wip 2

Author: MaximeBICMTL

pyproject.toml

@@ -56,6 +56,8 @@ members = ["python/loris_*"]
 loris_bids_reader    = { workspace = true }
 loris_dicom_importer = { workspace = true }
 loris_ephys_chunker  = { workspace = true }
+loris_ephys_server   = { workspace = true }
+loris_server         = { workspace = true }
 loris_utils          = { workspace = true }
 
 [tool.ruff]
@@ -65,8 +67,8 @@ 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
@@ -91,11 +93,14 @@ include = [
     "python/lib/get_session_info.py",
     "python/lib/logging.py",
     "python/lib/make_env.py",
+    "python/lib/user.py",
     "python/scripts/import_bids_dataset.py",
     "python/loris_bids_reader",
     "python/loris_dicom_importer",
     "python/loris_ephys_chunker",
+    "python/loris_ephys_server",
     "python/loris_utils",
+    "python/loris_server",
 ]
 exclude = [
     "python/loris_ephys_chunker/src/loris_ephys_chunker/protocol_buffers",

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
@@ -34,22 +42,7 @@ def get_data_dir_path_config(env: Env) -> Path:
     """
 
     data_dir_path = Path(_get_config_value(env, 'dataDirBasepath'))
-
-    if not data_dir_path.is_dir():
-        log_error_exit(
-            env,
-            (
-                f"The LORIS base data directory path configuration value '{data_dir_path}' does not refer to an"
-                " existing directory."
-            )
-        )
-
-    if not os.access(data_dir_path, os.R_OK) or not os.access(data_dir_path, os.W_OK):
-        log_error_exit(
-            env,
-            f"Missing read or write permission on the LORIS base data directory '{data_dir_path}'.",
-        )
-
+    check_loris_directory(env, data_dir_path, "data")
     return data_dir_path
 
 
@@ -60,22 +53,7 @@ def get_dicom_archive_dir_path_config(env: Env) -> Path:
     """
 
     dicom_archive_dir_path = Path(_get_config_value(env, 'tarchiveLibraryDir'))
-
-    if not dicom_archive_dir_path.is_dir():
-        log_error_exit(
-            env,
-            (
-                f"The LORIS DICOM archive directory path configuration value '{dicom_archive_dir_path}' does not refer"
-                " to an existing directory."
-            ),
-        )
-
-    if not os.access(dicom_archive_dir_path, os.R_OK) or not os.access(dicom_archive_dir_path, os.W_OK):
-        log_error_exit(
-            env,
-            f"Missing read or write permission on the LORIS DICOM archive directory '{dicom_archive_dir_path}'.",
-        )
-
+    check_loris_directory(env, dicom_archive_dir_path, "DICOM archive")
     return dicom_archive_dir_path
 
 
@@ -87,75 +65,66 @@ def get_default_bids_visit_label_config(env: Env) -> str | None:
     return _try_get_config_value(env, 'default_bids_vl')
 
 
-def get_eeg_viz_enabled_config(env: Env) -> bool:
+def get_ephys_visualization_enabled_config(env: Env) -> bool:
     """
-    Get whether the EEG visualization is enabled from the in-database configuration.
+    Get whether the electrophysiology visualization is enabled from the in-database configuration.
     """
 
     eeg_viz_enabled = _try_get_config_value(env, 'useEEGBrowserVisualizationComponents')
     return eeg_viz_enabled == 'true' or eeg_viz_enabled == '1'
 
 
-def get_eeg_chunks_dir_path_config(env: Env) -> Path | None:
+def get_ephys_chunks_dir_path_config(env: Env) -> Path | None:
     """
-    Get the EEG chunks directory path configuration value from the in-database configuration.
+    Get the electrophysiology chunks directory path configuration value from the in-database
+    configuration.
     """
 
-    eeg_chunks_path = _try_get_config_value(env, 'EEGChunksPath')
-    if eeg_chunks_path is None:
+    ephys_chunks_path = _try_get_config_value(env, 'EEGChunksPath')
+    if ephys_chunks_path is None:
         return None
 
-    eeg_chunks_path = Path(eeg_chunks_path)
+    ephys_chunks_path = Path(ephys_chunks_path)
+    check_loris_directory(env, ephys_chunks_path, "electrophysiology chunks")
+    return ephys_chunks_path
 
-    if not eeg_chunks_path.is_dir():
-        log_error_exit(
-            env,
-            (
-                f"The configuration value for the LORIS EEG chunks directory path '{eeg_chunks_path}' does not refer to"
-                " an existing directory."
-            ),
-        )
 
