remdb 0.3.172__py3-none-any.whl → 0.3.223__py3-none-any.whl

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  1. rem/agentic/README.md +262 -2
  2. rem/agentic/context.py +173 -0
  3. rem/agentic/context_builder.py +12 -2
  4. rem/agentic/mcp/tool_wrapper.py +39 -16
  5. rem/agentic/providers/pydantic_ai.py +46 -43
  6. rem/agentic/schema.py +2 -2
  7. rem/agentic/tools/rem_tools.py +11 -0
  8. rem/api/main.py +1 -1
  9. rem/api/mcp_router/resources.py +64 -8
  10. rem/api/mcp_router/server.py +31 -24
  11. rem/api/mcp_router/tools.py +621 -166
  12. rem/api/routers/admin.py +30 -4
  13. rem/api/routers/auth.py +114 -15
  14. rem/api/routers/chat/completions.py +66 -18
  15. rem/api/routers/chat/sse_events.py +7 -3
  16. rem/api/routers/chat/streaming.py +254 -22
  17. rem/api/routers/common.py +18 -0
  18. rem/api/routers/dev.py +7 -1
  19. rem/api/routers/feedback.py +9 -1
  20. rem/api/routers/messages.py +176 -38
  21. rem/api/routers/models.py +9 -1
  22. rem/api/routers/query.py +12 -1
  23. rem/api/routers/shared_sessions.py +16 -0
  24. rem/auth/jwt.py +19 -4
  25. rem/auth/middleware.py +42 -28
  26. rem/cli/README.md +62 -0
  27. rem/cli/commands/ask.py +1 -1
  28. rem/cli/commands/db.py +148 -70
  29. rem/cli/commands/process.py +171 -43
  30. rem/models/entities/ontology.py +91 -101
  31. rem/schemas/agents/rem.yaml +1 -1
  32. rem/services/content/service.py +18 -5
  33. rem/services/email/service.py +11 -2
  34. rem/services/embeddings/worker.py +26 -12
  35. rem/services/postgres/__init__.py +28 -3
  36. rem/services/postgres/diff_service.py +57 -5
  37. rem/services/postgres/programmable_diff_service.py +635 -0
  38. rem/services/postgres/pydantic_to_sqlalchemy.py +2 -2
  39. rem/services/postgres/register_type.py +12 -11
  40. rem/services/postgres/repository.py +46 -25
  41. rem/services/postgres/schema_generator.py +5 -5
  42. rem/services/postgres/sql_builder.py +6 -5
  43. rem/services/session/__init__.py +8 -1
  44. rem/services/session/compression.py +40 -2
  45. rem/services/session/pydantic_messages.py +276 -0
  46. rem/settings.py +28 -0
  47. rem/sql/background_indexes.sql +5 -0
  48. rem/sql/migrations/001_install.sql +157 -10
  49. rem/sql/migrations/002_install_models.sql +160 -132
  50. rem/sql/migrations/004_cache_system.sql +7 -275
  51. rem/sql/migrations/migrate_session_id_to_uuid.sql +45 -0
  52. rem/utils/model_helpers.py +101 -0
  53. rem/utils/schema_loader.py +6 -6
  54. {remdb-0.3.172.dist-info → remdb-0.3.223.dist-info}/METADATA +1 -1
  55. {remdb-0.3.172.dist-info → remdb-0.3.223.dist-info}/RECORD +57 -53
  56. {remdb-0.3.172.dist-info → remdb-0.3.223.dist-info}/WHEEL +0 -0
  57. {remdb-0.3.172.dist-info → remdb-0.3.223.dist-info}/entry_points.txt +0 -0
rem/cli/README.md CHANGED
@@ -434,6 +434,68 @@ Ensure you're using the correct model format:
434
434
  - OpenAI: `openai:gpt-4o-mini`, `openai:gpt-4o`
435
435
  - Anthropic: `anthropic:claude-sonnet-4-5-20250929`
436
436
 
