omnigraph/docs/user/search/embeddings.md

# Embeddings

OmniGraph embeds text through a **single engine-side client** (Google Gemini). It is used in two places: the
query-time auto-embed of a string passed to `nearest($v, "string")`, and the offline `omnigraph embed` file
pipeline. Both paths use the same client, so query vectors and CLI-produced document vectors share one model
and one vector space.

## Engine embedding client

- Model: `gemini-embedding-2-preview`
- Env: `GEMINI_API_KEY`, `OMNIGRAPH_GEMINI_BASE_URL` (default Google generativelanguage v1beta), `OMNIGRAPH_EMBED_TIMEOUT_MS=30000`, `OMNIGRAPH_EMBED_RETRY_ATTEMPTS=4`, `OMNIGRAPH_EMBED_RETRY_BACKOFF_MS=200`, `OMNIGRAPH_EMBEDDINGS_MOCK`
- Two task types: `embed_query_text` (RETRIEVAL_QUERY) for query strings and `embed_document_text` (RETRIEVAL_DOCUMENT) for stored documents
- Exponential backoff with retryable detection (timeouts, 429, 5xx)
- Vectors are stored as L2-normalized `FixedSizeList(Float32, dim)`; the requested dimension is driven by the target column width

## `@embed` schema annotation

Mark a Vector property with `@embed("source_text_property")`. Today this is a **catalog annotation** consumed
by the query typechecker and linter: it records which String property is the embedding source and lets
`nearest($v, "string")` auto-embed a query string for comparison against that vector column.

**It does not embed at ingest.** Stored vectors are supplied directly in your load data, or pre-filled by the
offline `omnigraph embed` pipeline below. (Ingest-time execution of `@embed` is a planned enhancement; until
it ships, populate the vector column yourself.)

## CLI `omnigraph embed` (offline file pipeline)

Operates on **JSONL files** (not on a graph), using the same engine client. Three modes (mutually exclusive):

- (default) `fill_missing` — only embed rows whose target field is empty
- `--reembed-all` — overwrite all
- `--clean` — strip embeddings

Inputs are either a single seed manifest YAML or `--input/--output/--spec`. Selectors `--type T`, `--select T:field=value` filter rows. Streams JSONL → JSONL.
Refactor AGENTS.md from encyclopedia to map; move spec into docs/ Splits the 990-line AGENTS.md into a 184-line map (architecture, where-to-find index, always-on invariants, capability matrix, maintenance contract) plus 18 new docs/*.md files holding the deep content per topic (storage, schema and query languages, indexes, embeddings, branches/commits, runs, merge, changes, execution, policy, server, CLI reference, audit, errors, CI, constants, v0.3.1 notes). Adds scripts/check-agents-md.sh and a check_agents_md CI job that verifies every docs/ link in AGENTS.md resolves and every doc in the canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> 2026-04-28 23:31:08 +02:00			`# Embeddings`

