Maxime staging PR

.github/labeler.yml

@@ -5,3 +5,7 @@
 "Language: Python":
 - changed-files:
   - any-glob-to-any-file: '**/*.py'
+
+"Package: EEG chunker":
+- changed-files:
+  - any-glob-to-any-file: 'python/loris_eeg_chunker/**'

install/templates/environment_template

@@ -6,7 +6,7 @@ source ${MINC_TOOLKIT_DIR}/minc-toolkit-config.sh
 umask 0002
 
 # export PATH, PERL5LIB, TMPDIR and LORIS_CONFIG variables
-export PATH=/opt/${PROJECT}/bin/mri:/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/uploadNeuroDB/bin:/opt/${PROJECT}/bin/mri/dicom-archive:/opt/${PROJECT}/bin/mri/python/scripts:/opt/${PROJECT}/bin/mri/tools:/opt/${PROJECT}/bin/mri/python/loris_eeg_chunker:${MINC_TOOLKIT_DIR}/bin:/usr/local/bin/tpcclib:$PATH
+export PATH=/opt/${PROJECT}/bin/mri:/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/uploadNeuroDB/bin:/opt/${PROJECT}/bin/mri/dicom-archive:/opt/${PROJECT}/bin/mri/python/scripts:/opt/${PROJECT}/bin/mri/tools:${MINC_TOOLKIT_DIR}/bin:/usr/local/bin/tpcclib:$PATH
 export PERL5LIB=/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/dicom-archive:$PERL5LIB
 export TMPDIR=/tmp
 export LORIS_CONFIG=/opt/${PROJECT}/bin/mri/config

pyproject.toml

@@ -12,24 +12,21 @@ license-files = ["LICENSE"]
 requires-python = ">= 3.11"
 dependencies = [
     "boto3==1.35.99",
-    "google",
     "mat73",
     "matplotlib",
-    "mne",
-    "mne-bids>=0.14",
     "mysqlclient",
     "nibabel",
     "nilearn",
     "nose",
     "numpy",
-    "protobuf>=3.0.0",
     "pybids==0.17.0",
     "pydicom",
     "python-dateutil",
     "scikit-learn",
     "scipy",
     "sqlalchemy>=2.0.0",
     "virtualenv",
+    "loris-eeg-chunker @ {root:uri}/python/loris_eeg_chunker",
 ]
 
 [project.optional-dependencies]
@@ -42,10 +39,12 @@ dev = [
 [project.urls]
 Homepage = "https://github.com/aces/loris-mri"
 
+[tool.hatch.metadata]
+allow-direct-references = true
+
 [tool.hatch.build.targets.wheel]
 packages = [
     "python/lib",
-    "python/loris_eeg_chunker",
     "python/tests",
 ]
 

python/lib/config.py

@@ -1,4 +1,5 @@
 import os
+from pathlib import Path
 from typing import Literal
 
 from lib.db.queries.config import try_get_config_with_setting_name
@@ -26,15 +27,15 @@ def get_patient_id_dicom_header_config(env: Env) -> Literal['PatientID', 'Patien
     return patient_id_dicom_header
 
 
-def get_data_dir_path_config(env: Env) -> str:
+def get_data_dir_path_config(env: Env) -> Path:
     """
     Get the LORIS base data directory path from the in-database configuration, or exit the program
     with an error if that configuration value does not exist or is incorrect.
     """
 
-    data_dir_path = os.path.normpath(_get_config_value(env, 'dataDirBasepath'))
+    data_dir_path = Path(_get_config_value(env, 'dataDirBasepath'))
 
-    if not os.path.isdir(data_dir_path):
+    if not data_dir_path.is_dir():
         log_error_exit(
             env,
             (
@@ -52,20 +53,20 @@ def get_data_dir_path_config(env: Env) -> str:
     return data_dir_path
 