437
+ ## Data Visibility: PUBLIC vs PRIVATE
438
+
439
+ **IMPORTANT: All ingested data is PUBLIC by default.** This is the correct behavior
440
+ for shared knowledge bases (ontologies, procedures, reference data).
441
+
442
+ ### Why PUBLIC by Default?
443
+
444
+ Most data in REM should be searchable by all users:
445
+ - Clinical ontologies (disorders, symptoms, drugs)
446
+ - Procedures and protocols (SCID-5, PHQ-9, etc.)
447
+ - Reference documentation
448
+ - Shared domain knowledge
449
+
450
+ The `rem_lookup()` function searches for data where `user_id IS NULL`, which means
451
+ public data. If you set `user_id` on data, it becomes invisible to other users.
452
+
453
+ ### Ingesting Public Data (Default)
454
+
455
+ ```bash
456
+ # Standard ingestion - data is PUBLIC
457
+ rem process ingest ontology/procedures/ --table ontologies
458
+
459
+ # From S3 - also PUBLIC
460
+ rem process ingest s3://bucket/docs/reference.pdf
461
+ ```
462
+
463
+ ### Ingesting Private Data (Rare)
464
+
465
+ Private data requires explicit `--make-private` flag:
466
+
467
+ ```bash
468
+ # Private user data - requires --make-private and --user-id
469
+ rem process ingest personal-notes.md --make-private --user-id user-123
470
+ ```
471
+
472
+ **When to use private data:**
473
+ - User-uploaded personal documents
474
+ - Session-specific content
475
+ - User notes and annotations
476
+
477
+ **NEVER use private data for:**
478
+ - Ontologies and reference material
479
+ - Clinical procedures and protocols
480
+ - Shared knowledge bases
481
+ - Anything that should be searchable by agents
482
+
483
+ ### Common Mistake
484
+
485
+ If agents can't find data via `search_rem`, the most common cause is that the data
486
+ was ingested with a `user_id` set. Check with:
487
+
488
+ ```sql
489
+ SELECT name, user_id FROM ontologies WHERE name = 'phq-9-procedure';
490
+ -- user_id should be NULL for public data
491
+ ```
492
+
493
+ Fix by setting user_id to NULL:
494
+ ```sql
495
+ UPDATE ontologies SET user_id = NULL WHERE user_id IS NOT NULL;
496
+ UPDATE kv_store SET user_id = NULL WHERE entity_type = 'ontologies' AND user_id IS NOT NULL;
497
+ ```
498
+
437
499
  ## Next Steps
438
500
 
439
501
  1. **Implement Schema Registry**
rem/cli/commands/ask.py CHANGED
@@ -75,7 +75,7 @@ async def run_agent_streaming(
75
75
  """
76
76
  Run agent in streaming mode using agent.iter() with usage limits.
77
77
 
78
- Design Pattern (from carrier):
78
+ Design Pattern:
79
79
  - Use agent.iter() for complete execution with tool call visibility
80
80
  - run_stream() stops after first output, missing tool calls
81
81
  - Stream tool call markers: [Calling: tool_name]
rem/cli/commands/db.py CHANGED
@@ -333,64 +333,120 @@ def rebuild_cache(connection: str | None):
333
333
 
334
334
  @click.command()
335
335
  @click.argument("file_path", type=click.Path(exists=True, path_type=Path))
336
+ @click.option("--table", "-t", default=None, help="Target table name (required for non-YAML formats)")
336
337
  @click.option("--user-id", default=None, help="User ID to scope data privately (default: public/shared)")
337
338
  @click.option("--dry-run", is_flag=True, help="Show what would be loaded without loading")
338
- def load(file_path: Path, user_id: str | None, dry_run: bool):
339
+ def load(file_path: Path, table: str | None, user_id: str | None, dry_run: bool):
339
340
  """
340
- Load data from YAML file into database.
341
+ Load data from file into database.
341
342
 
342
- File format:
343
- - table: resources
344
- key_field: name
345
- rows:
346
- - name: Example
347
- content: Test data...
343
+ Supports YAML with embedded metadata, or any tabular format via Polars
344
+ (jsonl, parquet, csv, json, arrow, etc.). For non-YAML formats, use --table.
348
345
 
