SQLAlchemy proof-of-concept

python/lib/db/base.py

@@ -0,0 +1,9 @@
+from sqlalchemy.orm import DeclarativeBase
+
+
+class Base(DeclarativeBase):
+    """
+    Base SQLAlchemy class that must be inherited by all the ORM model classes.
+    """
+
+    pass

python/lib/db/connect.py

@@ -0,0 +1,17 @@
+from typing import Any
+from sqlalchemy import create_engine
+from sqlalchemy.orm import Session
+
+
+default_port = 3306
+
+
+def connect_to_db(credentials: dict[str, Any]):
+    host     = credentials['host']
+    port     = credentials['port']
+    username = credentials['username']
+    password = credentials['passwd']
+    database = credentials['database']
+    port     = int(port) if port else default_port
+    engine = create_engine(f'mariadb+mysqlconnector://{username}:{password}@{host}:{port}/{database}')
+    return Session(engine)

python/lib/db/orm/dicom_archive.py

@@ -0,0 +1,51 @@
+from datetime import date, datetime
+from typing import List, Optional
+from sqlalchemy import String
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+from lib.db.base import Base
+import lib.db.orm.dicom_archive_file as db_dicom_archive_file
+import lib.db.orm.dicom_archive_series as db_dicom_archive_series
+import lib.db.orm.mri_upload as db_mri_upload
+
+
+class DbDicomArchive(Base):
+    __tablename__ = 'tarchive'
+
+    id                       : Mapped[int]                = mapped_column('TarchiveID', primary_key=True)
+    series                   : Mapped[List['db_dicom_archive_series.DbDicomArchiveSeries']] \
+        = relationship('DbDicomArchiveSeries', back_populates='archive')
+    files                    : Mapped[List['db_dicom_archive_file.DbDicomArchiveFile']] \
+        = relationship('DbDicomArchiveFile', back_populates='archive')
+    upload                   : Mapped[Optional['db_mri_upload.DbMriUpload']] \
+        = relationship('DbMriUpload', back_populates='dicom_archive')
+    study_uid                : Mapped[str]                = mapped_column('DicomArchiveID', type_ = String())
+    patient_id               : Mapped[str]                = mapped_column('PatientID')
+    patient_name             : Mapped[str]                = mapped_column('PatientName')
+    patient_birthdate        : Mapped[Optional[date]]     = mapped_column('PatientDoB')
+    patient_sex              : Mapped[Optional[str]]      = mapped_column('PatientSex')
+    neuro_db_center_name     : Mapped[Optional[str]]      = mapped_column('neurodbCenterName')
+    center_name              : Mapped[str]                = mapped_column('CenterName')
+    last_update              : Mapped[Optional[date]]     = mapped_column('LastUpdate')
+    date_acquired            : Mapped[Optional[date]]     = mapped_column('DateAcquired')
+    date_first_archived      : Mapped[Optional[datetime]] = mapped_column('DateFirstArchived')
+    date_last_archived       : Mapped[Optional[datetime]] = mapped_column('DateLastArchived')
+    acquisition_count        : Mapped[int]                = mapped_column('AcquisitionCount')
+    dicom_file_count         : Mapped[int]                = mapped_column('DicomFileCount')
+    non_dicom_file_count     : Mapped[int]                = mapped_column('NonDicomFileCount')
+    md5_sum_dicom_only       : Mapped[Optional[str]]      = mapped_column('md5sumDicomOnly')
+    md5_sum_archive          : Mapped[Optional[str]]      = mapped_column('md5sumArchive')
+    creating_user            : Mapped[str]                = mapped_column('CreatingUser')
+    sum_type_version         : Mapped[int]                = mapped_column('sumTypeVersion')
+    tar_type_version         : Mapped[Optional[int]]      = mapped_column('tarTypeVersion')
+    source_location          : Mapped[str]                = mapped_column('SourceLocation')
+    archive_location         : Mapped[Optional[str]]      = mapped_column('ArchiveLocation')
+    scanner_manufacturer     : Mapped[str]                = mapped_column('ScannerManufacturer')
+    scanner_model            : Mapped[str]                = mapped_column('ScannerModel')
+    scanner_serial_number    : Mapped[str]                = mapped_column('ScannerSerialNumber')
+    scanner_software_version : Mapped[str]                = mapped_column('ScannerSoftwareVersion')
+    session_id               : Mapped[Optional[int]]      = mapped_column('SessionID')
+    upload_attempt           : Mapped[int]                = mapped_column('uploadAttempt')
+    create_info              : Mapped[Optional[str]]      = mapped_column('CreateInfo')
+    acquisition_metadata     : Mapped[str]                = mapped_column('AcquisitionMetadata')
+    date_sent                : Mapped[Optional[datetime]] = mapped_column('DateSent')
+    pending_transfer         : Mapped[int]                = mapped_column('PendingTransfer')

