temdb 3.0.0__py3-none-any.whl

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Files changed (51) hide show
  1. temdb/alembic.ini +29 -0
  2. temdb/migrations/env.py +66 -0
  3. temdb/migrations/script.py.mako +28 -0
  4. temdb/migrations/versions/.gitkeep +0 -0
  5. temdb/migrations/versions/20260612_0001_initial_schema.py +542 -0
  6. temdb/migrations/versions/20260717_ec4c96d0bf77_add_description_to_block_table.py +32 -0
  7. temdb/migrations/versions/20260721_44f75ed44d66_updated_at_nullable_no_server_default.py +165 -0
  8. temdb/migrations/versions/20260721_bec991e0d0eb_dataset_status_server_default.py +38 -0
  9. temdb/migrations/versions/20260801_a1d2f3e4b5c6_add_sections_run_parameters.py +67 -0
  10. temdb/server/__init__.py +3 -0
  11. temdb/server/api/__init__.py +0 -0
  12. temdb/server/api/v2/__init__.py +0 -0
  13. temdb/server/api/v2/acquisition.py +1094 -0
  14. temdb/server/api/v2/block.py +228 -0
  15. temdb/server/api/v2/cutting_session.py +229 -0
  16. temdb/server/api/v2/dataset.py +139 -0
  17. temdb/server/api/v2/lens_correction.py +121 -0
  18. temdb/server/api/v2/microscope.py +93 -0
  19. temdb/server/api/v2/quality_control.py +185 -0
  20. temdb/server/api/v2/roi.py +372 -0
  21. temdb/server/api/v2/section.py +457 -0
  22. temdb/server/api/v2/specimen.py +246 -0
  23. temdb/server/api/v2/substrate.py +180 -0
  24. temdb/server/api/v2/tasks.py +508 -0
  25. temdb/server/cli.py +48 -0
  26. temdb/server/config.py +46 -0
  27. temdb/server/database.py +75 -0
  28. temdb/server/dependencies.py +24 -0
  29. temdb/server/exception_handlers.py +109 -0
  30. temdb/server/ids.py +12 -0
  31. temdb/server/main.py +172 -0
  32. temdb/server/sqlmodels/__init__.py +29 -0
  33. temdb/server/sqlmodels/acquisition.py +101 -0
  34. temdb/server/sqlmodels/base.py +41 -0
  35. temdb/server/sqlmodels/block.py +18 -0
  36. temdb/server/sqlmodels/cutting_session.py +27 -0
  37. temdb/server/sqlmodels/dataset.py +34 -0
  38. temdb/server/sqlmodels/lens_correction.py +36 -0
  39. temdb/server/sqlmodels/microscope.py +22 -0
  40. temdb/server/sqlmodels/roi.py +55 -0
  41. temdb/server/sqlmodels/section.py +55 -0
  42. temdb/server/sqlmodels/specimen.py +17 -0
  43. temdb/server/sqlmodels/substrate.py +23 -0
  44. temdb/server/sqlmodels/task.py +60 -0
  45. temdb/server/sqlmodels/tile.py +53 -0
  46. temdb/server/sqlmodels/tile_partition.py +147 -0
  47. temdb-3.0.0.dist-info/METADATA +16 -0
  48. temdb-3.0.0.dist-info/RECORD +51 -0
  49. temdb-3.0.0.dist-info/WHEEL +4 -0
  50. temdb-3.0.0.dist-info/entry_points.txt +3 -0
  51. temdb-3.0.0.dist-info/licenses/LICENSE +11 -0
temdb/alembic.ini ADDED
@@ -0,0 +1,29 @@
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+ [alembic]
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+ script_location = %(here)s/migrations
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+ file_template = %%(year)d%%(month).2d%%(day).2d_%%(rev)s_%%(slug)s
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+ prepend_sys_path = src
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+
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+ [loggers]
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+ keys = root,sqlalchemy,alembic
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+ [handlers]
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+ keys = console
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+ [formatters]
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+ keys = generic
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+ [logger_root]
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+ level = WARNING
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+ handlers = console
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+ [logger_sqlalchemy]
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+ level = WARNING
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+ handlers =
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+ qualname = sqlalchemy.engine
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+ [logger_alembic]
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+ level = INFO
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+ handlers =
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+ qualname = alembic
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+ [handler_console]
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+ class = StreamHandler
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+ args = (sys.stderr,)
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+ level = NOTSET
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+ formatter = generic
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+ [formatter_generic]
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+ format = %(levelname)-5.5s [%(name)s] %(message)s
@@ -0,0 +1,66 @@
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+ import asyncio
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+ import os
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+
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+ import sqlalchemy as sa
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+ from alembic import context
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+ from sqlalchemy.ext.asyncio import async_engine_from_config
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+
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+ from temdb.server.config import get_config
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+ from temdb.server.sqlmodels import Base
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+
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+ target_metadata = Base.metadata
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+
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+ MIGRATION_LOCK_KEY = 7_323_488_513_002_001
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+
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+
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+ def include_object(obj, name, type_, reflected, compare_to):
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+ if type_ == "table" and name.startswith("tile_d_"):
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+ return False
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+ return True
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+
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+
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+ def _database_url() -> str:
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+ url = os.environ.get("TEMDB_MIGRATION_URL") or get_config().database_url
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+ if not url:
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+ raise RuntimeError("No database_url configured (set TEMDB_MIGRATION_URL or dev.env)")
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+ return url
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+
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+
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+ def _configure(connection):
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+ connection.execute(sa.text(f"SELECT pg_advisory_lock({MIGRATION_LOCK_KEY})"))
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+ context.configure(
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+ connection=connection,
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+ target_metadata=target_metadata,
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+ include_object=include_object,
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+ compare_type=True,
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+ compare_server_default=True,
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+ )
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+ with context.begin_transaction():
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+ context.run_migrations()
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+ connection.commit()
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+
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+
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+ def run_migrations_offline():
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+ context.configure(
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+ url=_database_url(),
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+ target_metadata=target_metadata,
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+ literal_binds=True,
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+ include_object=include_object,
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+ )
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+ with context.begin_transaction():
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+ context.run_migrations()
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+
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+
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+ async def run_async_migrations():
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+ cfg = context.config.get_section(context.config.config_ini_section, {})
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+ cfg["sqlalchemy.url"] = _database_url()
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+ engine = async_engine_from_config(cfg, prefix="sqlalchemy.")
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+ async with engine.connect() as conn:
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+ await conn.run_sync(_configure)
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+ await engine.dispose()
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+
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+
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+ if context.is_offline_mode():
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+ run_migrations_offline()
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+ else:
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+ asyncio.run(run_async_migrations())
@@ -0,0 +1,28 @@
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+ """${message}
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+
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+ Revision ID: ${up_revision}
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+ Revises: ${down_revision | comma,n}
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+ Create Date: ${create_date}
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+
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+ """
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+ from collections.abc import Sequence
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+
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+ import sqlalchemy as sa
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+ from alembic import op
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+ ${imports if imports else ""}
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+
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+ # revision identifiers, used by Alembic.
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+ revision: str = ${repr(up_revision)}
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+ down_revision: str | Sequence[str] | None = ${repr(down_revision)}
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+ branch_labels: str | Sequence[str] | None = ${repr(branch_labels)}
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+ depends_on: str | Sequence[str] | None = ${repr(depends_on)}
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+
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+
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+ def upgrade() -> None:
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+ """Upgrade schema."""
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+ ${upgrades if upgrades else "pass"}
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+
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+
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+ def downgrade() -> None:
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+ """Downgrade schema."""
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+ ${downgrades if downgrades else "pass"}
File without changes