refactor(compiler): remove dead OpenAI embedding client (RFC-012 Phase 1) The compiler-side EmbeddingClient (OpenAI/`text-embedding-3-small`) was pub(crate), #![allow(dead_code)], and had zero callers anywhere in the workspace; the live nearest("string") path and the offline `omnigraph embed` CLI both use the engine Gemini client. It carried the only NANOGRAPH_* env vars (vestigial 'nanograph os' naming) and was the sole user of reqwest+tokio in omnigraph-compiler — dropping them removes an HTTP client and async runtime from a crate that advertises 'Zero Lance dependency' (invariant 11). Rewrites docs/user/search/embeddings.md to the single-client reality and corrects the false 'engine embeds @embed at ingest' claim. Verified: build green, 238 compiler tests pass, `rg NANOGRAPH_` empty. 2026-06-15 15:07:54 +02:00			`OmniGraph embeds text through a single engine-side client (Google Gemini). It is used in two places: the`
			query-time auto-embed of a string passed to `nearest($v, "string")`, and the offline `omnigraph embed` file
			`pipeline. Both paths use the same client, so query vectors and CLI-produced document vectors share one model`
			`and one vector space.`
Refactor AGENTS.md from encyclopedia to map; move spec into docs/ Splits the 990-line AGENTS.md into a 184-line map (architecture, where-to-find index, always-on invariants, capability matrix, maintenance contract) plus 18 new docs/*.md files holding the deep content per topic (storage, schema and query languages, indexes, embeddings, branches/commits, runs, merge, changes, execution, policy, server, CLI reference, audit, errors, CI, constants, v0.3.1 notes). Adds scripts/check-agents-md.sh and a check_agents_md CI job that verifies every docs/ link in AGENTS.md resolves and every doc in the canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> 2026-04-28 23:31:08 +02:00
refactor(compiler): remove dead OpenAI embedding client (RFC-012 Phase 1) The compiler-side EmbeddingClient (OpenAI/`text-embedding-3-small`) was pub(crate), #![allow(dead_code)], and had zero callers anywhere in the workspace; the live nearest("string") path and the offline `omnigraph embed` CLI both use the engine Gemini client. It carried the only NANOGRAPH_* env vars (vestigial 'nanograph os' naming) and was the sole user of reqwest+tokio in omnigraph-compiler — dropping them removes an HTTP client and async runtime from a crate that advertises 'Zero Lance dependency' (invariant 11). Rewrites docs/user/search/embeddings.md to the single-client reality and corrects the false 'engine embeds @embed at ingest' claim. Verified: build green, 238 compiler tests pass, `rg NANOGRAPH_` empty. 2026-06-15 15:07:54 +02:00			`## Engine embedding client`
Refactor AGENTS.md from encyclopedia to map; move spec into docs/ Splits the 990-line AGENTS.md into a 184-line map (architecture, where-to-find index, always-on invariants, capability matrix, maintenance contract) plus 18 new docs/*.md files holding the deep content per topic (storage, schema and query languages, indexes, embeddings, branches/commits, runs, merge, changes, execution, policy, server, CLI reference, audit, errors, CI, constants, v0.3.1 notes). Adds scripts/check-agents-md.sh and a check_agents_md CI job that verifies every docs/ link in AGENTS.md resolves and every doc in the canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> 2026-04-28 23:31:08 +02:00
			- Model: `gemini-embedding-2-preview`
			- Env: `GEMINI_API_KEY`, `OMNIGRAPH_GEMINI_BASE_URL` (default Google generativelanguage v1beta), `OMNIGRAPH_EMBED_TIMEOUT_MS=30000`, `OMNIGRAPH_EMBED_RETRY_ATTEMPTS=4`, `OMNIGRAPH_EMBED_RETRY_BACKOFF_MS=200`, `OMNIGRAPH_EMBEDDINGS_MOCK`
refactor(compiler): remove dead OpenAI embedding client (RFC-012 Phase 1) The compiler-side EmbeddingClient (OpenAI/`text-embedding-3-small`) was pub(crate), #![allow(dead_code)], and had zero callers anywhere in the workspace; the live nearest("string") path and the offline `omnigraph embed` CLI both use the engine Gemini client. It carried the only NANOGRAPH_* env vars (vestigial 'nanograph os' naming) and was the sole user of reqwest+tokio in omnigraph-compiler — dropping them removes an HTTP client and async runtime from a crate that advertises 'Zero Lance dependency' (invariant 11). Rewrites docs/user/search/embeddings.md to the single-client reality and corrects the false 'engine embeds @embed at ingest' claim. Verified: build green, 238 compiler tests pass, `rg NANOGRAPH_` empty. 2026-06-15 15:07:54 +02:00			- Two task types: `embed_query_text` (RETRIEVAL_QUERY) for query strings and `embed_document_text` (RETRIEVAL_DOCUMENT) for stored documents
Refactor AGENTS.md from encyclopedia to map; move spec into docs/ Splits the 990-line AGENTS.md into a 184-line map (architecture, where-to-find index, always-on invariants, capability matrix, maintenance contract) plus 18 new docs/*.md files holding the deep content per topic (storage, schema and query languages, indexes, embeddings, branches/commits, runs, merge, changes, execution, policy, server, CLI reference, audit, errors, CI, constants, v0.3.1 notes). Adds scripts/check-agents-md.sh and a check_agents_md CI job that verifies every docs/ link in AGENTS.md resolves and every doc in the canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> 2026-04-28 23:31:08 +02:00			`- Exponential backoff with retryable detection (timeouts, 429, 5xx)`
refactor(compiler): remove dead OpenAI embedding client (RFC-012 Phase 1) The compiler-side EmbeddingClient (OpenAI/`text-embedding-3-small`) was pub(crate), #![allow(dead_code)], and had zero callers anywhere in the workspace; the live nearest("string") path and the offline `omnigraph embed` CLI both use the engine Gemini client. It carried the only NANOGRAPH_* env vars (vestigial 'nanograph os' naming) and was the sole user of reqwest+tokio in omnigraph-compiler — dropping them removes an HTTP client and async runtime from a crate that advertises 'Zero Lance dependency' (invariant 11). Rewrites docs/user/search/embeddings.md to the single-client reality and corrects the false 'engine embeds @embed at ingest' claim. Verified: build green, 238 compiler tests pass, `rg NANOGRAPH_` empty. 2026-06-15 15:07:54 +02:00			- Vectors are stored as L2-normalized `FixedSizeList(Float32, dim)`; the requested dimension is driven by the target column width

