OpenREM 1.0.0b2__py3-none-any.whl → 1.0.0b3__py3-none-any.whl

openrem/remapp/extractors/ptsizecsv2db.py

@@ -1,368 +1,368 @@
-#    OpenREM - Radiation Exposure Monitoring tools for the physicist
-#    Copyright (C) 2012,2013  The Royal Marsden NHS Foundation Trust
-#
-#    This program is free software: you can redistribute it and/or modify
-#    it under the terms of the GNU General Public License as published by
-#    the Free Software Foundation, either version 3 of the License, or
-#    (at your option) any later version.
-#
-#    This program is distributed in the hope that it will be useful,
-#    but WITHOUT ANY WARRANTY; without even the implied warranty of
-#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#    GNU General Public License for more details.
-#
-#    Additional permission under section 7 of GPLv3:
-#    You shall not make any use of the name of The Royal Marsden NHS
-#    Foundation trust in connection with this Program in any press or
-#    other public announcement without the prior written consent of
-#    The Royal Marsden NHS Foundation Trust.
-#
-#    You should have received a copy of the GNU General Public License
-#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-"""
-..  module:: ptsizecsv2db.
-    :synopsis: Use to import height and weight data from csv file to existing studies in the database.
-
-..  moduleauthor:: Ed McDonagh
-
-"""
-import argparse
-import csv
-import datetime
-from decimal import Decimal
-import logging
-import os
-import sys
-import uuid
-
-import django
-from django import db
-from django.core.exceptions import ObjectDoesNotExist
-from django.core.files.base import ContentFile
-from openrem.remapp.tools.background import (
-    get_or_generate_task_uuid,
-    record_task_error_exit,
-)
-
-
-logger = logging.getLogger(__name__)
-
-
-basepath = os.path.dirname(__file__)
-projectpath = os.path.abspath(os.path.join(basepath, "..", ".."))
-if projectpath not in sys.path:
-    sys.path.insert(1, projectpath)
-os.environ["DJANGO_SETTINGS_MODULE"] = "openremproject.settings"
-django.setup()
-
-
-# Absolute import path to prevent issues with script
-from remapp.models import (
-    GeneralStudyModuleAttr,
-    SizeUpload,
-)  # pylint: disable=wrong-import-position
-
-
-def _patientstudymoduleattributes(
-    size_upload=None, exam=None, size_dict=None
-):  # C.7.2.2
-
-    log_file = size_upload.logfile
-    try:
-        patient_attributes = exam.patientstudymoduleattr_set.get()
-    except ObjectDoesNotExist:
-        error = (
-            f"Attempt to import pt size info for study UID {exam.study_instance_uid}/acc. number"
-            f" {exam.accession_number} failed due to a failed import"
-        )
-        logger.error(error)
-        record_task_error_exit(error)
-        log_file.file.open("a")
-        log_file.write(
-            "\r\n    ********* Failed to insert size - database entry incomplete *********"
-        )
-        log_file.file.close()
-        if size_dict["verbose"]:
-            print(
-                "    ********* Failed to insert size - database entry incomplete *********"
-            )
-        return
-
-    if size_dict["height"]:
-        if not patient_attributes.patient_size:
-            patient_attributes.patient_size = Decimal(size_dict["height"]) / Decimal(
-                100.0
-            )
-            log_file.file.open("a")
-            log_file.write(f"\r\n    Inserted height of {size_dict['height']} cm")
-            log_file.file.close()
-            if size_dict["verbose"]:
-                print(f"    Inserted height of {size_dict['height']} cm")
-        elif size_upload.overwrite:
-            existing_height = patient_attributes.patient_size * Decimal(100.0)
-            patient_attributes.patient_size = Decimal(size_dict["height"]) / Decimal(
-                100.0
-            )
-            log_file.file.open("a")
-            log_file.write(
-                f"\r\n    Inserted height of {size_dict['height']} cm replacing {existing_height:.0f} cm"
-            )
-            log_file.file.close()
-            if size_dict["verbose"]:
-                print(
-                    f"    Inserted height of {size_dict['height']} cm replacing {existing_height:.0f} cm"
-                )
-        else:
-            existing_height = patient_attributes.patient_size * Decimal(100.0)
-            log_file.file.open("a")
-            log_file.write(
-                f"\r\n    Height of {size_dict['height']} cm not inserted as {existing_height:.0f} cm "
-                f"already in the database"
-            )
-            log_file.file.close()
-            if size_dict["verbose"]:
-                print(
-                    f"    Height of {size_dict['height']} cm not inserted as {existing_height:.0f} cm already in "
-                    f"the database"
-                )
-
-    if size_dict["weight"]:
-        if not patient_attributes.patient_weight:
-            patient_attributes.patient_weight = size_dict["weight"]
-            log_file.file.open("a")
-            log_file.write(f"\r\n    Inserted weight of {size_dict['weight']} kg")
-            log_file.file.close()
-            if size_dict["verbose"]:
-                print(f"    Inserted weight of {size_dict['weight']} kg")
-        elif size_upload.overwrite:
-            existing_weight = patient_attributes.patient_weight
-            patient_attributes.patient_weight = size_dict["weight"]
-            log_file.file.open("a")
-            log_file.write(
-                f"\r\n    Inserted weight of {size_dict['weight']} kg replacing {existing_weight:.1f} kg"
-            )
-            log_file.file.close()
-            if size_dict["verbose"]:
-                print(
-                    f"    Inserted weight of {size_dict['weight']} kg replacing {existing_weight:.1f} kg"
-                )
-        else:
-            log_file.file.open("a")
-            log_file.write(
-                f"\r\n    Weight of {size_dict['weight']} kg not inserted as "
-                f"{patient_attributes.patient_weight:.1f} kg already in the database"
-            )
-            log_file.file.close()
-            if size_dict["verbose"]:
-                print(
-                    f"    Weight of {size_dict['weight']} kg not inserted as "
-                    f"{patient_attributes.patient_weight:.1f} kg already in the database"
-                )
-
-    patient_attributes.save()
-
-
-def _ptsizeinsert(size_upload=None, size_dict=None):
-
-    log_file = size_upload.logfile
-    if (size_dict["height"] or size_dict["weight"]) and size_dict["acc_no"]:
-        if not size_dict["si_uid"]:
-            exams = GeneralStudyModuleAttr.objects.filter(
-                accession_number__exact=size_dict["acc_no"]
-            )
-        else:
-            exams = GeneralStudyModuleAttr.objects.filter(
-                study_instance_uid__exact=size_dict["acc_no"]
-            )
-        if exams:
-            for exam in exams:
-                log_file.file.open("a")
-                log_file.write(f"\r\n{size_dict['acc_no']}:")
-                log_file.file.close()
-                if size_dict["verbose"]:
-                    print(size_dict["acc_no"])
-                _patientstudymoduleattributes(
-                    size_upload=size_upload, exam=exam, size_dict=size_dict
-                )
-
-    db.reset_queries()
-
-
-def websizeimport(csv_pk=None):
-    """Task to import patient size data from the OpenREM web interface.
-
-    :param csv_pk: Database index key for the import record, containing
-        the path to the import csv file and the field header details.
-
-    """
-
-    if csv_pk:
-        size_upload = SizeUpload.objects.all().filter(id__exact=csv_pk)[0]
-        size_upload.task_id = get_or_generate_task_uuid()
-        datestamp = datetime.datetime.now()
-        size_upload.import_date = datestamp
-        size_upload.progress = "Patient size data import started"
-        size_upload.status = "CURRENT"
-        size_upload.save()
-        if (
-            size_upload.id_type
-            and size_upload.id_field
-            and size_upload.height_field
-            and size_upload.weight_field
-        ):
-            si_uid = False
-            verbose = False
-            if size_upload.id_type == "si-uid":
-                si_uid = True
-
-            log_file = "pt_size_import_log_{0}.txt".format(
-                datestamp.strftime("%Y%m%d-%H%M%S%f")
-            )
-            headerrow = ContentFile(
-                f"Patient size import from {size_upload.sizefile.name}\r\n"
-            )
-
-            try:
-                size_upload.logfile.save(log_file, headerrow)
-            except OSError as e:
-                error = (
-                    "Error saving export file - please contact an administrator. "
-                    "Error({0}): {1}".format(e.errno, e.strerror)
-                )
-                size_upload.progress = error
-                size_upload.status = "ERROR"
-                size_upload.save()
-                record_task_error_exit(error)
-                return
-            except:
-                error = (
-                    "Unexpected error saving export file - please contact an "
-                    "administrator: {0}".format(sys.exc_info()[0])
-                )
-                size_upload.progress = error
-                size_upload.status = "ERROR"
-                size_upload.save()
-                record_task_error_exit(error)
-                return
-
-            log_file = size_upload.logfile
-            log_file.file.close()
-            # Method used for opening and writing to file as per https://code.djangoproject.com/ticket/13809
-
-            size_upload.sizefile.open(mode="r")
-            csv_file = size_upload.sizefile.readlines()