349
346
  Examples:
350
- rem db load rem/tests/data/graph_seed.yaml
351
- rem db load data.yaml --user-id my-user # Private to user
352
- rem db load data.yaml --dry-run
347
+ rem db load data.yaml # YAML with metadata
348
+ rem db load data.jsonl -t resources # Any Polars-supported format
353
349
  """
354
- asyncio.run(_load_async(file_path, user_id, dry_run))
350
+ asyncio.run(_load_async(file_path, table, user_id, dry_run))
355
351
 
356
352
 
357
- async def _load_async(file_path: Path, user_id: str | None, dry_run: bool):
353
+ def _load_dataframe_from_file(file_path: Path) -> "pl.DataFrame":
354
+ """Load any Polars-supported file format into a DataFrame."""
355
+ import polars as pl
356
+
357
+ suffix = file_path.suffix.lower()
358
+
359
+ if suffix in {".jsonl", ".ndjson"}:
360
+ return pl.read_ndjson(file_path)
361
+ elif suffix in {".parquet", ".pq"}:
362
+ return pl.read_parquet(file_path)
363
+ elif suffix == ".csv":
364
+ return pl.read_csv(file_path)
365
+ elif suffix == ".json":
366
+ return pl.read_json(file_path)
367
+ elif suffix in {".ipc", ".arrow"}:
368
+ return pl.read_ipc(file_path)
369
+ else:
370
+ raise ValueError(f"Unsupported file format: {suffix}. Use any Polars-supported format.")
371
+
372
+
373
+ async def _load_async(file_path: Path, table: str | None, user_id: str | None, dry_run: bool):
358
374
  """Async implementation of load command."""
375
+ import polars as pl
359
376
  import yaml
360
377
  from ...models.core.inline_edge import InlineEdge
361
- from ...models.entities import Resource, Moment, User, Message, SharedSession, Schema
378
+ from ...models.entities import SharedSession
362
379
  from ...services.postgres import get_postgres_service
380
+ from ...utils.model_helpers import get_table_name
381
+ from ... import get_model_registry
363
382
 
364
383
  logger.info(f"Loading data from: {file_path}")
365
384
  scope_msg = f"user: {user_id}" if user_id else "public"
366
385
  logger.info(f"Scope: {scope_msg}")
367
386
 
368
- # Load YAML file
369
- with open(file_path) as f:
370
- data = yaml.safe_load(f)
371
-
372
- if not isinstance(data, list):
373
- logger.error("YAML must be a list of table definitions")
374
- raise click.Abort()
375
-
376
- if dry_run:
377
- logger.info("DRY RUN - Would load:")
378
- logger.info(yaml.dump(data, default_flow_style=False))
379
- return
387
+ suffix = file_path.suffix.lower()
388
+ is_yaml = suffix in {".yaml", ".yml"}
380
389
 
381
- # Map table names to model classes
382
- # CoreModel subclasses use Repository.upsert()
390
+ # Build MODEL_MAP dynamically from registry
391
+ registry = get_model_registry()
392
+ registry.register_core_models()
383
393
  MODEL_MAP = {
384
- "users": User,
385
- "moments": Moment,
386
- "resources": Resource,
387
- "messages": Message,
388
- "schemas": Schema,
394
+ get_table_name(model): model
395
+ for model in registry.get_model_classes().values()
389
396
  }
390
397
 
391
398
  # Non-CoreModel tables that need direct SQL insertion
392
399
  DIRECT_INSERT_TABLES = {"shared_sessions"}
393
400
 
