Maxime's branch

.github/actions/setup-python/action.yml

@@ -17,7 +17,7 @@ runs:
   - name: Install Python project
     shell: bash
     run: |
-      pip install --no-cache-dir --editable .[dev] && \
+      pip install --no-cache-dir --editable .[all,dev] && \
       for pkg in python/loris_*; do \
           pip install --no-cache-dir --no-deps --editable "$pkg"; \
       done

pyproject.toml

@@ -32,6 +32,11 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
+all = [
+    "loris-ephys-visualizer-module @ {root:uri}/python/loris_ephys_visualizer_module",
+    "loris-meegqc-module           @ {root:uri}/python/loris_meegqc_module",
+    "loris-server                  @ {root:uri}/python/loris_server",
+]
 dev = [
     "pyright",
     "pytest",
@@ -55,11 +60,14 @@ packages = [
 members = ["python/loris_*"]
 
 [tool.uv.sources]
-loris_bids_importer  = { workspace = true }
-loris_bids_utils     = { workspace = true }
-loris_dicom_importer = { workspace = true }
-loris_ephys_chunker  = { workspace = true }
-loris_utils          = { workspace = true }
+loris_bids_importer           = { workspace = true }
+loris_bids_utils              = { workspace = true }
+loris_dicom_importer          = { workspace = true }
+loris_ephys_chunker           = { workspace = true }
+loris_ephys_visualizer_module = { workspace = true }
+loris_meegqc_module           = { workspace = true }
+loris_server                  = { workspace = true }
+loris_utils                   = { workspace = true }
 
 [tool.ruff]
 src = ["python"]
@@ -68,15 +76,18 @@ line-length = 120
 preview = true
 
 [tool.ruff.lint]
-ignore = ["E202", "E203", "E221", "E241", "E251", "E272"]
-select = ["E", "EXE", "F", "I", "N", "RUF", "UP", "W"]
+ignore = ["E202", "E203", "E221", "E241", "E251", "E272", "FAST003"]
+select = ["E", "EXE", "F", "FAST", "I", "N", "RUF", "UP", "W"]
 
 [tool.ruff.lint.pycodestyle]
 max-doc-length = 100
 
 [tool.ruff.lint.per-file-ignores]
 # ORM models often have very long lines.
 "python/lib/db/models/*.py" = ["E501"]
+# ORM queries can use booleans and `None` in comparisons.
+"python/lib/db/queries/*.py" = ["E711", "E712"]
+"python/loris_meegqc_module/src/loris_meegqc_module/database/models/*.py" = ["E501"]
 
 # The strict type checking configuration is used to type check only the modern (typed) modules. An
 # additional basic type checking configuration to type check legacy modules can be found in the

python/lib/config.py

@@ -7,6 +7,14 @@
 from lib.logging import log_error_exit
 
 
+def get_jwt_secret_key_config(env: Env) -> str:
+    """
+    Get the LORIS JWT secret key from the in-database configuration.
+    """
+
+    return _get_config_value(env, 'JWTKey')
+
+
 def get_patient_id_dicom_header_config(env: Env) -> Literal['PatientID', 'PatientName']:
     """
     Get the DICOM header in which to look for the patient ID from the in-database configuration, or

python/lib/db/decorators/y_n_bool.py

@@ -13,6 +13,7 @@ class YNBool(TypeDecorator[bool]):
     """
 
     impl = Enum('Y', 'N')
+    cache_ok = True
 
     def process_bind_param(self, value: bool | None, dialect: Dialect) -> Literal['Y', 'N'] | None:
         match value:

python/lib/db/misc.py

@@ -0,0 +1,12 @@
+from datetime import datetime
+
+from sqlalchemy import func, select
+from sqlalchemy.orm import Session as Database
+
+
+def get_database_time(db: Database) -> datetime:
+    """
+    Get the current time from the database server.
+    """
+
+    return db.execute(select(func.now())).scalar_one()