 
-def get_dicom_archive_dir_path_config(env: Env) -> str:
+def get_dicom_archive_dir_path_config(env: Env) -> Path:
     """
     Get the LORIS DICOM archive directory path from the in-database configuration, or exit the
     program with an error if that configuration value does not exist or is incorrect.
     """
 
-    dicom_archive_dir_path = os.path.normpath(_get_config_value(env, 'tarchiveLibraryDir'))
+    dicom_archive_dir_path = Path(_get_config_value(env, 'tarchiveLibraryDir'))
 
-    if not os.path.isdir(dicom_archive_dir_path):
+    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 diretory."
+                " to an existing directory."
             ),
         )
 

python/lib/db/decorators/string_path.py

@@ -0,0 +1,28 @@
+from pathlib import Path
+
+from sqlalchemy import String
+from sqlalchemy.engine import Dialect
+from sqlalchemy.types import TypeDecorator
+
+
+class StringPath(TypeDecorator[Path]):
+    """
+    Decorator for a database path type.
+    In SQL, the type will appear as a string.
+    In Python, the type will appear as a path object.
+    """
+
+    impl = String
+    cache_ok = True
+
+    def process_bind_param(self, value: Path | None, dialect: Dialect) -> str | None:
+        if value is None:
+            return None
+
+        return str(value)
+
+    def process_result_value(self, value: str | None, dialect: Dialect) -> Path | None:
+        if value is None:
+            return None
+
+        return Path(value)

python/lib/db/models/dicom_archive.py

@@ -1,4 +1,5 @@
 from datetime import date, datetime
+from pathlib import Path
 from typing import Optional
 
 from sqlalchemy import ForeignKey
@@ -12,6 +13,7 @@
 import lib.db.models.session as db_session
 from lib.db.base import Base
 from lib.db.decorators.int_bool import IntBool
+from lib.db.decorators.string_path import StringPath
 
 
 class DbDicomArchive(Base):
@@ -37,8 +39,8 @@ class DbDicomArchive(Base):
     creating_user            : Mapped[str]             = mapped_column('CreatingUser')
     sum_type_version         : Mapped[int]             = mapped_column('sumTypeVersion')
     tar_type_version         : Mapped[int | None]      = mapped_column('tarTypeVersion')
-    source_location          : Mapped[str]             = mapped_column('SourceLocation')
-    archive_location         : Mapped[str | None]      = mapped_column('ArchiveLocation')
+    source_path              : Mapped[Path]            = mapped_column('SourceLocation', StringPath)
+    archive_path             : Mapped[Path | None]     = mapped_column('ArchiveLocation', StringPath)
     scanner_manufacturer     : Mapped[str]             = mapped_column('ScannerManufacturer')
     scanner_model            : Mapped[str]             = mapped_column('ScannerModel')
     scanner_serial_number    : Mapped[str]             = mapped_column('ScannerSerialNumber')

python/lib/db/models/file.py

@@ -1,4 +1,5 @@
 from datetime import date, datetime
+from pathlib import Path
 
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
@@ -8,14 +9,15 @@
 from lib.db.base import Base
 from lib.db.decorators.int_bool import IntBool
 from lib.db.decorators.int_datetime import IntDatetime
+from lib.db.decorators.string_path import StringPath
 
 
 class DbFile(Base):
     __tablename__ = 'files'
 
     id                             : Mapped[int]          = mapped_column('FileID', primary_key=True)
     session_id                     : Mapped[int]          = mapped_column('SessionID', ForeignKey('session.ID'))
-    rel_path                       : Mapped[str]          = mapped_column('File')
+    path                           : Mapped[Path]         = mapped_column('File', StringPath)
     series_uid                     : Mapped[str | None]   = mapped_column('SeriesUID')
     echo_time                      : Mapped[float | None] = mapped_column('EchoTime')
     phase_encoding_direction       : Mapped[str | None]   = mapped_column('PhaseEncodingDirection')

python/lib/db/models/mri_protocol_violated_scan.py

@@ -1,4 +1,5 @@
 from datetime import datetime
+from pathlib import Path
 from typing import Optional
 