401
+ # Parse file based on format
402
+ if is_yaml:
403
+ # YAML with embedded metadata
404
+ with open(file_path) as f:
405
+ data = yaml.safe_load(f)
406
+
407
+ if not isinstance(data, list):
408
+ logger.error("YAML must be a list of table definitions")
409
+ raise click.Abort()
410
+
411
+ if dry_run:
412
+ logger.info("DRY RUN - Would load:")
413
+ logger.info(yaml.dump(data, default_flow_style=False))
414
+ return
415
+
416
+ table_defs = data
417
+ else:
418
+ # Polars-supported format - require --table
419
+ if not table:
420
+ logger.error(f"For {suffix} files, --table is required. Example: rem db load {file_path.name} -t resources")
421
+ raise click.Abort()
422
+
423
+ try:
424
+ df = _load_dataframe_from_file(file_path)
425
+ except Exception as e:
426
+ logger.error(f"Failed to load file: {e}")
427
+ raise click.Abort()
428
+
429
+ rows = df.to_dicts()
430
+
431
+ if dry_run:
432
+ logger.info(f"DRY RUN - Would load {len(rows)} rows to table '{table}':")
433
+ logger.info(f"Columns: {list(df.columns)}")
434
+
435
+ # Validate first row against model if table is known
436
+ if table in MODEL_MAP and rows:
437
+ from ...utils.model_helpers import validate_data_for_model
438
+ result = validate_data_for_model(MODEL_MAP[table], rows[0])
439
+ if result.extra_fields:
440
+ logger.warning(f"Unknown fields (ignored): {result.extra_fields}")
441
+ if result.valid:
442
+ logger.success(f"Sample row validates OK. Required: {result.required_fields or '(none)'}")
443
+ else:
444
+ result.log_errors("Sample row")
445
+ return
446
+
447
+ # Wrap as single table definition
448
+ table_defs = [{"table": table, "rows": rows}]
449
+
394
450
  # Connect to database
395
451
  pg = get_postgres_service()
396
452
  if not pg:
@@ -399,23 +455,23 @@ async def _load_async(file_path: Path, user_id: str | None, dry_run: bool):
399
455
 
400
456
  await pg.connect()
401
457
 
458
+ # Start embedding worker for generating embeddings
459
+ if pg.embedding_worker:
460
+ await pg.embedding_worker.start()
461
+
402
462
  try:
403
463
  total_loaded = 0
404
464
 
405
- for table_def in data:
465
+ for table_def in table_defs:
406
466
  table_name = table_def["table"]
407
- key_field = table_def.get("key_field", "id")
408
467
  rows = table_def.get("rows", [])
409
468
 
410
469
  # Handle direct insert tables (non-CoreModel)
411
470
  if table_name in DIRECT_INSERT_TABLES:
412
471
  for row_data in rows:
413
- # Add tenant_id if not present
414
- if "tenant_id" not in row_data:
415
- row_data["tenant_id"] = "default"
472
+ # tenant_id is optional - NULL means public/shared
416
473
 
417
474
  if table_name == "shared_sessions":
418
- # Insert shared_session directly
419
475
  await pg.fetch(
420
476
  """INSERT INTO shared_sessions
421
477
  (session_id, owner_user_id, shared_with_user_id, tenant_id)
@@ -424,7 +480,7 @@ async def _load_async(file_path: Path, user_id: str | None, dry_run: bool):
424
480
  row_data["session_id"],
425
481
  row_data["owner_user_id"],
426
482
  row_data["shared_with_user_id"],
427
- row_data["tenant_id"],
483
+ row_data.get("tenant_id"), # Optional - NULL means public
428
484
  )
429
485
  total_loaded += 1
430
486
  logger.success(f"Loaded shared_session: {row_data['owner_user_id']} -> {row_data['shared_with_user_id']}")
@@ -434,16 +490,11 @@ async def _load_async(file_path: Path, user_id: str | None, dry_run: bool):
434
490
  logger.warning(f"Unknown table: {table_name}, skipping")
435
491
  continue
436
492
 
437
- model_class = MODEL_MAP[table_name] # Type is inferred from MODEL_MAP
493
+ model_class = MODEL_MAP[table_name]
438
494
 
439
- for row_data in rows:
440
- # Add user_id and tenant_id only if explicitly provided
441
- # Default is public (None) - data is shared/visible to all
442
- # Pass --user-id to scope data privately to a specific user
443
- if "user_id" not in row_data and user_id is not None:
444
- row_data["user_id"] = user_id
445
- if "tenant_id" not in row_data and user_id is not None:
446
- row_data["tenant_id"] = row_data.get("user_id", user_id)
495
+ for row_idx, row_data in enumerate(rows):
496
+ # tenant_id and user_id are optional - NULL means public/shared data
497
+ # Data files can explicitly set tenant_id/user_id if needed
447
498
 
