diff --git a/embeddings/cli.py b/embeddings/cli.py index e761686..26ae866 100644 --- a/embeddings/cli.py +++ b/embeddings/cli.py @@ -9,6 +9,7 @@ import click import jsonlines +import smart_open from timdex_dataset_api import TIMDEXDataset from embeddings.config import configure_logger, configure_sentry @@ -156,32 +157,41 @@ def test_model_load(ctx: click.Context) -> None: @click.pass_context @model_required @click.option( - "-d", "--dataset-location", - required=True, + required=False, type=click.Path(), help="TIMDEX dataset location, e.g. 's3://timdex/dataset', to read records from.", ) @click.option( "--run-id", - required=True, + required=False, type=str, help="TIMDEX ETL run id.", ) @click.option( "--run-record-offset", - required=True, + required=False, type=int, default=0, help="TIMDEX ETL run record offset to start from, default = 0.", ) @click.option( "--record-limit", - required=True, + required=False, type=int, default=None, help="Limit number of records after --run-record-offset, default = None (unlimited).", ) +@click.option( + "--input-jsonl", + required=False, + type=str, + default=None, + help=( + "Optional filepath to JSONLines file containing " + "TIMDEX records to create embeddings from." + ), +) @click.option( "--strategy", type=click.Choice(list(STRATEGY_REGISTRY.keys())), @@ -205,6 +215,7 @@ def create_embeddings( run_id: str, run_record_offset: int, record_limit: int, + input_jsonl: str, strategy: list[str], output_jsonl: str, ) -> None: @@ -212,22 +223,37 @@ def create_embeddings( model: BaseEmbeddingModel = ctx.obj["model"] model.load() - # init TIMDEXDataset - timdex_dataset = TIMDEXDataset(dataset_location) - - # query TIMDEX dataset for an iterator of records - timdex_records = timdex_dataset.read_dicts_iter( - columns=[ - "timdex_record_id", - "run_id", - "run_record_offset", - "transformed_record", - ], - run_id=run_id, - where=f"""run_record_offset >= {run_record_offset}""", - limit=record_limit, - action="index", - ) + # read input records from TIMDEX dataset (default) or a JSONLines file + if input_jsonl: + with ( + smart_open.open(input_jsonl, "r") as file_obj, # type: ignore[no-untyped-call] + jsonlines.Reader(file_obj) as reader, + ): + timdex_records = iter(list(reader)) + + else: + if not dataset_location or not run_id: + raise click.UsageError( + "Both '--dataset-location' and '--run-id' are required arguments " + "when reading input records from the TIMDEX dataset." + ) + + # init TIMDEXDataset + timdex_dataset = TIMDEXDataset(dataset_location) + + # query TIMDEX dataset for an iterator of records + timdex_records = timdex_dataset.read_dicts_iter( + columns=[ + "timdex_record_id", + "run_id", + "run_record_offset", + "transformed_record", + ], + run_id=run_id, + where=f"""run_record_offset >= {run_record_offset}""", + limit=record_limit, + action="index", + ) # create an iterator of EmbeddingInputs applying all requested strategies embedding_inputs = create_embedding_inputs(timdex_records, list(strategy)) @@ -235,20 +261,17 @@ def create_embeddings( # create embeddings via the embedding model embeddings = model.create_embeddings(embedding_inputs) - # if requested, write embeddings to a local JSONLines file + # write embeddings to TIMDEX dataset (default) or to a JSONLines file if output_jsonl: - with jsonlines.open( - output_jsonl, - mode="w", - dumps=lambda obj: json.dumps( - obj, - default=str, - ), - ) as writer: + with ( + smart_open.open(output_jsonl, "w") as s3_file, # type: ignore[no-untyped-call] + jsonlines.Writer( + s3_file, + dumps=lambda obj: json.dumps(obj, default=str), + ) as writer, + ): for embedding in embeddings: writer.write(embedding.to_dict()) - - # else, default writing embeddings back to TIMDEX dataset else: # WIP NOTE: write via anticipated timdex_dataset.embeddings.write(...) # NOTE: will likely use an imported TIMDEXEmbedding class from TDA, which the diff --git a/embeddings/strategies/processor.py b/embeddings/strategies/processor.py index 5316729..a5131c5 100644 --- a/embeddings/strategies/processor.py +++ b/embeddings/strategies/processor.py @@ -33,7 +33,12 @@ def create_embedding_inputs( for timdex_dataset_record in timdex_dataset_records: # decode and parse the TIMDEX JSON record once for all requested strategies - timdex_record = json.loads(timdex_dataset_record["transformed_record"].decode()) + transformed_record_raw = timdex_dataset_record["transformed_record"] + timdex_record = json.loads( + transformed_record_raw.decode() + if isinstance(transformed_record_raw, bytes) + else transformed_record_raw + ) for transformer in transformers: # prepare text for embedding from transformer strategy diff --git a/pyproject.toml b/pyproject.toml index c311b0d..f81f003 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,6 +12,7 @@ dependencies = [ "huggingface-hub>=0.26.0", "jsonlines>=4.0.0", "sentry-sdk>=2.34.1", + "smart-open[s3]>=7.4.4", "timdex-dataset-api", "torch>=2.9.0", "transformers>=4.57.1", @@ -41,7 +42,10 @@ exclude = [ ] [[tool.mypy.overrides]] -module = ["timdex_dataset_api.