-    if not os.access(eeg_chunks_path, os.R_OK) or not os.access(eeg_chunks_path, os.W_OK):
-        log_error_exit(
-            env,
-            f"Missing read or write permission on the LORIS EEG chunks directory '{eeg_chunks_path}'.",
-        )
-
-    return eeg_chunks_path
-
-
-def get_eeg_pre_package_download_dir_path_config(env: Env) -> Path | None:
+def get_ephys_archive_dir_path_config(env: Env) -> Path | None:
     """
-    Get the EEG pre-packaged download path configuration value from the in-database configuration.
+    Get the electrophysiology archive directory path configuration value from the in-database
+    configuration.
     """
 
-    eeg_pre_package_path = _try_get_config_value(env, 'prePackagedDownloadPath')
-    if eeg_pre_package_path is None:
+    ephys_archive_dir_path = _try_get_config_value(env, 'prePackagedDownloadPath')
+    if ephys_archive_dir_path is None:
         return None
 
-    eeg_pre_package_path = Path(eeg_pre_package_path)
+    ephys_archive_dir_path = Path(ephys_archive_dir_path)
+    check_loris_directory(env, ephys_archive_dir_path, "electrophysiology archive")
+    return ephys_archive_dir_path
 
-    if not eeg_pre_package_path.is_dir():
+
+def check_loris_directory(env: Env, dir_path: Path, display_name: str):
+    """
+    Check that a LORIS directory exists and is readable and writable, or exit the program with an
+    error otherwise.
+    """
+
+    if not dir_path.is_dir():
         log_error_exit(
             env,
             (
-                "The configuration value for the LORIS EEG pre-packaged download directory path"
-                f" '{eeg_pre_package_path}' does not refer to an existing directory."
+                f"The LORIS {display_name} directory path configuration value '{dir_path}' does not refer to an"
+                " existing directory."
             ),
         )
 
-    if not os.access(eeg_pre_package_path, os.R_OK) or not os.access(eeg_pre_package_path, os.W_OK):
+    if not os.access(dir_path, os.R_OK) or not os.access(dir_path, os.W_OK):
         log_error_exit(
             env,
-            (
-                "Missing read or write permission on the LORIS EEG pre-packaged download directory"
-                f" '{eeg_pre_package_path}'."
-            ),
+            f"Missing read or write permission on the {display_name} directory '{dir_path}'.",
         )
 
-    return eeg_pre_package_path
-
 
 def _get_config_value(env: Env, setting_name: str) -> str:
     """

python/lib/db/models/user.py

@@ -1,7 +1,11 @@
 from datetime import date
 
-from sqlalchemy.orm import Mapped, mapped_column
+from sqlalchemy.orm import Mapped, mapped_column, relationship
 
+import lib.db.models.project as db_project
+import lib.db.models.site as db_site
+import lib.db.models.user_project  # type: ignore  # noqa: F401
+import lib.db.models.user_site  # type: ignore  # noqa: F401
 from lib.db.base import Base
 from lib.db.decorators.int_bool import IntBool
 from lib.db.decorators.y_n_bool import YNBool
@@ -11,7 +15,7 @@ class DbUser(Base):
     __tablename__ = 'users'
 
     id                       : Mapped[int]          = mapped_column('ID', primary_key=True)
-    user_id                  : Mapped[str]          = mapped_column('UserID')
+    username                 : Mapped[str]          = mapped_column('UserID')
     password                 : Mapped[str | None]   = mapped_column('Password')
     real_name                : Mapped[str | None]   = mapped_column('Real_name')
     first_name               : Mapped[str | None]   = mapped_column('First_name')
@@ -41,3 +45,13 @@ class DbUser(Base):
     active_from              : Mapped[date | None]  = mapped_column('active_from')
     active_to                : Mapped[date | None]  = mapped_column('active_to')
     account_request_date     : Mapped[date | None]  = mapped_column('account_request_date')
+
+    projects: Mapped[list['db_project.DbProject']] = relationship('DbProject', secondary='user_project_rel')
+    """
+    The projects to which this user belongs to.
+    """
+
+    sites: Mapped[list['db_site.DbSite']] = relationship('DbSite', secondary='user_psc_rel')
+    """
+    The sites to which this user belongs to.
+    """

python/lib/db/models/user_project.py

@@ -0,0 +1,15 @@
+from sqlalchemy import ForeignKey
+from sqlalchemy.orm import Mapped, mapped_column
+
+from lib.db.base import Base
+
+
+class DbUserProject(Base):
+    """
+    Relationship between users and projects.
+    """
+
+    __tablename__ = 'user_project_rel'
+
+    user_id    : Mapped[int] = mapped_column('UserID',    ForeignKey('users.ID'),          primary_key=True)
+    project_id : Mapped[int] = mapped_column('ProjectID', ForeignKey('Project.ProjectID'), primary_key=True)