python/lib/db/models/bids_dataset.py

@@ -0,0 +1,35 @@
+from datetime import datetime
+from pathlib import Path
+
+from sqlalchemy.orm import Mapped, mapped_column
+
+from lib.db.base import Base
+from lib.db.decorators.string_path import StringPath
+
+
+class DbBidsDataset(Base):
+    """
+    A LORIS BIDS dataset.
+    """
+
+    __tablename__ = 'bids_dataset'
+
+    id: Mapped[int] = mapped_column('ID', primary_key=True, autoincrement=True)
+    """
+    The ID of this BIDS dataset.
+    """
+
+    path: Mapped[Path] = mapped_column('Path', StringPath, unique=True)
+    """
+    The path of this BIDS dataset, relative to the LORIS data directory.
+    """
+
+    insert_time: Mapped[datetime] = mapped_column('InsertTime', default=datetime.now)
+    """
+    The time at which this BIDS dataset was created in LORIS.
+    """
+
+    update_time: Mapped[datetime] = mapped_column('UpdateTime', default=datetime.now)
+    """
+    The last time at which this BIDS dataset was updated in LORIS.
+    """

python/lib/db/models/bids_file.py

@@ -0,0 +1,61 @@
+from datetime import datetime
+from pathlib import Path
+
+from sqlalchemy import ForeignKey, UniqueConstraint
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+import lib.db.models.bids_dataset as db_bids_dataset
+from lib.db.base import Base
+from lib.db.decorators.int_bool import IntBool
+from lib.db.decorators.string_path import StringPath
+
+
+class DbBidsFile(Base):
+    """
+    A file within a LORIS BIDS dataset.
+    """
+
+    __tablename__ = 'bids_file'
+    __table_args__ = (
+        UniqueConstraint('DatasetID', 'Path', name='bids_file_dataset_id_path_unique'),
+    )
+
+    id: Mapped[int] = mapped_column('ID', primary_key=True, autoincrement=True)
+    """
+    The ID of this BIDS file.
+    """
+
+    dataset_id: Mapped[int] = mapped_column('DatasetID', ForeignKey('bids_dataset.ID', ondelete='CASCADE'))
+    """
+    The ID of the BIDS dataset to which this file belongs.
+    """
+
+    path: Mapped[Path] = mapped_column('Path', StringPath)
+    """
+    The path of this file relative to its LORIS BIDS dataset.
+    """
+
+    source_path: Mapped[Path | None] = mapped_column('SourcePath', StringPath)
+    """
+    The source path of this file relative to the BIDS dataset from which it was imported.
+    """
+
+    insert_time: Mapped[datetime] = mapped_column('InsertTime', default=datetime.now)
+    """
+    The time at which this BIDS dataset was created in LORIS.
+    """
+
+    blake2b_hash: Mapped[str] = mapped_column('Blake2bHash')
+    """
+    The BLAKE2b hash of this file.
+    """
+
+    derivative: Mapped[bool] = mapped_column('Derivative', IntBool)
+    """
+    Whether this file is a BIDS derivative.
+    """
+
+    dataset: Mapped['db_bids_dataset.DbBidsDataset'] = relationship('DbBidsDataset')
+    """
+    The BIDS dataset to which this file belongs.
+    """

python/lib/db/models/file.py

@@ -4,6 +4,7 @@
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
+import lib.db.models.bids_file as db_bids_file
 import lib.db.models.dicom_archive as db_dicom_archive
 import lib.db.models.file_parameter as db_file_parameter
 import lib.db.models.session as db_session
@@ -40,6 +41,16 @@ class DbFile(Base):
     acquisition_order_per_modality : Mapped[int | None]   = mapped_column('AcqOrderPerModality')
     acquisition_date               : Mapped[date | None]  = mapped_column('AcquisitionDate')
 
+    bids_info_id: Mapped[int | None] = mapped_column('BidsInfoID', ForeignKey('bids_file.ID', ondelete='SET NULL'))
+    """
+    The ID of the BIDS information of this file, if any.
+    """
+
+    bids_info: Mapped['db_bids_file.DbBidsFile | None'] = relationship('DbBidsFile')
+    """
+    The BIDS information of this file, if any.
+    """
+
     session: Mapped['db_session.DbSession'] = relationship('DbSession', back_populates='files')
     """
     The session to which this file belongs.