-            size_upload.num_records = len(csv_file) - 1
-            size_upload.save()
-            try:
-                dataset = csv.DictReader(csv_file)
-                for i, line in enumerate(dataset):
-                    size_upload.progress = (
-                        f"Processing row {i + 1} of {size_upload.num_records}"
-                    )
-                    size_upload.save()
-                    size_dict = {
-                        "acc_no": line[size_upload.id_field],
-                        "height": line[size_upload.height_field],
-                        "weight": line[size_upload.weight_field],
-                        "si_uid": si_uid,
-                        "verbose": verbose,
-                    }
-                    _ptsizeinsert(size_upload=size_upload, size_dict=size_dict)
-            finally:
-                size_upload.sizefile.delete()
-                size_upload.processtime = (
-                    datetime.datetime.now() - datestamp
-                ).total_seconds()
-                size_upload.status = "COMPLETE"
-                size_upload.save()
-
-
-def _create_parser():
-    parser = argparse.ArgumentParser(
-        description="Import height and weight data from a CSV file into an OpenREM database. If either height or "
-        "weight is missing just add a blank column with an appropriate title."
-    )
-    parser.add_argument(
-        "-u",
-        "--si-uid",
-        action="store_true",
-        help="use Study Instance UID instead of Accession Number",
-    )
-    parser.add_argument(
-        "-v", "--verbose", help="also print log to shell", action="store_true"
-    )
-    parser.add_argument(
-        "-o", "--overwrite", help="overwrite existing values", action="store_true"
-    )
-    parser.add_argument(
-        "csvfile", help="csv file with height, weight and study identifier"
-    )
-    parser.add_argument(
-        "id", help="column title for the accession number or study instance UID"
-    )
-    parser.add_argument(
-        "height", help="column title for the patient height, values in cm"
-    )
-    parser.add_argument(
-        "weight", help="column title for the patient weight, values in kg"
-    )
-
-    return parser
-
-
-def csv2db():
-    """Import patient height and weight data from csv RIS exports. Called from ``openrem_ptsizecsv.py`` script
-
-    :param args: sys.argv from the command line call
-
-    Example::
-
-        openrem_ptsizecsv.py -s MyRISExport.csv StudyInstanceUID height weight
-
-    """
-
-    args = _create_parser().parse_args()
-
-    with open(args.csvfile) as csv_file:
-        dataset = csv.DictReader(csv_file)
-        fieldnames = dataset.fieldnames
-        arg_headers = [args.id, args.height, args.weight]
-        if not all(header in fieldnames for header in arg_headers):
-            msg = f"Error: one or more of {arg_headers} not found in csv file"
-            print(msg)
-            record_task_error_exit(msg)
-            return
-        size_upload = SizeUpload()
-        date_stamp = datetime.datetime.now()
-        size_upload.import_date = date_stamp
-        size_upload.task_id = uuid.uuid4()
-        size_upload.progress = "Patient size data import from shell started"
-        size_upload.status = "CURRENT"
-        size_upload.overwrite = args.overwrite
-        size_upload.save()
-        log_file_name = "pt_size_import_log_{0}.txt".format(
-            date_stamp.strftime("%Y%m%d-%H%M%S%f")
-        )
-        log_header_row = ContentFile(f"Patient size import from {args.csvfile}\r\n")
-        size_upload.logfile.save(log_file_name, log_header_row)
-        size_upload.save()
-        log_file = size_upload.logfile
-        log_file.file.close()
-        size_upload.num_records = len(csv_file.readlines())
-        size_upload.save()
-        csv_file.seek(0)
-
-        for line in dataset:
-            size_dict = {
-                "acc_no": line[args.id],
-                "height": line[args.height],
-                "weight": line[args.weight],
-                "si_uid": args.si_uid,
-                "verbose": args.verbose,
-            }
-            _ptsizeinsert(size_upload=size_upload, size_dict=size_dict)
-
-    size_upload.processtime = (datetime.datetime.now() - date_stamp).total_seconds()
-    size_upload.status = "COMPLETE"
-    size_upload.save()
+#    OpenREM - Radiation Exposure Monitoring tools for the physicist
+#    Copyright (C) 2012,2013  The Royal Marsden NHS Foundation Trust
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    Additional permission under section 7 of GPLv3:
+#    You shall not make any use of the name of The Royal Marsden NHS
+#    Foundation trust in connection with this Program in any press or
+#    other public announcement without the prior written consent of
+#    The Royal Marsden NHS Foundation Trust.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+"""
+..  module:: ptsizecsv2db.