*"] +module = [ + "timdex_dataset_api.*", + "smart_open.*", +] follow_untyped_imports = true diff --git a/tests/fixtures/cli_inputs/test-3-records.jsonl b/tests/fixtures/cli_inputs/test-3-records.jsonl new file mode 100644 index 0000000..9aa3b34 --- /dev/null +++ b/tests/fixtures/cli_inputs/test-3-records.jsonl @@ -0,0 +1,3 @@ +{"timdex_record_id": "record:1", "run_id": "abc123", "run_record_offset": 0, "transformed_record": "{\"title\":\"Record 1\",\"description\":\"This is a record about coffee in the mountains.\"}"} +{"timdex_record_id": "record:2", "run_id": "abc123", "run_record_offset": 1, "transformed_record": "{\"title\":\"Record 2\",\"description\":\"Sometimes poetry is made accidentally by the fabrication of metadata.\"}"} +{"timdex_record_id": "record:3", "run_id": "abc123", "run_record_offset": 2, "transformed_record": "{\"title\":\"Record 3\",\"description\":\"This is an oddball record, meant to evoke the peculiar nature of mathematics.\"}"} \ No newline at end of file diff --git a/tests/test_cli.py b/tests/test_cli.py index f360be6..9f78a93 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -133,10 +133,38 @@ def test_model_required_decorator_works_across_commands( assert "OK" in result.output +def test_create_embeddings_requires_strategy(register_mock_model, runner): + result = runner.invoke( + main, + [ + "create-embeddings", + "--model-uri", + "test/mock-model", + "--dataset-location", + "s3://test", + "--run-id", + "run-1", + ], + ) + assert result.exit_code != 0 + assert "Missing option '--strategy'" in result.output + + def test_create_embeddings_requires_dataset_location(register_mock_model, runner): - result = runner.invoke(main, ["create-embeddings", "--model-uri", "test/mock-model"]) + result = runner.invoke( + main, + [ + "create-embeddings", + "--model-uri", + "test/mock-model", + "--run-id", + "run-1", + "--strategy", + "full_record", + ], + ) assert result.exit_code != 0 - assert "--dataset-location" in result.output + assert "Both '--dataset-location' and '--run-id' are required" in result.output def test_create_embeddings_requires_run_id(register_mock_model, runner): @@ -148,24 +176,54 @@ def test_create_embeddings_requires_run_id(register_mock_model, runner): "test/mock-model", "--dataset-location", "s3://test", + "--strategy", + "full_record", ], ) assert result.exit_code != 0 - assert "Missing option '--run-id'" in result.output + assert "Both '--dataset-location' and '--run-id' are required" in result.output -def test_create_embeddings_requires_strategy(register_mock_model, runner): +def test_create_embeddings_optional_input_jsonl(register_mock_model, runner, tmp_path): + input_file = "tests/fixtures/cli_inputs/test-3-records.jsonl" + output_file = tmp_path / "output.jsonl" + result = runner.invoke( main, [ "create-embeddings", "--model-uri", "test/mock-model", - "--dataset-location", - "s3://test", - "--run-id", - "run-1", + "--input-jsonl", + input_file, + "--strategy", + "full_record", + "--output-jsonl", + str(output_file), ], ) - assert result.exit_code != 0 - assert "Missing option '--strategy'" in result.output + assert result.exit_code == 0 + assert output_file.exists() + + +def test_create_embeddings_optional_input_jsonl_does_not_require_dataset_params( + register_mock_model, runner, tmp_path +): + input_file = "tests/fixtures/cli_inputs/test-3-records.jsonl" + output_file = tmp_path / "output.jsonl" + + result = runner.invoke( + main, + [ + "create-embeddings", + "--model-uri", + "test/mock-model", + "--input-jsonl", + input_file, + "--strategy", + "full_record", + "--output-jsonl", + str(output_file), + ], + ) + assert result.exit_code == 0 diff --git a/uv.lock b/uv.lock index 23f47f5..9f521ef 100644 --- a/uv.lock +++ b/uv.lock @@ -1583,6 +1583,23 @@ wheels = [ { url = 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