python/lib/db/models/meg_ctf_head_shape_file.py

@@ -1,7 +1,10 @@
+from datetime import datetime
 from pathlib import Path
 
+from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
+import lib.db.models.bids_file as db_bids_file
 import lib.db.models.meg_ctf_head_shape_point as db_meg_ctf_head_shape_point
 from lib.db.base import Base
 from lib.db.decorators.string_path import StringPath
@@ -20,11 +23,21 @@ class DbMegCtfHeadShapeFile(Base):
     ID of the head shape file.
     """
 
+    bids_info_id: Mapped[int | None] = mapped_column('BidsInfoID', ForeignKey('bids_file.ID', ondelete='SET NULL'))
+    """
+    The ID of the BIDS information of this head shape file, if any.
+    """
+
     path: Mapped[Path] = mapped_column('Path', StringPath)
     """
     Path of the head shape file relative to the LORIS data directory.
     """
 
+    insert_time: Mapped[datetime] = mapped_column('InsertTime', default=datetime.now)
+    """
+    The time at which this head shape file was created in LORIS.
+    """
+
     blake2b_hash: Mapped[str] = mapped_column('Blake2bHash')
     """
     Blake2B hash of the head shape file, which may be used to check that the on-disk file data
@@ -35,3 +48,8 @@ class DbMegCtfHeadShapeFile(Base):
     """
     3D points present in the head shape file.
     """
+
+    bids_info: Mapped['db_bids_file.DbBidsFile | None'] = relationship('DbBidsFile')
+    """
+    The BIDS information of this head shape file, if any.
+    """

python/lib/db/models/module.py

@@ -0,0 +1,15 @@
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+import lib.db.models.permission as db_permission
+from lib.db.base import Base
+from lib.db.decorators.y_n_bool import YNBool
+
+
+class DbModule(Base):
+    __tablename__ = 'modules'
+
+    id     : Mapped[int]  = mapped_column('ID', primary_key=True)
+    name   : Mapped[str]  = mapped_column('Name', unique=True)
+    active : Mapped[bool] = mapped_column('Active', YNBool)
+
+    permissions: Mapped[list['db_permission.DbPermission']] = relationship('DbPermission', back_populates='module')

python/lib/db/models/permission.py

@@ -0,0 +1,19 @@
+from sqlalchemy import ForeignKey
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+import lib.db.models.module as db_module
+import lib.db.models.permission_category as db_permission_category
+from lib.db.base import Base
+
+
+class DbPermission(Base):
+    __tablename__ = 'permissions'
+
+    id          : Mapped[int]        = mapped_column('permID', primary_key=True)
+    code        : Mapped[str]        = mapped_column('code', default='', unique=True)
+    description : Mapped[str]        = mapped_column('description', default='')
+    module_id   : Mapped[int | None] = mapped_column('moduleID', ForeignKey('modules.ID'))
+    category_id : Mapped[int]        = mapped_column('categoryID', ForeignKey('permissions_category.ID'), default=2)
+
+    module   : Mapped['db_module.DbModule | None']                   = relationship('DbModule', back_populates='permissions')
+    category : Mapped['db_permission_category.DbPermissionCategory'] = relationship('DbPermissionCategory')

python/lib/db/models/permission_category.py

@@ -0,0 +1,10 @@
+from sqlalchemy.orm import Mapped, mapped_column
+
+from lib.db.base import Base
+
+
+class DbPermissionCategory(Base):
+    __tablename__ = 'permissions_category'
+
+    id          : Mapped[int] = mapped_column('ID', primary_key=True)
+    description : Mapped[str] = mapped_column('Description')

python/lib/db/models/physio_event_file.py

@@ -4,6 +4,7 @@
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
+import lib.db.models.bids_file as db_bids_file
 import lib.db.models.imaging_file_type as db_imaging_file_type
 import lib.db.models.physio_event_parameter as db_physio_event_parameter
 import lib.db.models.physio_file as db_physio_file
@@ -24,8 +25,18 @@ class DbPhysioEventFile(Base):
     last_update    : Mapped[datetime]    = mapped_column('LastUpdate', default=datetime.now)
     last_written   : Mapped[datetime]    = mapped_column('LastWritten', default=datetime.now)
 