448
499
  # Convert graph_edges to InlineEdge format if present
449
500
  if "graph_edges" in row_data:
@@ -452,30 +503,40 @@ async def _load_async(file_path: Path, user_id: str | None, dry_run: bool):
452
503
  for edge in row_data["graph_edges"]
453
504
  ]
454
505
 
455
- # Convert any ISO timestamp strings with Z suffix to naive datetime
456
- # This handles fields like starts_timestamp, ends_timestamp, etc.
506
+ # Convert ISO timestamp strings
457
507
  from ...utils.date_utils import parse_iso
458
508
  for key, value in list(row_data.items()):
459
509
  if isinstance(value, str) and (key.endswith("_timestamp") or key.endswith("_at")):
460
510
  try:
461
511
  row_data[key] = parse_iso(value)
462
512
  except (ValueError, TypeError):
463
- pass # Not a valid datetime string, leave as-is
513
+ pass
464
514
 
465
- # Create model instance and upsert via repository
466
515
  from ...services.postgres.repository import Repository
516
+ from ...utils.model_helpers import validate_data_for_model
467
517
 
468
- instance = model_class(**row_data)
469
- repo = Repository(model_class, table_name, pg) # Type inferred from MODEL_MAP
470
- await repo.upsert(instance) # type: ignore[arg-type]
518
+ result = validate_data_for_model(model_class, row_data)
519
+ if not result.valid:
520
+ result.log_errors(f"Row {row_idx + 1} ({table_name})")
521
+ raise click.Abort()
522
+
523
+ repo = Repository(model_class, table_name, pg)
524
+ await repo.upsert(result.instance) # type: ignore[arg-type]
471
525
  total_loaded += 1
472
526
 
473
- # Log based on model type
474
- name = getattr(instance, 'name', getattr(instance, 'id', '?'))
527
+ name = getattr(result.instance, 'name', getattr(result.instance, 'id', '?'))
475
528
  logger.success(f"Loaded {table_name[:-1]}: {name}")
476
529
 
477
530
  logger.success(f"Data loaded successfully! Total rows: {total_loaded}")
478
531
 
532
+ # Wait for embeddings to complete
533
+ if pg.embedding_worker and pg.embedding_worker.running:
534
+ queue_size = pg.embedding_worker.task_queue.qsize()
535
+ if queue_size > 0:
536
+ logger.info(f"Waiting for {queue_size} embeddings to complete...")
537
+ await pg.embedding_worker.stop()
538
+ logger.success("Embeddings generated successfully")
539
+
479
540
  finally:
480
541
  await pg.disconnect()
481
542
 
@@ -580,7 +641,7 @@ async def _diff_async(
580
641
 
581
642
  if not result.has_changes:
582
643
  click.secho("✓ No schema drift detected", fg="green")
583
- click.echo(" Database matches Pydantic models")
644
+ click.echo(" Database matches source (tables, functions, triggers, views)")
584
645
  if result.filtered_count > 0:
585
646
  click.echo()
586
647
  click.secho(f" ({result.filtered_count} destructive change(s) hidden by '{strategy}' strategy)", fg="yellow")
@@ -592,17 +653,34 @@ async def _diff_async(
592
653
  if result.filtered_count > 0:
593
654
  click.secho(f" ({result.filtered_count} destructive change(s) hidden by '{strategy}' strategy)", fg="yellow")
594
655
  click.echo()
595
- click.echo("Changes:")
596
- for line in result.summary:
597
- if line.startswith("+"):
598
- click.secho(f" {line}", fg="green")
599
- elif line.startswith("-"):
600
- click.secho(f" {line}", fg="red")
601
- elif line.startswith("~"):
602
- click.secho(f" {line}", fg="yellow")
603
- else:
604
- click.echo(f" {line}")
605
- click.echo()
656
+
657
+ # Table/column changes (Alembic)
658
+ if result.summary:
659
+ click.echo("Table Changes:")
660
+ for line in result.summary:
661
+ if line.startswith("+"):
662
+ click.secho(f" {line}", fg="green")
663
+ elif line.startswith("-"):
664
+ click.secho(f" {line}", fg="red")
665
+ elif line.startswith("~"):
666
+ click.secho(f" {line}", fg="yellow")
667
+ else:
668
+ click.echo(f" {line}")
669
+ click.echo()
670
+
671
+ # Programmable object changes (functions, triggers, views)
672
+ if result.programmable_summary:
673
+ click.echo("Programmable Objects (functions/triggers/views):")
674
+ for line in result.programmable_summary:
675
+ if line.startswith("+"):
676
+ click.secho(f" {line}", fg="green")
677
+ elif line.startswith("-"):
678
+ click.secho(f" {line}", fg="red")
679
+ elif line.startswith("~"):
680
+ click.secho(f" {line}", fg="yellow")
681
+ else:
682
+ click.echo(f" {line}")
683
+ click.echo()
606
684
 
