Add more integration tests for run_nifti_insertion.py

python/lib/db/models/mri_protocol_violated_scan.py

@@ -19,7 +19,7 @@ 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')
-    minc_location            : Mapped[str | None]      = mapped_column('minc_location')
+    file_rel_path            : Mapped[str | None]      = mapped_column('minc_location')
     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_violation_log.py

@@ -19,7 +19,7 @@ class DbMriViolationLog(Base):
     series_uid              : Mapped[str | None]       = mapped_column('SeriesUID')
     dicom_archive_id        : Mapped[int | None]       \
         = mapped_column('TarchiveID', ForeignKey('tarchive.TarchiveID'))
-    minc_file               : Mapped[str | None]       = mapped_column('MincFile')
+    file_rel_path           : Mapped[str | None]       = mapped_column('MincFile')
     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/queries/mri_protocol_violated_scans.py → python/lib/db/queries/mri_protocol_violated_scan.py

@@ -1,24 +1,26 @@
+from collections.abc import Sequence
+
 from sqlalchemy import select
 from sqlalchemy.orm import Session as Database
 
 from lib.db.models.mri_protocol_violated_scan import DbMriProtocolViolatedScan
 
 
-def try_get_protocol_violated_scans_with_unique_series_combination(
+def get_protocol_violated_scans_with_unique_series_combination(
         db: Database,
         series_uid: str,
         echo_time: str | None,
         echo_number: str | None,
         phase_encoding_direction: str | None
-) -> DbMriProtocolViolatedScan | None:
+) -> Sequence[DbMriProtocolViolatedScan]:
     """
-    Get the protocol violated scans from the database using its SeriesInstanceUID, or return `None` if
-    no protocol violated scan was found.
+    Get all protocol violated scans from the database using the file's SeriesInstanceUID,
+    echo time, echo number and phase encoding direction.
     """
 
     return db.execute(select(DbMriProtocolViolatedScan)
         .where(DbMriProtocolViolatedScan.series_uid == series_uid)
         .where(DbMriProtocolViolatedScan.te_range == echo_time)
         .where(DbMriProtocolViolatedScan.echo_number == echo_number)
         .where(DbMriProtocolViolatedScan.phase_encoding_direction == phase_encoding_direction)
-    ).scalar_one_or_none()
+    ).scalars().all()

python/lib/db/queries/mri_violations_log.py → python/lib/db/queries/mri_violation_log.py

@@ -1,24 +1,26 @@
+from collections.abc import Sequence
+
 from sqlalchemy import select
 from sqlalchemy.orm import Session as Database
 
 from lib.db.models.mri_violation_log import DbMriViolationLog
 
 
-def try_get_violations_log_with_unique_series_combination(
+def get_violations_log_with_unique_series_combination(
         db: Database,
         series_uid: str,
         echo_time: str | None,
         echo_number: str | None,
         phase_encoding_direction: str | None
-) -> DbMriViolationLog | None:
+) -> Sequence[DbMriViolationLog]:
     """
-    Get the violations log from the database using its SeriesInstanceUID, or return `None` if
-    no violations log was found.
+    Get all violations log from the database using the file's SeriesInstanceUID,
+    echo time, echo number and phase encoding direction.
     """
 
     return db.execute(select(DbMriViolationLog)
         .where(DbMriViolationLog.series_uid == series_uid)
         .where(DbMriViolationLog.echo_time == echo_time)
         .where(DbMriViolationLog.echo_number == echo_number)
         .where(DbMriViolationLog.phase_encoding_direction == phase_encoding_direction)
-    ).scalar_one_or_none()
+    ).scalars().all()

python/lib/dcm2bids_imaging_pipeline_lib/nifti_insertion_pipeline.py

@@ -53,6 +53,7 @@ def __init__(self, loris_getopt_obj, script_name):
         self.bvec_blake2 = compute_file_blake2b_hash(self.bvec_path) if self.bval_path else None
         self.loris_scan_type = self.options_dict["loris_scan_type"]["value"]
         self.bypass_extra_checks = self.options_dict["bypass_extra_checks"]["value"]
+        self.create_pic_bool = self.options_dict["create_pic"]["value"]
 
         # ---------------------------------------------------------------------------------------------
         # Set 'Inserting' flag to 1 in mri_upload
@@ -164,8 +165,8 @@ def __init__(self, loris_getopt_obj, script_name):
             log_error_exit(
                 self.env,
                 (
-                    f"{self.nifti_path} violates exclusionary checks listed in mri_protocol_checks. "
-                    f"  List of violations are: {self.exclude_violations_list}"
+                    f"{self.nifti_path} violates exclusionary checks listed in mri_protocol_checks."
+                    f" List of violations are: {self.exclude_violations_list}"
                 ),
                 lib.exitcode.UNKNOWN_PROTOCOL,
             )
@@ -175,7 +176,8 @@ def __init__(self, loris_getopt_obj, script_name):
         # ---------------------------------------------------------------------------------------------
         # Create the pic images
         # ---------------------------------------------------------------------------------------------
-        self._create_pic_image()
+        if self.create_pic_bool:
+            self._create_pic_image()
 
         # ---------------------------------------------------------------------------------------------
         # Remove the tmp directory from the file system