+    :synopsis: Use to import height and weight data from csv file to existing studies in the database.
+
+..  moduleauthor:: Ed McDonagh
+
+"""
+import argparse
+import csv
+import datetime
+from decimal import Decimal
+import logging
+import os
+import sys
+import uuid
+
+import django
+from django import db
+from django.core.exceptions import ObjectDoesNotExist
+from django.core.files.base import ContentFile
+from openrem.remapp.tools.background import (
+    get_or_generate_task_uuid,
+    record_task_error_exit,
+)
+
+
+logger = logging.getLogger(__name__)
+
+
+basepath = os.path.dirname(__file__)
+projectpath = os.path.abspath(os.path.join(basepath, "..", ".."))
+if projectpath not in sys.path:
+    sys.path.insert(1, projectpath)
+os.environ["DJANGO_SETTINGS_MODULE"] = "openremproject.settings"
+django.setup()
+
+
+# Absolute import path to prevent issues with script
+from remapp.models import (
+    GeneralStudyModuleAttr,
+    SizeUpload,
+)  # pylint: disable=wrong-import-position
+
+
+def _patientstudymoduleattributes(
+    size_upload=None, exam=None, size_dict=None
+):  # C.7.2.2
+
+    log_file = size_upload.logfile
+    try:
+        patient_attributes = exam.patientstudymoduleattr_set.get()
+    except ObjectDoesNotExist:
+        error = (
+            f"Attempt to import pt size info for study UID {exam.study_instance_uid}/acc. number"
+            f" {exam.accession_number} failed due to a failed import"
+        )
+        logger.error(error)
+        record_task_error_exit(error)
+        log_file.file.open("a")
+        log_file.write(
+            "\r\n    ********* Failed to insert size - database entry incomplete *********"
+        )
+        log_file.file.close()
+        if size_dict["verbose"]:
+            print(
+                "    ********* Failed to insert size - database entry incomplete *********"
+            )
+        return
+
+    if size_dict["height"]:
+        if not patient_attributes.patient_size:
+            patient_attributes.patient_size = Decimal(size_dict["height"]) / Decimal(
+                100.0
+            )
+            log_file.file.open("a")
+            log_file.write(f"\r\n    Inserted height of {size_dict['height']} cm")
+            log_file.file.close()
+            if size_dict["verbose"]:
+                print(f"    Inserted height of {size_dict['height']} cm")
+        elif size_upload.overwrite:
+            existing_height = patient_attributes.patient_size * Decimal(100.0)
+            patient_attributes.patient_size = Decimal(size_dict["height"]) / Decimal(
+                100.0
+            )
+            log_file.file.open("a")
+            log_file.write(
+                f"\r\n    Inserted height of {size_dict['height']} cm replacing {existing_height:.0f} cm"
+            )
+            log_file.file.close()
+            if size_dict["verbose"]:
+                print(
+                    f"    Inserted height of {size_dict['height']} cm replacing {existing_height:.0f} cm"
+                )
+        else:
+            existing_height = patient_attributes.patient_size * Decimal(100.0)
+            log_file.file.open("a")
+            log_file.write(
+                f"\r\n    Height of {size_dict['height']} cm not inserted as {existing_height:.0f} cm "
+                f"already in the database"
+            )
+            log_file.file.close()
+            if size_dict["verbose"]:
+                print(
+                    f"    Height of {size_dict['height']} cm not inserted as {existing_height:.0f} cm already in "
+                    f"the database"
+                )
+
+    if size_dict["weight"]:
+        if not patient_attributes.patient_weight:
+            patient_attributes.patient_weight = size_dict["weight"]
+            log_file.file.open("a")
+            log_file.write(f"\r\n    Inserted weight of {size_dict['weight']} kg")
+            log_file.file.close()
+            if size_dict["verbose"]:
+                print(f"    Inserted weight of {size_dict['weight']} kg")
+        elif size_upload.overwrite:
+            existing_weight = patient_attributes.patient_weight
+            patient_attributes.patient_weight = size_dict["weight"]
+            log_file.file.open("a")
+            log_file.write(
