color": palette[9]} — skip if color slot 9 is already taken by a real tag.

Mode: by-category

First detect the vault layout — this decides which query type to emit:

• Folder layout: categories are top-level folders (concepts/, entities/, …). Detect by checking whether those folders exist and hold .md files.
• Flat layout: all notes live in one notes/ folder and the category is in frontmatter (category: concept). Detect by checking that notes carry a category: frontmatter key. (The vault-template shipped with this kit is flat.)

If both signals appear, prefer flat when most notes sit in a single folder; otherwise use folder.

Folder layout → path: queries

Use these top-level folders in this fixed order so colors are stable across runs:

Emit one entry per folder that exists AND contains at least one .md file:

{"query": "path:\"<folder>\"", "color": {"a": 1, "rgb": <int>}}

Flat layout → frontmatter property queries

Scan the actual category: values in notes/**/*.md (e.g. grep -rh "^category:" notes/ | sort | uniq -c). Map each value to a color using this fixed order so colors stay stable across runs:

For any category value not in this table, assign the next unused palette color. Emit one entry per category value that actually occurs, using Obsidian's property search syntax (note the escaped quotes inside the JSON string):

{"query": "[\"category\":\"concept\"]", "color": {"a": 1, "rgb": 5142951}}

Property queries require a reasonably recent Obsidian (1.4+). If the user reports the groups appear in the panel but nodes stay uncolored, their Obsidian is too old for property search — fall back to by-tag, or add a category/<value> nested tag to each note's frontmatter tags and color by tag:#category/<value>.

Mode: by-visibility

Emit exactly three entries, in this order (first-match wins, so most restrictive comes first):

1. visibility/pii → #E15759 (red, rgb 14767961)
2. visibility/internal → #F28E2B (orange, rgb 15896107)
3. visibility/public → #59A14F (green, rgb 5873999)

{"query": "tag:#visibility/pii", "color": {"a": 1, "rgb": 14767961}}

Pages with no visibility/ tag remain Obsidian's default color — do not add a catch-all.

Mode: combined

Emit by-visibility entries first, then by-tag entries. Visibility wins on conflict because it appears first in the list.

Mode: custom

If the user gave explicit mappings, honor them literally. Convert any hex they give (e.g. #FF00FF) to packed int using int(hex_without_hash, 16). Wrap each as {"a": 1, "rgb": <int>}.

Step 3: Merge into graph.json (Do Not Clobber)

1. Read the existing $VAULT_PATH/.obsidian/graph.json. If it doesn't exist, start from this minimal default:

   {
     "collapse-filter": true,
     "search": "",
     "showTags": false,
     "showAttachments": false,
     "hideUnresolved": false,
     "showOrphans": true,
     "collapse-color-groups": false,
     "colorGroups": [],
     "collapse-display": true,
     "showArrow": false,
     "textFadeMultiplier": 0,
     "nodeSizeMultiplier": 1,
     "lineSizeMultiplier": 1,
     "collapse-forces": true,
     "centerStrength": 0.518713248970312,
     "repelStrength": 10,
     "linkStrength": 1,
     "linkDistance": 250,
     "scale": 1,
     "close": true
   }

2. Back up first: copy the existing file to .obsidian/graph.json.backup-<YYYYMMDD-HHMM> before writing. If a backup from the same minute exists, reuse it — don't pile up duplicates.
3. Replace only the colorGroups field with your new array. Leave every other field untouched. This preserves the user's zoom, physics, filter, search, and display preferences.
4. Write the file back with the same JSON style as the original (usually compact single-line or 2-space indent — preserve what's there).

Step 4: Report and Log

Print a summary like:

Graph colorized → .obsidian/graph.json
  Mode:    by-tag
  Groups:  7 color assignments
  Palette: blue, orange, red, teal, green, yellow, purple
  Backup:  .obsidian/graph.json.backup-20260424-1432

Re-open Obsidian to see the new colors (open Graph view → expand "Color groups").
This write was made with Obsidian fully quit, so it will persist. Editing graph.json
while Obsidian is running gets overwritten — always quit first.

Append to $VAULT_PATH/log.md:

- [TIMESTAMP] GRAPH_COLORIZE mode=<mode> groups=<N> backup=graph.json.backup-<stamp>

Edge Cases

• No tags in vault in by-tag mode → fall back to by-category and tell the user.
• User wants to undo → restore from the latest graph.json.backup-* and note that in log.md.
• User wants to clear all color groups → set colorGroups: [], back up, log as GRAPH_COLORIZE mode=clear.
• .obsidian/ missing → the vault hasn't been opened in Obsidian yet. Tell the user to open it once, then re-run. Don't create .obsidian/ yourself — Obsidian populates many files there on first open.
• Query syntax gotchas: folder paths with spaces need quoting (path:"my folder"); tags with nested slashes work literally (tag:#visibility/internal); don't URL-encode.
• Obsidian open during edit (most common failure): Obsidian rewrites graph.json from memory on close and periodically while running, so writes made while it is open are clobbered within seconds — Cmd/Ctrl+R does not reliably help. Always have the user fully quit (Cmd+Q) first, verify with pgrep -x Obsidian, then write, then re-open. See "Before You Start" step 3.
• Groups show in panel but nodes stay gray (flat-layout vaults): the Obsidian version is too old for ["category":...] property search. Fall back to by-tag, or add category/<value> nested tags and color by tag:.
• New category value appears later: a category not in the mapping gets no entry and its nodes stay default gray — re-run to pick it up.

Notes

• This is a pure config edit — no page content changes, no frontmatter writes.
• Re-running is safe: each run creates a new backup, only colorGroups is rewritten.
• If the user has manually curated color groups they want to keep, offer combined mode or ask before overwriting.
• The palette here matches wiki-export's graph.html community colors, so the Obsidian graph and the exported visualization look consistent.