 from sqlalchemy import ForeignKey
@@ -8,6 +9,7 @@
 import lib.db.models.dicom_archive as db_dicom_archive
 import lib.db.models.mri_protocol_group as db_mri_protocol_group
 from lib.db.base import Base
+from lib.db.decorators.string_path import StringPath
 
 
 class DbMriProtocolViolatedScan(Base):
@@ -19,7 +21,7 @@ class DbMriProtocolViolatedScan(Base):
     dicom_archive_id         : Mapped[int | None]      = mapped_column('TarchiveID', ForeignKey('tarchive.TarchiveID'))
     time_run                 : Mapped[datetime | None] = mapped_column('time_run')
     series_description       : Mapped[str | None]      = mapped_column('series_description')
-    file_rel_path            : Mapped[str | None]      = mapped_column('minc_location')
+    file_path                : Mapped[Path | None]     = mapped_column('minc_location', StringPath)
     patient_name             : Mapped[str | None]      = mapped_column('PatientName')
     tr_range                 : Mapped[str | None]      = mapped_column('TR_range')
     te_range                 : Mapped[str | None]      = mapped_column('TE_range')

python/lib/db/models/mri_upload.py

@@ -1,4 +1,5 @@
 from datetime import datetime
+from pathlib import Path
 from typing import Optional
 
 from sqlalchemy import ForeignKey
@@ -8,6 +9,7 @@
 import lib.db.models.session as db_session
 from lib.db.base import Base
 from lib.db.decorators.int_bool import IntBool
+from lib.db.decorators.string_path import StringPath
 from lib.db.decorators.y_n_bool import YNBool
 
 
@@ -17,8 +19,8 @@ class DbMriUpload(Base):
     id                          : Mapped[int]             = mapped_column('UploadID', primary_key=True)
     uploaded_by                 : Mapped[str]             = mapped_column('UploadedBy')
     upload_date                 : Mapped[datetime | None] = mapped_column('UploadDate')
-    upload_location             : Mapped[str]             = mapped_column('UploadLocation')
-    decompressed_location       : Mapped[str]             = mapped_column('DecompressedLocation')
+    upload_path                 : Mapped[Path]            = mapped_column('UploadLocation', StringPath)
+    decompressed_path           : Mapped[Path]            = mapped_column('DecompressedLocation', StringPath)
     insertion_complete          : Mapped[bool]            = mapped_column('InsertionComplete', IntBool)
     inserting                   : Mapped[bool | None]     = mapped_column('Inserting', IntBool)
     patient_name                : Mapped[str]             = mapped_column('PatientName')

python/lib/db/models/mri_violation_log.py

@@ -1,4 +1,5 @@
 from datetime import datetime
+from pathlib import Path
 from typing import Optional
 
 from sqlalchemy import ForeignKey
@@ -9,6 +10,7 @@
 import lib.db.models.mri_protocol_check_group as db_mri_protocol_check_group
 import lib.db.models.mri_scan_type as db_mri_scan_type
 from lib.db.base import Base
+from lib.db.decorators.string_path import StringPath
 
 
 class DbMriViolationLog(Base):
@@ -19,7 +21,7 @@ class DbMriViolationLog(Base):
     series_uid              : Mapped[str | None]       = mapped_column('SeriesUID')
     dicom_archive_id        : Mapped[int | None]       \
         = mapped_column('TarchiveID', ForeignKey('tarchive.TarchiveID'))
-    file_rel_path           : Mapped[str | None]       = mapped_column('MincFile')
+    file_path               : Mapped[Path | None]      = mapped_column('MincFile', StringPath)
     patient_name            : Mapped[str | None]       = mapped_column('PatientName')
     candidate_id            : Mapped[int | None]       = mapped_column('CandidateID', ForeignKey('candidate.ID'))
     visit_label             : Mapped[str | None]       = mapped_column('Visit_label')

python/lib/db/models/physio_channel.py

@@ -1,5 +1,6 @@
 from datetime import datetime
 from decimal import Decimal
+from pathlib import Path
 