+                f"\r\n    Inserted weight of {size_dict['weight']} kg replacing {existing_weight:.1f} kg"
+            )
+            log_file.file.close()
+            if size_dict["verbose"]:
+                print(
+                    f"    Inserted weight of {size_dict['weight']} kg replacing {existing_weight:.1f} kg"
+                )
+        else:
+            log_file.file.open("a")
+            log_file.write(
+                f"\r\n    Weight of {size_dict['weight']} kg not inserted as "
+                f"{patient_attributes.patient_weight:.1f} kg already in the database"
+            )
+            log_file.file.close()
+            if size_dict["verbose"]:
+                print(
+                    f"    Weight of {size_dict['weight']} kg not inserted as "
+                    f"{patient_attributes.patient_weight:.1f} kg already in the database"
+                )
+
+    patient_attributes.save()
+
+
+def _ptsizeinsert(size_upload=None, size_dict=None):
+
+    log_file = size_upload.logfile
+    if (size_dict["height"] or size_dict["weight"]) and size_dict["acc_no"]:
+        if not size_dict["si_uid"]:
+            exams = GeneralStudyModuleAttr.objects.filter(
+                accession_number__exact=size_dict["acc_no"]
+            )
+        else:
+            exams = GeneralStudyModuleAttr.objects.filter(
+                study_instance_uid__exact=size_dict["acc_no"]
+            )
+        if exams:
+            for exam in exams:
+                log_file.file.open("a")
+                log_file.write(f"\r\n{size_dict['acc_no']}:")
+                log_file.file.close()
+                if size_dict["verbose"]:
+                    print(size_dict["acc_no"])
+                _patientstudymoduleattributes(
+                    size_upload=size_upload, exam=exam, size_dict=size_dict
+                )
+
+    db.reset_queries()
+
+
+def websizeimport(csv_pk=None):
+    """Task to import patient size data from the OpenREM web interface.
+
+    :param csv_pk: Database index key for the import record, containing
+        the path to the import csv file and the field header details.
+
+    """
+
+    if csv_pk:
+        size_upload = SizeUpload.objects.all().filter(id__exact=csv_pk)[0]
+        size_upload.task_id = get_or_generate_task_uuid()
+        datestamp = datetime.datetime.now()
+        size_upload.import_date = datestamp
+        size_upload.progress = "Patient size data import started"
+        size_upload.status = "CURRENT"
+        size_upload.save()
+        if (
+            size_upload.id_type
+            and size_upload.id_field
+            and size_upload.height_field
+            and size_upload.weight_field
+        ):
+            si_uid = False
+            verbose = False
+            if size_upload.id_type == "si-uid":
+                si_uid = True
+
+            log_file = "pt_size_import_log_{0}.txt".format(
+                datestamp.strftime("%Y%m%d-%H%M%S%f")
+            )
+            headerrow = ContentFile(
+                f"Patient size import from {size_upload.sizefile.name}\r\n"
+            )
+
+            try:
+                size_upload.logfile.save(log_file, headerrow)
+            except OSError as e:
+                error = (
+                    "Error saving export file - please contact an administrator. "
+                    "Error({0}): {1}".format(e.errno, e.strerror)
+                )
+                size_upload.progress = error
+                size_upload.status = "ERROR"
+                size_upload.save()
+                record_task_error_exit(error)
+                return
+            except:
+                error = (
+                    "Unexpected error saving export file - please contact an "
+                    "administrator: {0}".format(sys.exc_info()[0])
+                )
+                size_upload.progress = error
+                size_upload.status = "ERROR"
+                size_upload.save()
+                record_task_error_exit(error)
+                return
+
+            log_file = size_upload.logfile
+            log_file.file.close()
+            # Method used for opening and writing to file as per https://code.djangoproject.com/ticket/13809
+
+            size_upload.sizefile.open(mode="r")
+            csv_file = size_upload.sizefile.readlines()
+            size_upload.num_records = len(csv_file) - 1
