factorize subject session

pyproject.toml

@@ -17,6 +17,7 @@ include = [
     "python/tests",
     "python/lib/db",
     "python/lib/exception",
+    "python/lib/get_subject_session.py",
     "python/lib/validate_subject_ids.py",
 ]
 typeCheckingMode = "strict"

python/lib/database_lib/session_db.py

@@ -1,9 +1,11 @@
 """This class performs session table related database queries and common checks"""
 
+from typing_extensions import deprecated
 
 __license__ = "GPLv3"
 
 
+@deprecated('Use `lib.db.model.session.DbSession` instead')
 class SessionDB:
     """
     This class performs database queries for session table.
@@ -35,6 +37,7 @@ def __init__(self, db, verbose):
         self.db = db
         self.verbose = verbose
 
+    @deprecated('Use `lib.db.query.try_get_candidate_with_cand_id_visit_label` instead')
     def create_session_dict(self, cand_id, visit_label):
         """
         Queries the session table for a particular candidate ID and visit label and returns a dictionary
@@ -56,6 +59,7 @@ def create_session_dict(self, cand_id, visit_label):
 
         return results[0] if results else None
 
+    @deprecated('Use `lib.db.query.site.try_get_site_with_psc_id_visit_label` instead')
     def get_session_center_info(self, pscid, visit_label):
         """
         Get site information for a given visit.
@@ -77,6 +81,7 @@ def get_session_center_info(self, pscid, visit_label):
 
         return results[0] if results else None
 
+    @deprecated('Use `lib.get_subject_session.get_candidate_next_visit_number` instead')
     def determine_next_session_site_id_and_visit_number(self, cand_id):
         """
         Determines the next session site and visit number based on the last session inserted for a given candidate.
@@ -99,6 +104,7 @@ def determine_next_session_site_id_and_visit_number(self, cand_id):
 
         return results[0] if results else None
 
+    @deprecated('Use `lib.db.model.session.DbSession` instead')
     def insert_into_session(self, fields, values):
         """
         Insert a new row in the session table using fields list as column names and values as values.

python/lib/db/model/candidate.py

@@ -1,7 +1,9 @@
 from datetime import date
-from typing import Optional
-from sqlalchemy.orm import Mapped, mapped_column
+from typing import List, Optional
+from sqlalchemy.orm import Mapped, mapped_column, relationship
 from lib.db.base import Base
+import lib.db.model.session as db_session
+import lib.db.model.site as db_site
 
 
 class DbCandidate(Base):
@@ -31,3 +33,8 @@ class DbCandidate(Base):
     entity_type             : Mapped[str]            = mapped_column('Entity_type')
     proband_sex             : Mapped[Optional[str]]  = mapped_column('ProbandSex')
     proband_sate_of_birth   : Mapped[Optional[date]] = mapped_column('ProbandDoB')
+
+    sessions          : Mapped[List['db_session.DbSession']] \
+        = relationship('DbSession', back_populates='candidate')
+    registration_site : Mapped['db_site.DbSite'] \
+        = relationship('DbSite')

python/lib/db/model/dicom_archive.py

@@ -1,6 +1,5 @@
 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.model.dicom_archive_file as db_dicom_archive_file
@@ -12,13 +11,7 @@ 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())
+    study_uid                : Mapped[str]                = mapped_column('DicomArchiveID')
     patient_id               : Mapped[str]                = mapped_column('PatientID')
     patient_name             : Mapped[str]                = mapped_column('PatientName')
     patient_birthdate        : Mapped[Optional[date]]     = mapped_column('PatientDoB')
@@ -49,3 +42,10 @@ class DbDicomArchive(Base):
     acquisition_metadata     : Mapped[str]                = mapped_column('AcquisitionMetadata')
     date_sent                : Mapped[Optional[datetime]] = mapped_column('DateSent')
     pending_transfer         : Mapped[int]                = mapped_column('PendingTransfer')
+
+    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')

python/lib/db/model/dicom_archive_file.py

@@ -11,15 +11,16 @@ class DbDicomArchiveFile(Base):
 
     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')
+
+    archive : Mapped['db_dicom_archive.DbDicomArchive'] \
+        = relationship('DbDicomArchive', back_populates='files')
+    series  : Mapped[Optional['db_dicom_archive_series.DbDicomArchiveSeries']] \
+        = relationship('DbDicomArchiveSeries', back_populates="files")

python/lib/db/model/dicom_archive_series.py

@@ -11,10 +11,6 @@ class DbDicomArchiveSeries(Base):
 