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
@@ -8,6 +9,7 @@
 import lib.db.models.physio_file as db_physio_file
 import lib.db.models.physio_status_type as db_physio_status_type
 from lib.db.base import Base
+from lib.db.decorators.string_path import StringPath
 
 
 class DbPhysioChannel(Base):
@@ -28,7 +30,7 @@ class DbPhysioChannel(Base):
     reference          : Mapped[str | None]     = mapped_column('Reference')
     status_description : Mapped[str | None]     = mapped_column('StatusDescription')
     unit               : Mapped[str | None]     = mapped_column('Unit')
-    file_path          : Mapped[str | None]     = mapped_column('FilePath')
+    file_path          : Mapped[Path | None]    = mapped_column('FilePath', StringPath)
 
     physio_file  : Mapped['db_physio_file.DbPhysioFile']                = relationship('DbPhysioFile', back_populates='channels')
     channel_type : Mapped['db_physio_channel_type.DbPhysioChannelType'] = relationship('DbPhysioChannelType')

python/lib/db/models/physio_coord_system.py

@@ -1,3 +1,5 @@
+from pathlib import Path
+
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
@@ -6,17 +8,18 @@
 import lib.db.models.physio_coord_system_unit as db_physio_coord_system_unit
 import lib.db.models.physio_modality as db_physio_modality
 from lib.db.base import Base
+from lib.db.decorators.string_path import StringPath
 
 
 class DbPhysioCoordSystem(Base):
     __tablename__ = 'physiological_coord_system'
 
-    id          : Mapped[int]        = mapped_column('PhysiologicalCoordSystemID', primary_key=True)
-    name_id     : Mapped[int]        = mapped_column('NameID', ForeignKey('physiological_coord_system_name.PhysiologicalCoordSystemNameID'))
-    type_id     : Mapped[int]        = mapped_column('TypeID', ForeignKey('physiological_coord_system_type.PhysiologicalCoordSystemTypeID'))
-    unit_id     : Mapped[int]        = mapped_column('UnitID', ForeignKey('physiological_coord_system_unit.PhysiologicalCoordSystemUnitID'))
-    modality_id : Mapped[int]        = mapped_column('ModalityID', ForeignKey('physiological_modality.PhysiologicalModalityID'))
-    file_path   : Mapped[str | None] = mapped_column('FilePath')
+    id          : Mapped[int]         = mapped_column('PhysiologicalCoordSystemID', primary_key=True)
+    name_id     : Mapped[int]         = mapped_column('NameID', ForeignKey('physiological_coord_system_name.PhysiologicalCoordSystemNameID'))
+    type_id     : Mapped[int]         = mapped_column('TypeID', ForeignKey('physiological_coord_system_type.PhysiologicalCoordSystemTypeID'))
+    unit_id     : Mapped[int]         = mapped_column('UnitID', ForeignKey('physiological_coord_system_unit.PhysiologicalCoordSystemUnitID'))
+    modality_id : Mapped[int]         = mapped_column('ModalityID', ForeignKey('physiological_modality.PhysiologicalModalityID'))
+    file_path   : Mapped[Path | None] = mapped_column('FilePath', StringPath)
 
     name     : Mapped['db_physio_coord_system_name.DbPhysioCoordSystemName'] = relationship('DbPhysioCoordSystemName')
     type     : Mapped['db_physio_coord_system_type.DbPhysioCoordSystemType'] = relationship('DbPhysioCoordSystemType')

python/lib/db/models/physio_event_file.py

@@ -1,4 +1,5 @@
 from datetime import datetime
+from pathlib import Path
 
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
@@ -9,18 +10,19 @@
 import lib.db.models.physio_task_event as db_physio_task_event
 import lib.db.models.project as db_project
 from lib.db.base import Base
+from lib.db.decorators.string_path import StringPath
 
 
 class DbPhysioEventFile(Base):
     __tablename__ = 'physiological_event_file'
 
