* fix(cli): write embed generate output in the format embed index reads
* Address review: structured results get their own --output writer
deduplicate --output and ontology align --output were routed through
_write_embeddings_output, a helper for numeric matrices: it rejects the
dict/list shapes these commands produce and the .csv extension deduplicate
documents. New _write_result_output serializes structured results — JSON,
JSON-lines for lists, CSV for rows — and both commands use it. embed
generate keeps the embeddings writer, whose strictness is what #994 fixed.
On the pyarrow gap: the parquet writer already fails with an actionable
message (install pyarrow or use .json). Silently writing JSON bytes to a
.parquet path would recreate #994's magic-bytes failure, so the error stays
an error and the default suggestion stays .json.
* fix(cli): improve structured output serialization
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Co-authored-by: Sameer6305 <sskadam6305@gmail.com>
Per the Qodo review: only string application ids are recorded in (and
resolved through) _app_node_id_map. Internal ids are commonly integers,
so an integer application id could collide with — and silently remap —
a caller-supplied internal id of the same value. Also pass a labels list
to create_node in the regression test, matching the API signature.
GraphStore.add_edges reads application-level string ids from
source_id/target_id and passed them straight to the backend, while
Neo4jStore.create_relationship matches on internal integer ids (id(n)).
Nothing resolved one to the other, so persisting a graph created every
node and zero relationships — each edge failed with 'nodes not found'
as a logger.warning and the call appeared to succeed (#1136).
add_nodes already receives the application-id/internal-id pair from
create_nodes (the app id is preserved in properties['id']) and discarded
it one statement before add_edges needed it. Keep the map on the store,
populate it from both add_nodes and create_node, and resolve known
application ids in create_relationship. Unknown ids pass through
unchanged, so direct internal-id callers and backends whose ids are the
application ids keep their existing behavior.
Fix DBIngestor calls in load_from_database , it was never actually reaching the db.
execute_query/export_table need the connection string as their first arg,
but we were only passing it to the constructor's config dict, which
those methods don't read. Every call blew up with a TypeError before
connecting.
Also split the ImportError/OSError handling , they were caught together
so a real connection failure got reported as "module not available",
which sent people looking in the wrong place. OSError now surfaces as
an actual failure with the original exception chained via `from e`.
Fixes#973.
yzxcj797