     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')
@@ -26,3 +22,8 @@ class DbDicomArchiveSeries(Base):
     number_of_files    : Mapped[int]             = mapped_column('NumberOfFiles')
     series_uid         : Mapped[Optional[str]]   = mapped_column('SeriesUID')
     modality           : Mapped[Optional[str]]   = mapped_column('Modality')
+
+    archive : Mapped['db_dicom_archive.DbDicomArchive'] \
+        = relationship('DbDicomArchive', back_populates="series")
+    files   : Mapped[List['db_dicom_archive_file.DbDicomArchiveFile']] \
+        = relationship('DbDicomArchiveFile', back_populates="series")

python/lib/db/model/mri_upload.py

@@ -21,9 +21,10 @@ class DbMriUpload(Base):
     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')
+
+    dicom_archive : Mapped[Optional['db_dicom_archive.DbDicomArchive']] \
+        = relationship('DicomArchive', back_populates='upload')

python/lib/db/model/project_cohort.py

@@ -0,0 +1,10 @@
+from sqlalchemy.orm import Mapped, mapped_column
+from lib.db.base import Base
+
+
+class DbProjectCohort(Base):
+    __tablename__ = 'project_cohort_rel'
+
+    id         : Mapped[int] = mapped_column('ProjectCohortRelID', primary_key=True)
+    project_id : Mapped[int] = mapped_column('ProjectID')
+    cohort_id  : Mapped[int] = mapped_column('CohortID')

python/lib/db/model/session.py

@@ -1,17 +1,20 @@
 from datetime import date, datetime
 from typing import Optional
-from sqlalchemy.orm import Mapped, mapped_column
+from sqlalchemy import ForeignKey
+from sqlalchemy.orm import Mapped, mapped_column, relationship
 from lib.db.base import Base
+import lib.db.model.candidate as db_candidate
+import lib.db.model.site as db_site
 
 
 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')
+    cand_id                  : Mapped[int]                = mapped_column('CandID', ForeignKey('candidate.CandID'))
+    site_id                  : Mapped[int]                = mapped_column('CenterID', ForeignKey('psc.ID'))
     project_id               : Mapped[int]                = mapped_column('ProjectID')
-    visit_no                 : Mapped[Optional[int]]      = mapped_column('VisitNo')
+    visit_number             : 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')
@@ -42,3 +45,6 @@ class DbSession(Base):
     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')
+
+    candidate : Mapped['db_candidate.DbCandidate'] = relationship('DbCandidate', back_populates='sessions')
+    site      : Mapped['db_site.DbSite']           = relationship('DbSite')

python/lib/db/model/site.py

@@ -0,0 +1,23 @@
+from typing import Optional
+from sqlalchemy.orm import Mapped, mapped_column
+from lib.db.base import Base
+
+
+class DbSite(Base):
+    __tablename__ = 'psc'
+
+    id         : Mapped[int]           = mapped_column('CenterID', primary_key=True)
+    name       : Mapped[str]           = mapped_column('Name')
+    area       : Mapped[Optional[str]] = mapped_column('PSCArea')
+    address    : Mapped[Optional[str]] = mapped_column('Address')
+    city       : Mapped[Optional[str]] = mapped_column('City')
+    state_id   : Mapped[Optional[int]] = mapped_column('StateID')
+    zip        : Mapped[Optional[str]] = mapped_column('ZIP')
+    phone_1    : Mapped[Optional[str]] = mapped_column('Phone1')
+    phone_2    : Mapped[Optional[str]] = mapped_column('Phone2')
+    contact_1  : Mapped[Optional[str]] = mapped_column('Contact1')
+    contact_2  : Mapped[Optional[str]] = mapped_column('Contact2')
+    alias      : Mapped[str]           = mapped_column('Alias')
+    mri_alias  : Mapped[str]           = mapped_column('MRI_alias')
+    account    : Mapped[Optional[str]] = mapped_column('Account')
+    study_site : Mapped[Optional[str]] = mapped_column('Study_site')

python/lib/db/query/project.py

@@ -0,0 +1,17 @@
+
+from sqlalchemy import select
+from sqlalchemy.orm import Session as Database
+
+from lib.db.model.project_cohort import DbProjectCohort
+
+
+def try_get_project_cohort_with_project_id_cohort_id(db: Database, project_id: int, cohort_id: int):
+    """
+    Get a project cohort relation from the database using its project ID and candidate ID, or
+    return `None` if no relation is found.
+    """
+
+    return db.execute(select(DbProjectCohort)
+        .where(DbProjectCohort.project_id == project_id)
+        .where(DbProjectCohort.cohort_id == cohort_id)
+    ).scalar_one_or_none()

python/lib/db/query/session.py

@@ -0,0 +1,17 @@
+
+from sqlalchemy import select
+from sqlalchemy.orm import Session as Database
+
+from lib.db.model.session import DbSession
+
+
+def try_get_session_with_cand_id_visit_label(db: Database, cand_id: int, visit_label: str):
+    """
+    Get a session from the database using its candidate CandID and visit label, or return `None`
+    if no session is found.
+    """
+
+    return db.execute(select(DbSession)
+        .where(DbSession.cand_id == cand_id)
+        .where(DbSession.visit_label == visit_label)
+    ).scalar_one_or_none()

python/lib/db/query/site.py

@@ -0,0 +1,20 @@
+from sqlalchemy import select
+from sqlalchemy.orm import Session as Database
+
+from lib.db.model.candidate import DbCandidate
+from lib.db.model.session import DbSession
+from lib.db.model.site import DbSite
+
+
+def try_get_site_with_psc_id_visit_label(db: Database, psc_id: str, visit_label: str):
+    """
+    Get a session from the database using its candidate CandID and visit label, or return `None`
+    if no session is found.
+    """
+
+    return db.execute(select(DbSite)
+        .join(DbSession.site)
+        .join(DbSession.candidate)
+        .where(DbCandidate.psc_id == psc_id)
+        .where(DbSession.visit_label == visit_label)
+    ).scalar_one_or_none()