-    id             : Mapped[int]        = mapped_column('EventFileID', primary_key=True)
-    physio_file_id : Mapped[int | None] = mapped_column('PhysiologicalFileID', ForeignKey('physiological_file.PhysiologicalFileID'))
-    project_id     : Mapped[int | None] = mapped_column('ProjectID', ForeignKey('Project.ProjectID'))
-    file_type      : Mapped[str]        = mapped_column('FileType', ForeignKey('ImagingFileTypes.type'))
-    file_path      : Mapped[str | None] = mapped_column('FilePath')
-    last_update    : Mapped[datetime]   = mapped_column('LastUpdate')
-    last_written   : Mapped[datetime]   = mapped_column('LastWritten')
+    id             : Mapped[int]         = mapped_column('EventFileID', primary_key=True)
+    physio_file_id : Mapped[int | None]  = mapped_column('PhysiologicalFileID', ForeignKey('physiological_file.PhysiologicalFileID'))
+    project_id     : Mapped[int | None]  = mapped_column('ProjectID', ForeignKey('Project.ProjectID'))
+    file_type      : Mapped[str]         = mapped_column('FileType', ForeignKey('ImagingFileTypes.type'))
+    file_path      : Mapped[Path | None] = mapped_column('FilePath', StringPath)
+    last_update    : Mapped[datetime]    = mapped_column('LastUpdate')
+    last_written   : Mapped[datetime]    = mapped_column('LastWritten')
 
     physio_file       : Mapped['db_physio_file.DbPhysioFile | None']                     = relationship('PhysiologicalFile')
     project           : Mapped['db_project.DbProject | None']                            = relationship('Project')

python/lib/db/models/physio_file.py

@@ -1,4 +1,5 @@
 from datetime import datetime
+from pathlib import Path
 
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
@@ -7,6 +8,7 @@
 import lib.db.models.physio_modality as db_physio_modality
 import lib.db.models.physio_output_type as db_physio_output_type
 from lib.db.base import Base
+from lib.db.decorators.string_path import StringPath
 
 
 class DbPhysioFile(Base):
@@ -20,7 +22,7 @@ class DbPhysioFile(Base):
     file_type        : Mapped[str | None]      = mapped_column('FileType')
     acquisition_time : Mapped[datetime | None] = mapped_column('AcquisitionTime')
     inserted_by_user : Mapped[str]             = mapped_column('InsertedByUser')
-    path             : Mapped[str]             = mapped_column('FilePath')
+    path             : Mapped[Path]            = mapped_column('FilePath', StringPath)
     index            : Mapped[int | None]      = mapped_column('Index')
     parent_id        : Mapped[int | None]      = mapped_column('ParentID')
 

python/lib/db/queries/dicom_archive.py

@@ -1,4 +1,6 @@
 
+from pathlib import Path
+
 from sqlalchemy import delete, select
 from sqlalchemy.orm import Session as Database
 
@@ -29,14 +31,14 @@ def try_get_dicom_archive_with_patient_name(db: Database, patient_name: str) ->
     ).scalar_one_or_none()
 
 
-def try_get_dicom_archive_with_archive_location(db: Database, archive_location: str) -> DbDicomArchive | None:
+def try_get_dicom_archive_with_archive_path(db: Database, archive_path: Path) -> DbDicomArchive | None:
     """
-    Get a DICOM archive from the database using its archive location, or return `None` if no DICOM
+    Get a DICOM archive from the database using its archive path, or return `None` if no DICOM
     archive is found.
     """
 
     return db.execute(select(DbDicomArchive)
-        .where(DbDicomArchive.archive_location.like(f'%{archive_location}%'))
+        .where(DbDicomArchive.archive_path.like(f'%{archive_path}%'))
     ).scalar_one_or_none()