python/lib/db/orm/dicom_archive_file.py

@@ -0,0 +1,25 @@
+from typing import Optional
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+from sqlalchemy import ForeignKey
+from lib.db.base import Base
+import lib.db.orm.dicom_archive as db_dicom_archive
+import lib.db.orm.dicom_archive_series as db_dicom_archive_series
+
+
+class DbDicomArchiveFile(Base):
+    __tablename__ = 'tarchive_files'
+
+    id                 : Mapped[int]           = mapped_column('TarchiveFileID', primary_key=True)
+    archive_id         : Mapped[int]           = mapped_column('TarchiveID', ForeignKey('tarchive.TarchiveID'))
+    archive            : Mapped['db_dicom_archive.DbDicomArchive'] \
+        = relationship('DbDicomArchive', back_populates='files')
+    series_id          : Mapped[Optional[int]] \
+        = mapped_column('TarchiveSeriesID', ForeignKey('tarchive_series.TarchiveSeriesID'))
+    series             : Mapped[Optional['db_dicom_archive_series.DbDicomArchiveSeries']] \
+        = relationship('DbDicomArchiveSeries', back_populates="files")
+    series_number      : Mapped[Optional[int]] = mapped_column('SeriesNumber')
+    series_description : Mapped[Optional[str]] = mapped_column('SeriesDescription')
+    file_number        : Mapped[Optional[int]] = mapped_column('FileNumber')
+    echo_number        : Mapped[Optional[int]] = mapped_column('EchoNumber')
+    md5_sum            : Mapped[str]           = mapped_column('Md5Sum')
+    file_name          : Mapped[str]           = mapped_column('FileName')

python/lib/db/orm/dicom_archive_series.py

@@ -0,0 +1,28 @@
+from typing import List, Optional
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+from sqlalchemy import ForeignKey
+from lib.db.base import Base
+import lib.db.orm.dicom_archive as db_dicom_archive
+import lib.db.orm.dicom_archive_file as db_dicom_archive_file
+
+
+class DbDicomArchiveSeries(Base):
+    __tablename__ = 'tarchive_series'
+
+    id                 : Mapped[int]             = mapped_column('TarchiveSeriesID', primary_key=True)
+    archive_id         : Mapped[int]             = mapped_column('TarchiveID', ForeignKey("tarchive.TarchiveID"))
+    archive            : Mapped['db_dicom_archive.DbDicomArchive'] \
+        = relationship('DbDicomArchive', back_populates="series")
+    files              : Mapped[List['db_dicom_archive_file.DbDicomArchiveFile']] \
+        = relationship('DbDicomArchiveFile', back_populates="series")
+    series_number      : Mapped[int]             = mapped_column('SeriesNumber')
+    series_description : Mapped[Optional[str]]   = mapped_column('SeriesDescription')
+    sequence_name      : Mapped[Optional[str]]   = mapped_column('SequenceName')
+    echo_time          : Mapped[Optional[float]] = mapped_column('EchoTime')
+    repetition_time    : Mapped[Optional[float]] = mapped_column('RepetitionTime')
+    inversion_time     : Mapped[Optional[float]] = mapped_column('InversionTime')
+    slice_thickness    : Mapped[Optional[float]] = mapped_column('SliceThickness')
+    phase_encoding     : Mapped[Optional[str]]   = mapped_column('PhaseEncoding')
+    number_of_files    : Mapped[int]             = mapped_column('NumberOfFiles')
+    series_uid         : Mapped[Optional[str]]   = mapped_column('SeriesUID')
+    modality           : Mapped[Optional[str]]   = mapped_column('Modality')

python/lib/db/orm/mri_upload.py

@@ -0,0 +1,29 @@
+from datetime import datetime
+from typing import Optional
+from sqlalchemy import ForeignKey
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+from lib.db.base import Base
+import lib.db.orm.dicom_archive as db_dicom_archive
+
+
+class DbMriUpload(Base):
+    __tablename__ = 'mri_upload'
+
+    id                          : Mapped[int]                = mapped_column('UploadID', primary_key=True)
+    uploaded_by                 : Mapped[str]                = mapped_column('UploadedBy')
+    upload_date                 : Mapped[Optional[datetime]] = mapped_column('UploadDate')
+    upload_location             : Mapped[str]                = mapped_column('UploadLocation')
+    decompressed_location       : Mapped[str]                = mapped_column('DecompressedLocation')
+    insertion_complete          : Mapped[bool]               = mapped_column('InsertionComplete')
+    inserting                   : Mapped[Optional[bool]]     = mapped_column('Inserting')
+    patient_name                : Mapped[str]                = mapped_column('PatientName')
+    number_of_minc_inserted     : Mapped[Optional[int]]      = mapped_column('number_of_mincInserted')
+    number_of_minc_created      : Mapped[Optional[int]]      = mapped_column('number_of_mincCreated')
+    dicom_archive_id            : Mapped[Optional[int]] \
+        = mapped_column('TarchiveID', ForeignKey('tarchive.TarchiveID'))
+    dicom_archive               : Mapped[Optional['db_dicom_archive.DbDicomArchive']] \
+        = relationship('DicomArchive', back_populates='upload')
+    session_id                  : Mapped[Optional[int]]      = mapped_column('SessionID')
+    is_candidate_info_validated : Mapped[Optional[bool]]     = mapped_column('IsCandidateInfoValidated')
+    is_dicom_archive_validated  : Mapped[bool]               = mapped_column('IsTarchiveValidated')
+    is_phantom                  : Mapped[str]                = mapped_column('IsPhantom')