607
685
  # Generate migration if requested
608
686
  if generate:
@@ -11,39 +11,102 @@ from rem.services.content import ContentService
11
11
 
12
12
 
13
13
  @click.command(name="ingest")
14
- @click.argument("file_path", type=click.Path(exists=True))
15
- @click.option("--user-id", default=None, help="User ID to scope file privately (default: public/shared)")
14
+ @click.argument("path", type=click.Path(exists=True))
15
+ @click.option("--table", "-t", default=None, help="Target table (e.g., ontologies, resources). Auto-detected for schemas.")
16
+ @click.option("--make-private", is_flag=True, help="Make data private to a specific user. RARELY NEEDED - most data should be public/shared.")
17
+ @click.option("--user-id", default=None, help="User ID for private data. REQUIRES --make-private flag.")
16
18
  @click.option("--category", help="Optional file category")
17
19
  @click.option("--tags", help="Optional comma-separated tags")
20
+ @click.option("--pattern", "-p", default="**/*.md", help="Glob pattern for directory ingestion (default: **/*.md)")
21
+ @click.option("--dry-run", is_flag=True, help="Show what would be ingested without making changes")
18
22
  def process_ingest(
19
- file_path: str,
23
+ path: str,
24
+ table: str | None,
25
+ make_private: bool,
20
26
  user_id: str | None,
21
27
  category: str | None,
22
28
  tags: str | None,
29
+ pattern: str,
30
+ dry_run: bool,
23
31
  ):
24
32
  """
25
- Ingest a file into REM (storage + parsing + embedding).
33
+ Ingest files into REM (storage + parsing + embedding).
26
34
 
27
- This command performs the full ingestion pipeline:
28
- 1. Reads the file from the local path.
29
- 2. Stores it in the configured storage (local/S3).
30
- 3. Parses the content.
31
- 4. Chunks and embeds the content into Resources.
32
- 5. Creates a File entity record.
35
+ Supports both single files and directories. For directories, recursively
36
+ processes files matching the pattern (default: **/*.md).
37
+
38
+ **IMPORTANT: Data is PUBLIC by default.** This is the correct behavior for
39
+ shared knowledge bases (ontologies, procedures, reference data). Private
40
+ user-scoped data is rarely needed and requires explicit --make-private flag.
41
+
42
+ Target table is auto-detected for schemas (agent.yaml → schemas table).
43
+ Use --table to explicitly set the target (e.g., ontologies for clinical knowledge).
33
44
 
34
45
  Examples:
35
46
  rem process ingest sample.pdf
36
47
  rem process ingest contract.docx --category legal --tags contract,2023
37
48
  rem process ingest agent.yaml # Auto-detects kind=agent, saves to schemas table
49
+
50
+ # Directory ingestion into ontologies table (PUBLIC - no user-id needed)
51
+ rem process ingest ontology/procedures/scid-5/ --table ontologies
52
+ rem process ingest ontology/ --table ontologies --pattern "**/*.md"
53
+
54
+ # Preview what would be ingested
55
+ rem process ingest ontology/ --table ontologies --dry-run
56
+
57
+ # RARE: Private user-scoped data (requires --make-private)
58
+ rem process ingest private-notes.md --make-private --user-id user-123
38
59
  """
39
60
  import asyncio
61
+
62
+ # Validate: user_id requires --make-private flag
63
+ if user_id and not make_private:
64
+ raise click.UsageError(
65
+ "Setting --user-id requires the --make-private flag.\n\n"
66
+ "Data should be PUBLIC by default (no user-id). Private user-scoped data\n"
67
+ "is rarely needed - only use --make-private for truly personal content.\n\n"
68
+ "Example: rem process ingest file.md --make-private --user-id user-123"
69
+ )
70
+
71
+ # If --make-private is set, user_id is required
72
+ if make_private and not user_id:
73
+ raise click.UsageError(
74
+ "--make-private requires --user-id to specify which user owns the data.\n\n"
75
+ "Example: rem process ingest file.md --make-private --user-id user-123"
76
+ )
77
+
78
+ # Clear user_id if not making private (ensure None for public data)
79
+ effective_user_id = user_id if make_private else None
80
+ from pathlib import Path
40
81
  from ...services.content import ContentService
41
82
 