			## `@embed` schema annotation
Refactor AGENTS.md from encyclopedia to map; move spec into docs/ Splits the 990-line AGENTS.md into a 184-line map (architecture, where-to-find index, always-on invariants, capability matrix, maintenance contract) plus 18 new docs/*.md files holding the deep content per topic (storage, schema and query languages, indexes, embeddings, branches/commits, runs, merge, changes, execution, policy, server, CLI reference, audit, errors, CI, constants, v0.3.1 notes). Adds scripts/check-agents-md.sh and a check_agents_md CI job that verifies every docs/ link in AGENTS.md resolves and every doc in the canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> 2026-04-28 23:31:08 +02:00
refactor(compiler): remove dead OpenAI embedding client (RFC-012 Phase 1) The compiler-side EmbeddingClient (OpenAI/`text-embedding-3-small`) was pub(crate), #![allow(dead_code)], and had zero callers anywhere in the workspace; the live nearest("string") path and the offline `omnigraph embed` CLI both use the engine Gemini client. It carried the only NANOGRAPH_* env vars (vestigial 'nanograph os' naming) and was the sole user of reqwest+tokio in omnigraph-compiler — dropping them removes an HTTP client and async runtime from a crate that advertises 'Zero Lance dependency' (invariant 11). Rewrites docs/user/search/embeddings.md to the single-client reality and corrects the false 'engine embeds @embed at ingest' claim. Verified: build green, 238 compiler tests pass, `rg NANOGRAPH_` empty. 2026-06-15 15:07:54 +02:00			Mark a Vector property with `@embed("source_text_property")`. Today this is a catalog annotation consumed
			`by the query typechecker and linter: it records which String property is the embedding source and lets`
			`nearest($v, "string")` auto-embed a query string for comparison against that vector column.
Refactor AGENTS.md from encyclopedia to map; move spec into docs/ Splits the 990-line AGENTS.md into a 184-line map (architecture, where-to-find index, always-on invariants, capability matrix, maintenance contract) plus 18 new docs/*.md files holding the deep content per topic (storage, schema and query languages, indexes, embeddings, branches/commits, runs, merge, changes, execution, policy, server, CLI reference, audit, errors, CI, constants, v0.3.1 notes). Adds scripts/check-agents-md.sh and a check_agents_md CI job that verifies every docs/ link in AGENTS.md resolves and every doc in the canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> 2026-04-28 23:31:08 +02:00
refactor(compiler): remove dead OpenAI embedding client (RFC-012 Phase 1) The compiler-side EmbeddingClient (OpenAI/`text-embedding-3-small`) was pub(crate), #![allow(dead_code)], and had zero callers anywhere in the workspace; the live nearest("string") path and the offline `omnigraph embed` CLI both use the engine Gemini client. It carried the only NANOGRAPH_* env vars (vestigial 'nanograph os' naming) and was the sole user of reqwest+tokio in omnigraph-compiler — dropping them removes an HTTP client and async runtime from a crate that advertises 'Zero Lance dependency' (invariant 11). Rewrites docs/user/search/embeddings.md to the single-client reality and corrects the false 'engine embeds @embed at ingest' claim. Verified: build green, 238 compiler tests pass, `rg NANOGRAPH_` empty. 2026-06-15 15:07:54 +02:00			`It does not embed at ingest. Stored vectors are supplied directly in your load data, or pre-filled by the`
			offline `omnigraph embed` pipeline below. (Ingest-time execution of `@embed` is a planned enhancement; until
			`it ships, populate the vector column yourself.)`
Refactor AGENTS.md from encyclopedia to map; move spec into docs/ Splits the 990-line AGENTS.md into a 184-line map (architecture, where-to-find index, always-on invariants, capability matrix, maintenance contract) plus 18 new docs/*.md files holding the deep content per topic (storage, schema and query languages, indexes, embeddings, branches/commits, runs, merge, changes, execution, policy, server, CLI reference, audit, errors, CI, constants, v0.3.1 notes). Adds scripts/check-agents-md.sh and a check_agents_md CI job that verifies every docs/ link in AGENTS.md resolves and every doc in the canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> 2026-04-28 23:31:08 +02:00
			## CLI `omnigraph embed` (offline file pipeline)