python/lib/db/models/user_site.py

@@ -0,0 +1,15 @@
+from sqlalchemy import ForeignKey
+from sqlalchemy.orm import Mapped, mapped_column
+
+from lib.db.base import Base
+
+
+class DbUserSite(Base):
+    """
+    Relationship between users and sites.
+    """
+
+    __tablename__ = 'user_psc_rel'
+
+    user_id: Mapped[int] = mapped_column('UserID', ForeignKey('users.ID'), primary_key=True)
+    site_id: Mapped[int] = mapped_column('CenterID', ForeignKey('psc.CenterID'), primary_key=True)

python/lib/db/queries/user.py

@@ -0,0 +1,24 @@
+from sqlalchemy import select
+from sqlalchemy.orm import Session as Database
+
+from lib.db.models.user import DbUser
+
+
+def try_get_user_with_id(db: Database, user_id: int) -> DbUser | None:
+    """
+    Get a user from the database using its ID, or return `None` if no user is found.
+    """
+
+    return db.execute(select(DbUser)
+        .where(DbUser.id == user_id)
+    ).scalar_one_or_none()
+
+
+def try_get_user_with_username(db: Database, username: str) -> DbUser | None:
+    """
+    Get a user from the database using its username, or return `None` if no user is found.
+    """
+
+    return db.execute(select(DbUser)
+        .where(DbUser.username == username)
+    ).scalar_one_or_none()

python/lib/eeg.py

@@ -14,7 +14,7 @@
 
 import lib.exitcode
 import lib.utilities as utilities
-from lib.config import get_eeg_viz_enabled_config
+from lib.config import get_ephys_visualization_enabled_config
 from lib.db.models.physio_file import DbPhysioFile
 from lib.db.models.session import DbSession
 from lib.db.queries.physio_file import try_get_physio_file_with_path
@@ -206,7 +206,7 @@ def register_data(self, derivatives=False, detect=True):
             import_physio_file_archive(self.env, eeg_file, files_to_archive)
 
             # create data chunks for React visualization
-            if get_eeg_viz_enabled_config(self.env):
+            if get_ephys_visualization_enabled_config(self.env):
                 create_physio_channels_chunks(self.env, eeg_file)
 
     def fetch_and_insert_eeg_files(self, derivatives=False, detect=True):

python/lib/import_bids_dataset/archive.py

@@ -4,7 +4,7 @@
 from loris_utils.crypto import compute_file_blake2b_hash
 from loris_utils.path import remove_path_extension
 
-from lib.config import get_data_dir_path_config, get_eeg_pre_package_download_dir_path_config
+from lib.config import get_data_dir_path_config, get_ephys_archive_dir_path_config
 from lib.db.models.physio_event_archive import DbPhysioEventArchive
 from lib.db.models.physio_file import DbPhysioFile
 from lib.db.models.physio_file_archive import DbPhysioFileArchive
@@ -70,9 +70,9 @@ def get_archive_path(env: Env, file_path: Path) -> Path:
     """
 
     archive_rel_path = remove_path_extension(file_path).with_suffix('.tgz')
-    archives_dir_path = get_eeg_pre_package_download_dir_path_config(env)
-    if archives_dir_path is not None:
+    archive_dir_path = get_ephys_archive_dir_path_config(env)
+    if archive_dir_path is not None:
         data_dir_path = get_data_dir_path_config(env)
-        return (archives_dir_path / 'raw' / archive_rel_path.name).relative_to(data_dir_path)
+        return (archive_dir_path / 'raw' / archive_rel_path.name).relative_to(data_dir_path)
     else:
         return archive_rel_path

python/lib/import_bids_dataset/main.py

@@ -23,7 +23,7 @@
 )
 from lib.import_bids_dataset.env import BidsImportEnv
 from lib.import_bids_dataset.events import get_root_events_metadata
-from lib.import_bids_dataset.meg import import_bids_meg_data_type
+from lib.import_bids_dataset.meg.ctf import import_bids_meg_data_type
 from lib.import_bids_dataset.mri import import_bids_mri_data_type
 from lib.import_bids_dataset.print import print_bids_import_summary
 from lib.logging import log, log_error_exit, log_warning
@@ -93,7 +93,7 @@ def import_bids_dataset(env: Env, args: Args, legacy_db: Database):
 
     import_env = BidsImportEnv(
         data_dir_path     = data_dir_path,
-        loris_bids_path   = loris_bids_path,
+        loris_bids_path   = loris_bids_path.relative_to(data_dir_path) if loris_bids_path is not None else None,
         total_files_count = acquisitions_count,
     )