Migrate mri_scanner to the new database abstraction

pyproject.toml

@@ -23,6 +23,7 @@ include = [
     "python/lib/get_subject_session.py",
     "python/lib/logging.py",
     "python/lib/make_env.py",
+    "python/lib/scanner.py",
     "python/lib/validate_subject_info.py",
 ]
 typeCheckingMode = "strict"

python/lib/database_lib/mri_scanner.py

@@ -2,11 +2,14 @@
 
 import datetime
 
+from typing_extensions import deprecated
+
 from lib.candidate import Candidate
 
 __license__ = "GPLv3"
 
 
+@deprecated('Use `lib.scanner` instead')
 class MriScanner:
     """
     This class performs database queries for imaging dataset stored in the mri_scanner table.
@@ -38,6 +41,7 @@ def __init__(self, db, verbose):
         self.db = db
         self.verbose = verbose
 
+    @deprecated('Use `lib.scanner.get_or_create_scanner` instead')
     def determine_scanner_information(self, manufacturer, software_version, serial_number, scanner_model,
                                       center_id, project_id):
         """
@@ -81,6 +85,7 @@ def determine_scanner_information(self, manufacturer, software_version, serial_n
         )
         return scanner_id
 
+    @deprecated('Use `lib.scanner.get_or_create_scanner` instead')
     def register_new_scanner(self, manufacturer, software_version, serial_number, scanner_model, center_id, project_id):
         """
         Inserts a new entry in the mri_scanner table after having created a new candidate to
@@ -132,6 +137,7 @@ def register_new_scanner(self, manufacturer, software_version, serial_number, sc
 
         return scanner_id
 
+    @deprecated('Use `lib.db.models.mri_scanner.DbMriScanner.candidate` instead')
     def get_scanner_candid(self, scanner_id):
         """
         Select a ScannerID CandID based on the scanner ID in mri_scanner.

python/lib/db/queries/mri_scanner.py

@@ -0,0 +1,26 @@
+from typing import Optional
+
+from sqlalchemy import select
+from sqlalchemy.orm import Session as Database
+
+from lib.db.models.mri_scanner import DbMriScanner
+
+
+def try_get_scanner_with_info(
+    db: Database,
+    manufacturer: str,
+    software_version: str,
+    serial_number: str,
+    model: str,
+) -> Optional[DbMriScanner]:
+    """
+    Get an MRI scanner from the database using the provided information, or return `None` if no
+    scanner is found.
+    """
+
+    return db.execute(select(DbMriScanner)
+        .where(DbMriScanner.manufacturer     == manufacturer)
+        .where(DbMriScanner.model            == model)
+        .where(DbMriScanner.serial_number    == serial_number)
+        .where(DbMriScanner.software_version == software_version)
+    ).scalar_one_or_none()

python/lib/dcm2bids_imaging_pipeline_lib/base_pipeline.py

@@ -14,6 +14,7 @@
 from lib.imaging import Imaging
 from lib.logging import log_error_exit, log_verbose, log_warning
 from lib.make_env import make_env
+from lib.scanner import get_or_create_scanner
 from lib.validate_subject_info import validate_subject_info
 
 
@@ -110,7 +111,7 @@ def __init__(self, loris_getopt_obj, script_name):
         ))
 
         # grep scanner information based on what is in the DICOM headers
-        self.scanner_id = self.determine_scanner_info()
+        self.mri_scanner = self.determine_scanner_info()
 
     def load_mri_upload_and_dicom_archive(self):
         """
@@ -240,17 +241,19 @@ def determine_scanner_info(self):
         """
         Determine the scanner information found in the database for the uploaded DICOM archive.
         """
-        scanner_id = self.imaging_obj.get_scanner_id(
+
+        mri_scanner = get_or_create_scanner(
+            self.env,
             self.dicom_archive.scanner_manufacturer,
-            self.dicom_archive.scanner_software_version,
-            self.dicom_archive.scanner_serial_number,
             self.dicom_archive.scanner_model,
+            self.dicom_archive.scanner_serial_number,
+            self.dicom_archive.scanner_software_version,
             self.site_dict['CenterID'],
             self.session.project_id if self.session is not None else None,
         )
 
-        log_verbose(self.env, f"Found Scanner ID: {scanner_id}")
-        return scanner_id
+        log_verbose(self.env, f"Found scanner ID: {mri_scanner.id}")
+        return mri_scanner
 
     def validate_subject_info(self):
         """

python/lib/dcm2bids_imaging_pipeline_lib/nifti_insertion_pipeline.py

@@ -14,6 +14,7 @@
 from lib.exception.validate_subject_info_error import ValidateSubjectInfoError
 from lib.get_subject_session import get_subject_session
 from lib.logging import log_error_exit, log_verbose
+from lib.scanner import get_or_create_scanner
 from lib.validate_subject_info import validate_subject_info
 
 __license__ = "GPLv3"
@@ -84,7 +85,7 @@ def __init__(self, loris_getopt_obj, script_name):
         if self.dicom_archive is not None:
             self._validate_nifti_patient_name_with_dicom_patient_name()
             self.subject_info = self.imaging_obj.determine_subject_info(
-                self.dicom_archive, self.scanner_id
+                self.dicom_archive, self.mri_scanner.id
             )
         else:
             self._determine_subject_info_based_on_json_patient_name()
@@ -357,12 +358,13 @@ def _determine_acquisition_protocol(self):
         scan_param = self.json_file_dict
 