refactor(compiler): remove dead OpenAI embedding client (RFC-012 Phase 1) The compiler-side EmbeddingClient (OpenAI/`text-embedding-3-small`) was pub(crate), #![allow(dead_code)], and had zero callers anywhere in the workspace; the live nearest("string") path and the offline `omnigraph embed` CLI both use the engine Gemini client. It carried the only NANOGRAPH_* env vars (vestigial 'nanograph os' naming) and was the sole user of reqwest+tokio in omnigraph-compiler — dropping them removes an HTTP client and async runtime from a crate that advertises 'Zero Lance dependency' (invariant 11). Rewrites docs/user/search/embeddings.md to the single-client reality and corrects the false 'engine embeds @embed at ingest' claim. Verified: build green, 238 compiler tests pass, `rg NANOGRAPH_` empty. 2026-06-15 15:07:54 +02:00			`Operates on JSONL files (not on a graph), using the same engine client. Three modes (mutually exclusive):`
Refactor AGENTS.md from encyclopedia to map; move spec into docs/ Splits the 990-line AGENTS.md into a 184-line map (architecture, where-to-find index, always-on invariants, capability matrix, maintenance contract) plus 18 new docs/*.md files holding the deep content per topic (storage, schema and query languages, indexes, embeddings, branches/commits, runs, merge, changes, execution, policy, server, CLI reference, audit, errors, CI, constants, v0.3.1 notes). Adds scripts/check-agents-md.sh and a check_agents_md CI job that verifies every docs/ link in AGENTS.md resolves and every doc in the canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> 2026-04-28 23:31:08 +02:00
			- (default) `fill_missing` — only embed rows whose target field is empty
			- `--reembed-all` — overwrite all
			- `--clean` — strip embeddings

			Inputs are either a single seed manifest YAML or `--input/--output/--spec`. Selectors `--type T`, `--select T:field=value` filter rows. Streams JSONL → JSONL.