+            size_upload.save()
+            try:
+                dataset = csv.DictReader(csv_file)
+                for i, line in enumerate(dataset):
+                    size_upload.progress = (
+                        f"Processing row {i + 1} of {size_upload.num_records}"
+                    )
+                    size_upload.save()
+                    size_dict = {
+                        "acc_no": line[size_upload.id_field],
+                        "height": line[size_upload.height_field],
+                        "weight": line[size_upload.weight_field],
+                        "si_uid": si_uid,
+                        "verbose": verbose,
+                    }
+                    _ptsizeinsert(size_upload=size_upload, size_dict=size_dict)
+            finally:
+                size_upload.sizefile.delete()
+                size_upload.processtime = (
+                    datetime.datetime.now() - datestamp
+                ).total_seconds()
+                size_upload.status = "COMPLETE"
+                size_upload.save()
+
+
+def _create_parser():
+    parser = argparse.ArgumentParser(
+        description="Import height and weight data from a CSV file into an OpenREM database. If either height or "
+        "weight is missing just add a blank column with an appropriate title."
+    )
+    parser.add_argument(
+        "-u",
+        "--si-uid",
+        action="store_true",
+        help="use Study Instance UID instead of Accession Number",
+    )
+    parser.add_argument(
+        "-v", "--verbose", help="also print log to shell", action="store_true"
+    )
+    parser.add_argument(
+        "-o", "--overwrite", help="overwrite existing values", action="store_true"
+    )
+    parser.add_argument(
+        "csvfile", help="csv file with height, weight and study identifier"
+    )
+    parser.add_argument(
+        "id", help="column title for the accession number or study instance UID"
+    )
+    parser.add_argument(
+        "height", help="column title for the patient height, values in cm"
+    )
+    parser.add_argument(
+        "weight", help="column title for the patient weight, values in kg"
+    )
+
+    return parser
+
+
+def csv2db():
+    """Import patient height and weight data from csv RIS exports. Called from ``openrem_ptsizecsv.py`` script
+
+    :param args: sys.argv from the command line call
+
+    Example::
+
+        openrem_ptsizecsv.py -s MyRISExport.csv StudyInstanceUID height weight
+
+    """
+
+    args = _create_parser().parse_args()
+
+    with open(args.csvfile) as csv_file:
+        dataset = csv.DictReader(csv_file)
+        fieldnames = dataset.fieldnames
+        arg_headers = [args.id, args.height, args.weight]
+        if not all(header in fieldnames for header in arg_headers):
+            msg = f"Error: one or more of {arg_headers} not found in csv file"
+            print(msg)
+            record_task_error_exit(msg)
+            return
+        size_upload = SizeUpload()
+        date_stamp = datetime.datetime.now()
+        size_upload.import_date = date_stamp
+        size_upload.task_id = uuid.uuid4()
+        size_upload.progress = "Patient size data import from shell started"
+        size_upload.status = "CURRENT"
+        size_upload.overwrite = args.overwrite
+        size_upload.save()
+        log_file_name = "pt_size_import_log_{0}.txt".format(
+            date_stamp.strftime("%Y%m%d-%H%M%S%f")
+        )
+        log_header_row = ContentFile(f"Patient size import from {args.csvfile}\r\n")
+        size_upload.logfile.save(log_file_name, log_header_row)
+        size_upload.save()
+        log_file = size_upload.logfile
+        log_file.file.close()
+        size_upload.num_records = len(csv_file.readlines())
+        size_upload.save()
+        csv_file.seek(0)
+
+        for line in dataset:
+            size_dict = {
+                "acc_no": line[args.id],
+                "height": line[args.height],
+                "weight": line[args.weight],
+                "si_uid": args.si_uid,
+                "verbose": args.verbose,
+            }
+            _ptsizeinsert(size_upload=size_upload, size_dict=size_dict)
+
+    size_upload.processtime = (datetime.datetime.now() - date_stamp).total_seconds()
+    size_upload.status = "COMPLETE"
+    size_upload.save()