42
83
  async def _ingest():
43
- # Initialize ContentService with repositories for proper resource saving
44
84
  from rem.services.postgres import get_postgres_service
45
85
  from rem.services.postgres.repository import Repository
46
- from rem.models.entities import File, Resource
86
+ from rem.models.entities import File, Resource, Ontology
87
+
88
+ input_path = Path(path)
89
+ tag_list = tags.split(",") if tags else None
90
+
91
+ # Collect files to process
92
+ if input_path.is_dir():
93
+ files_to_process = list(input_path.glob(pattern))
94
+ if not files_to_process:
95
+ logger.error(f"No files matching '{pattern}' found in {input_path}")
96
+ sys.exit(1)
97
+ logger.info(f"Found {len(files_to_process)} files matching '{pattern}'")
98
+ else:
99
+ files_to_process = [input_path]
100
+
101
+ # Dry run: just show what would be processed
102
+ if dry_run:
103
+ logger.info("DRY RUN - Would ingest:")
104
+ for f in files_to_process[:20]:
105
+ entity_key = f.stem # filename without extension
106
+ logger.info(f" {f} → {table or 'auto-detect'} (key: {entity_key})")
107
+ if len(files_to_process) > 20:
108
+ logger.info(f" ... and {len(files_to_process) - 20} more files")
109
+ return
47
110
 
48
111
  db = get_postgres_service()
49
112
  if not db:
@@ -51,53 +114,118 @@ def process_ingest(
51
114
  await db.connect()
52
115
 
53
116
  try:
54
- file_repo = Repository(File, "files", db=db)
55
- resource_repo = Repository(Resource, "resources", db=db)
56
- service = ContentService(file_repo=file_repo, resource_repo=resource_repo)
57
-
58
- tag_list = tags.split(",") if tags else None
59
-
60
- scope_msg = f"user: {user_id}" if user_id else "public"
61
- logger.info(f"Ingesting file: {file_path} ({scope_msg})")
62
- result = await service.ingest_file(
63
- file_uri=file_path,
64
- user_id=user_id,
65
- category=category,
66
- tags=tag_list,
67
- is_local_server=True, # CLI is local
68
- )
69
-
70
- # Handle schema ingestion (agents/evaluators)
71
- if result.get("schema_name"):
72
- logger.success(f"Schema ingested: {result['schema_name']} (kind={result.get('kind', 'agent')})")
73
- logger.info(f"Version: {result.get('version', '1.0.0')}")
74
- # Handle file ingestion
75
- elif result.get("processing_status") == "completed":
76
- logger.success(f"File ingested: {result['file_name']}")
77
- logger.info(f"File ID: {result['file_id']}")
78
- logger.info(f"Resources created: {result['resources_created']}")
117
+ # Direct table ingestion (ontologies, etc.)
118
+ if table:
119
+ await _ingest_to_table(
120
+ db=db,
121
+ files=files_to_process,
122
+ table_name=table,
123
+ user_id=effective_user_id,
124
+ category=category,
125
+ tag_list=tag_list,
126
+ )
79
127
  else:
80
- logger.error(f"Ingestion failed: {result.get('message', 'Unknown error')}")
81
- sys.exit(1)
128
+ # Standard file ingestion via ContentService
129
+ file_repo = Repository(File, "files", db=db)
130
+ resource_repo = Repository(Resource, "resources", db=db)
131
+ service = ContentService(file_repo=file_repo, resource_repo=resource_repo)
132
+
133
+ for file_path in files_to_process:
134
+ scope_msg = f"user: {effective_user_id}" if effective_user_id else "public"
135
+ logger.info(f"Ingesting: {file_path} ({scope_msg})")
136
+
137
+ result = await service.ingest_file(
138
+ file_uri=str(file_path),
139
+ user_id=effective_user_id,
140
+ category=category,
141
+ tags=tag_list,
142
+ is_local_server=True,
143
+ )
144
+
145
+ # Handle schema ingestion (agents/evaluators)
146
+ if result.get("schema_name"):
147
+ logger.success(f"Schema: {result['schema_name']} (kind={result.get('kind', 'agent')})")
148
+ elif result.get("processing_status") == "completed":
149
+ logger.success(f"File: {result['file_name']} ({result['resources_created']} resources)")
150
+ else:
151
+ logger.error(f"Failed: {result.get('message', 'Unknown error')}")
82
152
 