python/lib/db/orm/session.py

@@ -0,0 +1,44 @@
+from datetime import date, datetime
+from typing import Optional
+from sqlalchemy.orm import Mapped, mapped_column
+from lib.db.base import Base
+
+
+class DbSession(Base):
+    __tablename__ = 'session'
+
+    id                       : Mapped[int]                = mapped_column('ID', primary_key=True)
+    cand_id                  : Mapped[int]                = mapped_column('CandID')
+    center_id                : Mapped[int]                = mapped_column('CenterID')
+    project_id               : Mapped[int]                = mapped_column('ProjectID')
+    visit_no                 : Mapped[Optional[int]]      = mapped_column('VisitNo')
+    visit_label              : Mapped[str]                = mapped_column('Visit_label')
+    cohort_id                : Mapped[int]                = mapped_column('CohortID')
+    submitted                : Mapped[str]                = mapped_column('Submitted')
+    current_stage            : Mapped[str]                = mapped_column('Current_stage')
+    date_stage_change        : Mapped[Optional[date]]     = mapped_column('Date_stage_change')
+    screening                : Mapped[Optional[str]]      = mapped_column('Screening')
+    date_screening           : Mapped[date]               = mapped_column('Date_screening')
+    visit                    : Mapped[Optional[str]]      = mapped_column('Visit')
+    date_visit               : Mapped[Optional[date]]     = mapped_column('Date_visit')
+    date_status_change       : Mapped[Optional[date]]     = mapped_column('Date_status_change')
+    approval                 : Mapped[Optional[str]]      = mapped_column('Approval')
+    date_approval            : Mapped[Optional[date]]     = mapped_column('Date_approval')
+    active                   : Mapped[str]                = mapped_column('Active')
+    date_active              : Mapped[Optional[date]]     = mapped_column('Date_active')
+    registered_by            : Mapped[Optional[str]]      = mapped_column('RegisteredBy')
+    user_id                  : Mapped[str]                = mapped_column('UserID')
+    date_registered          : Mapped[Optional[date]]     = mapped_column('Date_registered')
+    test_date                : Mapped[int]                = mapped_column('Testdate')
+    hardcopy_request         : Mapped[str]                = mapped_column('Hardcopy_request')
+    bvl_qc_status            : Mapped[Optional[str]]      = mapped_column('BVLQCStaus')
+    bvl_qc_type              : Mapped[Optional[str]]      = mapped_column('BVLQCType')
+    bvl_qc_exclusion         : Mapped[Optional[str]]      = mapped_column('BVLQCExclusion')
+    qcd                      : Mapped[Optional[str]]      = mapped_column('QCd')
+    scan_done                : Mapped[Optional[str]]      = mapped_column('Scan_done')
+    mri_qc_status            : Mapped[str]                = mapped_column('MRIQCStatus')
+    mri_qc_pending           : Mapped[str]                = mapped_column('MRIQCPending')
+    mri_qc_first_change_time : Mapped[Optional[datetime]] = mapped_column('MRIQCFirstChange')
+    mri_qc_last_change_time  : Mapped[Optional[datetime]] = mapped_column('MRIQCLastChange')
+    mri_caveat               : Mapped[str]                = mapped_column('MRICaveat')
+    language_id              : Mapped[Optional[int]]      = mapped_column('languageID')

python/requirements.txt

@@ -1,19 +1,20 @@
+boto3
+flake8
+google
+mat73
+matplotlib
 mne
 mne-bids>=0.6
-protobuf>=3.0.0
-pybids==0.14.0
-mysqlclient
 mysql-connector
-google
-matplotlib
-nose
+mysqlclient
 nilearn
-scikit-learn
-virtualenv
-python-dateutil
 nibabel
+nose
 numpy
+protobuf>=3.0.0
+pybids==0.17.0
+python-dateutil
+scikit-learn
 scipy
-flake8
-boto3
-mat73
+sqlalchemy>=2.0.0
+virtualenv