         # get scanner ID if not already figured out
-        if not self.scanner_id:
-            self.scanner_id = self.imaging_obj.get_scanner_id(
+        if self.mri_scanner is None:
+            self.mri_scanner = get_or_create_scanner(
+                self.env,
                 self.json_file_dict['Manufacturer'],
-                self.json_file_dict['SoftwareVersions'],
-                self.json_file_dict['DeviceSerialNumber'],
                 self.json_file_dict['ManufacturersModelName'],
+                self.json_file_dict['DeviceSerialNumber'],
+                self.json_file_dict['SoftwareVersions'],
                 self.site_dict['CenterID'],
                 self.session.project_id,
             )
@@ -373,7 +375,7 @@ def _determine_acquisition_protocol(self):
             self.session.cohort_id,
             self.session.site_id,
             self.session.visit_label,
-            self.scanner_id
+            self.mri_scanner.id,
         )
 
         protocol_info = self.imaging_obj.get_acquisition_protocol_info(
@@ -701,7 +703,7 @@ def _register_into_files_and_parameter_file(self, nifti_rel_path):
             'InsertTime': datetime.datetime.now().timestamp(),
             'Caveat': 1 if self.warning_violations_list else 0,
             'TarchiveSource': self.dicom_archive.id,
-            'ScannerID': self.scanner_id,
+            'ScannerID': self.mri_scanner.id,
             'AcquisitionDate': acquisition_date,
             'SourceFileID': None
         }

python/lib/imaging.py

@@ -9,6 +9,7 @@
 
 import nibabel as nib
 from nilearn import image, plotting
+from typing_extensions import deprecated
 
 import lib.utilities as utilities
 from lib.config_file import SubjectInfo
@@ -18,7 +19,7 @@
 from lib.database_lib.mri_protocol import MriProtocol
 from lib.database_lib.mri_protocol_checks import MriProtocolChecks
 from lib.database_lib.mri_protocol_violated_scans import MriProtocolViolatedScans
 from lib.database_lib.mri_scan_type import MriScanType
 from lib.database_lib.mri_scanner import MriScanner
 from lib.database_lib.mri_violations_log import MriViolationsLog
 from lib.database_lib.parameter_file import ParameterFile
@@ -74,7 +75,7 @@
         self.mri_prot_db_obj = MriProtocol(db, verbose)
         self.mri_prot_check_db_obj = MriProtocolChecks(db, verbose)
         self.mri_prot_viol_scan_db_obj = MriProtocolViolatedScans(db, verbose)
         self.mri_scan_type_db_obj = MriScanType(db, verbose)
         self.mri_scanner_db_obj = MriScanner(db, verbose)
         self.mri_viol_log_db_obj = MriViolationsLog(db, verbose)
         self.param_type_db_obj = ParameterType(db, verbose)
@@ -832,6 +833,7 @@
                 'MriProtocolChecksGroupID': hdr_checks_list[0]['MriProtocolChecksGroupID']
             }
 
+    @deprecated('Use `lib.scanner.get_or_create_scanner` instead')
     def get_scanner_id(self, manufacturer, software_version, serial_nb, model_name, center_id, project_id):
         """
         Get the scanner ID based on the scanner information provided as input.
@@ -858,6 +860,7 @@
             project_id
         )
 
+    @deprecated('Use `lib.db.models.DbScanner.candidate` instead')
     def get_scanner_candid(self, scanner_id):
         """
         Select a ScannerID CandID based on the scanner ID in mri_scanner.

python/lib/scanner.py

@@ -0,0 +1,74 @@
+import random
+from datetime import datetime
+
+from sqlalchemy.orm import Session as Database
+
+from lib.db.models.candidate import DbCandidate
+from lib.db.models.mri_scanner import DbMriScanner
+from lib.db.queries.candidate import try_get_candidate_with_cand_id
+from lib.db.queries.mri_scanner import try_get_scanner_with_info
+from lib.env import Env
+
+
+def get_or_create_scanner(
+    env: Env,
+    manufacturer: str,
+    model: str,
+    serial_number: str,
+    software_version: str,
+    site_id: int,
+    project_id: int,
+) -> DbMriScanner:
+    """
+    Get an MRI scanner from the database using the provided information, or create it if it does
+    not already exist.
+    """
+
+    mri_scanner = try_get_scanner_with_info(env.db, manufacturer, model, serial_number, software_version)
+
+    if mri_scanner is not None:
+        return mri_scanner
+
+    cand_id = generate_new_cand_id(env.db)
+    now = datetime.now()
+
+    candidate = DbCandidate(
+        cand_id                 = cand_id,
+        psc_id                  = 'scanner',
+        registration_site_id    = site_id,
+        registration_project_id = project_id,
+        user_id                 = 'imaging.py',
+        entity_type             = 'Scanner',
+        date_active             = now,
+        date_registered         = now,
+        active                  = True,
+    )
+
+    env.db.add(candidate)
+    env.db.commit()
+
+    mri_scanner = DbMriScanner(
+        manufacturer     = manufacturer,
+        model            = model,
+        serial_number    = serial_number,
+        software_version = software_version,
+        candidate_id     = candidate.id,
+    )
+
+    env.db.add(mri_scanner)
+    env.db.commit()
+
+    return mri_scanner
+
+
+# TODO: Move this function to a more appropriate place.
+def generate_new_cand_id(db: Database) -> int:
+    """
+    Generate a new random CandID that is not already in the database.
+    """
+
+    while True:
+        cand_id = random.randint(100000, 999999)
+        candidate = try_get_candidate_with_cand_id(db, cand_id)
+        if candidate is None:
+            return cand_id