83
153
  except Exception as e:
84
154
  logger.error(f"Error during ingestion: {e}")
85
155
  sys.exit(1)
86
156
  finally:
87
- # Wait for global embedding worker to finish queued tasks
157
+ # Wait for embedding worker to finish
88
158
  from rem.services.embeddings.worker import get_global_embedding_worker
89
159
  try:
90
160
  worker = get_global_embedding_worker()
91
161
  if worker and worker.running and not worker.task_queue.empty():
92
- logger.info(f"Waiting for {worker.task_queue.qsize()} embedding tasks to complete...")
93
- # Worker.stop() waits for queue to drain (see worker.py line ~148)
162
+ logger.info(f"Waiting for {worker.task_queue.qsize()} embedding tasks...")
94
163
  await worker.stop()
95
164
  except RuntimeError:
96
- # Worker doesn't exist yet - no tasks queued
97
165
  pass
98
166
 
99
167
  await db.disconnect()
100
168
 
169
+ async def _ingest_to_table(db, files, table_name, user_id, category, tag_list):
170
+ """Direct ingestion of files to a specific table (ontologies, etc.)."""
171
+ from rem.services.postgres.repository import Repository
172
+ from rem import get_model_registry
173
+ from rem.utils.model_helpers import get_table_name
174
+
175
+ # Get model class for table
176
+ registry = get_model_registry()
177
+ registry.register_core_models()
178
+ model_class = None
179
+ for model in registry.get_model_classes().values():
180
+ if get_table_name(model) == table_name:
181
+ model_class = model
182
+ break
183
+
184
+ if not model_class:
185
+ logger.error(f"Unknown table: {table_name}")
186
+ sys.exit(1)
187
+
188
+ repo = Repository(model_class, table_name, db=db)
189
+ processed = 0
190
+ failed = 0
191
+
192
+ for file_path in files:
193
+ try:
194
+ # Read file content
195
+ content = file_path.read_text(encoding="utf-8")
196
+ entity_key = file_path.stem # filename without extension
197
+
198
+ # Build entity based on table
199
+ entity_data = {
200
+ "name": entity_key,
201
+ "content": content,
202
+ "tags": tag_list or [],
203
+ }
204
+
205
+ # Add optional fields
206
+ if category:
207
+ entity_data["category"] = category
208
+
209
+ # Scoping: user_id for private data, "public" for shared
210
+ # tenant_id="public" is the default for shared knowledge bases
211
+ entity_data["tenant_id"] = user_id or "public"
212
+ entity_data["user_id"] = user_id # None = public/shared
213
+
214
+ # For ontologies, add URI
215
+ if table_name == "ontologies":
216
+ entity_data["uri"] = f"file://{file_path.absolute()}"
217
+
218
+ entity = model_class(**entity_data)
219
+ await repo.upsert(entity, embeddable_fields=["content"], generate_embeddings=True)
220
+ processed += 1
221
+ logger.success(f" ✓ {entity_key}")
222
+
223
+ except Exception as e:
224
+ failed += 1
225
+ logger.error(f" ✗ {file_path.name}: {e}")
226
+
227
+ logger.info(f"Completed: {processed} succeeded, {failed} failed")
228
+
101
229
  asyncio.run(_ingest())
102
230
 
103
231
  def register_commands(group: click.Group):