+    bids_info_id: Mapped[int | None] = mapped_column('BidsInfoID', ForeignKey('bids_file.ID', ondelete='SET NULL'))
+    """
+    The ID of the BIDS information of this event file, if any.
+    """
+
     physio_file       : Mapped['db_physio_file.DbPhysioFile | None']                     = relationship('DbPhysioFile')
     project           : Mapped['db_project.DbProject | None']                            = relationship('DbProject')
     imaging_file_type : Mapped['db_imaging_file_type.DbImagingFileType | None']          = relationship('DbImagingFileType')
     task_events       : Mapped[list['db_physio_task_event.DbPhysioTaskEvent']]           = relationship('DbPhysioTaskEvent', back_populates='event_file')
     event_parameters  : Mapped[list['db_physio_event_parameter.DbPhysioEventParameter']] = relationship('DbPhysioEventParameter', back_populates='event_file')
+
+    bids_info: Mapped['db_bids_file.DbBidsFile | None'] = relationship('DbBidsFile')
+    """
+    The BIDS information of this event file, if any.
+    """

python/lib/db/models/physio_file.py

@@ -4,6 +4,7 @@
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
+import lib.db.models.bids_file as db_bids_file
 import lib.db.models.meg_ctf_head_shape_file as db_meg_ctf_head_shape_file
 import lib.db.models.physio_channel as db_physio_channel
 import lib.db.models.physio_event_archive as db_physio_event_archive
@@ -38,7 +39,12 @@ class DbPhysioFile(Base):
     be a directory for MEG CTF data.
     """
 
-    head_shape_file_id: Mapped[int | None] = mapped_column('HeadShapeFileID', ForeignKey('meg_ctf_head_shape_file.ID'))
+    bids_info_id: Mapped[int | None] = mapped_column('BidsInfoID', ForeignKey('bids_file.ID', ondelete='SET NULL'))
+    """
+    The ID of the BIDS information of this file, if any.
+    """
+
+    head_shape_file_id: Mapped[int | None] = mapped_column('HeadShapeFileID', ForeignKey('meg_ctf_head_shape_file.ID', ondelete='SET NULL'))
     """
     ID of the head shape file associated to this file, which is only present for MEG CTF files.
     """
@@ -53,6 +59,11 @@ class DbPhysioFile(Base):
     event_files   : Mapped[list['db_physio_event_file.DbPhysioEventFile']]         = relationship('DbPhysioEventFile', back_populates='physio_file')
     task_events   : Mapped[list['db_physio_task_event.DbPhysioTaskEvent']]         = relationship('DbPhysioTaskEvent', back_populates='physio_file')
 
+    bids_info: Mapped['db_bids_file.DbBidsFile | None'] = relationship('DbBidsFile')
+    """
+    The BIDS information of this file, if any.
+    """
+
     head_shape_file: Mapped['db_meg_ctf_head_shape_file.DbMegCtfHeadShapeFile | None'] = relationship('DbMegCtfHeadShapeFile')
     """
     The head shape file associated to this file, which is only present for MEG CTF files.

python/lib/db/models/user.py

@@ -2,8 +2,10 @@
 
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
+import lib.db.models.permission as db_permission
 import lib.db.models.project as db_project
 import lib.db.models.site as db_site
+import lib.db.models.user_permission  # type: ignore  # ruff:ignore[unused-import]
 import lib.db.models.user_project  # type: ignore  # ruff:ignore[unused-import]
 import lib.db.models.user_site  # type: ignore  # ruff:ignore[unused-import]
 from lib.db.base import Base
@@ -55,3 +57,8 @@ class DbUser(Base):
     """
     The sites to which this user belongs to.
     """
+
+    permissions: Mapped[list['db_permission.DbPermission']] = relationship('DbPermission', secondary='user_perm_rel')
+    """
+    The permissions granted to this user.
+    """