endoreg-db 0.3.6__py3-none-any.whl → 0.3.8__py3-none-any.whl

endoreg_db/management/commands/import_legacy_videos.py

@@ -1,76 +1,76 @@
-from endoreg_db.utils.hashs import get_video_hash
-import subprocess
-from django.core.files import File
-from django.core.management.base import BaseCommand
-from endoreg_db.models.data_file.video import LegacyVideo
-import os
-from tqdm import tqdm
-# import cv2
-
-def convert_mkv_to_mp4(source_path, target_path):
-    """
-    Convert a .mkv file to a .mp4 file using FFmpeg.
-    
-    Parameters:
-        mov_file_path (str): The file path of the input .MOV file.
-        mp4_file_path (str): The file path where the output .mp4 file should be saved.
-        
-    Returns:
-        None
-    """
-    cmd = ["ffmpeg", "-y", "-i", source_path, "-vcodec", "h264", "-acodec", "aac", target_path]
-    subprocess.run(cmd)
-
-
-class Command(BaseCommand):
-    """
-    Imports videos from a directory into the database
-
-    Usage:
-        python manage.py import_legacy_videos <directory>
-    """
-    help = 'Imports videos from a directory into the database'
-
-    def add_arguments(self, parser):
-        parser.add_argument('directory', type=str)
-
-    def handle(self, *args, **options):
-        directory = options['directory']
-        if not os.path.isdir(directory):
-            raise Exception(f"Directory {directory} does not exist")
-
-        # iterate over all subdirectories and gather all .mkv files
-        mkv_files = []
-        for root, dirs, files in os.walk(directory):
-            for file in files:
-                if file.endswith(".mkv"):
-                    mkv_files.append(os.path.join(root, file))
-
-        # create videos
-        for mkv_file in tqdm(mkv_files):
-            # get the name of the video
-            video_name = os.path.basename(mkv_file).replace(".mkv", "")
-
-            # convert the .mkv file to a .mp4 file
-            mp4_file = os.path.join(directory, video_name + ".mp4")
-            if not os.path.isfile(mp4_file):
-                convert_mkv_to_mp4(mkv_file, mp4_file)
-
-            # create the video object
-            video_hash = get_video_hash(mp4_file)
-
-            # check if the video already exists
-            if LegacyVideo.objects.filter(video_hash=video_hash).exists():
-                print(f"Video with hash {video_hash} already exists. Skipping...")
-                continue
-
-            video = LegacyVideo.objects.create(video_hash=video_hash, suffix = "mp4")
-
-            # open the .mp4 file
-            with open(mp4_file, 'rb') as f:
-                # create the Django File object
-                django_file = File(f)
-                # save the file to the video
-                video.file.save(video_name + ".mp4", django_file)
-            raise Exception("Stop here: NEED TO FIX OPENCV DEPENDENCY")
-            video.initialize_video_specs(cv2.VideoCapture(video.file.path))
+from endoreg_db.utils.hashs import get_video_hash
+import subprocess
+from django.core.files import File
+from django.core.management.base import BaseCommand
+from endoreg_db.models.data_file.video import LegacyVideo
+import os
+from tqdm import tqdm
+# import cv2
+
+def convert_mkv_to_mp4(source_path, target_path):
+    """
+    Convert a .mkv file to a .mp4 file using FFmpeg.
+    
+    Parameters:
+        mov_file_path (str): The file path of the input .MOV file.
+        mp4_file_path (str): The file path where the output .mp4 file should be saved.
+        
+    Returns:
+        None
+    """
+    cmd = ["ffmpeg", "-y", "-i", source_path, "-vcodec", "h264", "-acodec", "aac", target_path]
+    subprocess.run(cmd)
+
+
+class Command(BaseCommand):
+    """
+    Imports videos from a directory into the database
+
+    Usage:
+        python manage.py import_legacy_videos <directory>
+    """
+    help = 'Imports videos from a directory into the database'
+
+    def add_arguments(self, parser):
+        parser.add_argument('directory', type=str)
+
+    def handle(self, *args, **options):
+        directory = options['directory']
+        if not os.path.isdir(directory):
+            raise Exception(f"Directory {directory} does not exist")
+
+        # iterate over all subdirectories and gather all .mkv files
+        mkv_files = []
+        for root, dirs, files in os.walk(directory):
+            for file in files:
+                if file.endswith(".mkv"):
+                    mkv_files.append(os.path.join(root, file))
+
+        # create videos
+        for mkv_file in tqdm(mkv_files):
+            # get the name of the video
+            video_name = os.path.basename(mkv_file).replace(".mkv", "")
+
+            # convert the .mkv file to a .mp4 file
+            mp4_file = os.path.join(directory, video_name + ".mp4")
+            if not os.path.isfile(mp4_file):
+                convert_mkv_to_mp4(mkv_file, mp4_file)
+
+            # create the video object
+            video_hash = get_video_hash(mp4_file)
+
+            # check if the video already exists
+            if LegacyVideo.objects.filter(video_hash=video_hash).exists():
+                print(f"Video with hash {video_hash} already exists. Skipping...")
+                continue
+
+            video = LegacyVideo.objects.create(video_hash=video_hash, suffix = "mp4")
+
+            # open the .mp4 file
+            with open(mp4_file, 'rb') as f:
+                # create the Django File object
+                django_file = File(f)
+                # save the file to the video
+                video.file.save(video_name + ".mp4", django_file)
+            raise Exception("Stop here: NEED TO FIX OPENCV DEPENDENCY")
+            video.initialize_video_specs(cv2.VideoCapture(video.file.path))

endoreg_db/management/commands/load_active_model_data.py

@@ -1,45 +1,45 @@
-from django.conf import settings
-import os
-from django.core.management.base import BaseCommand
-from ...models import ActiveModel
-from ...utils import load_model_data_from_yaml
-from ...data import ACTIVE_MODEL_DATA_DIR
-
-SOURCE_DIR = ACTIVE_MODEL_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
-
-MODEL_0 = ActiveModel
-
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
-    MODEL_0.__name__,
-]
-
-IMPORT_METADATA = {
-    MODEL_0.__name__: {
-        "dir": SOURCE_DIR, # e.g. "interventions"
-        "model": MODEL_0, # e.g. Intervention
-        "foreign_keys": [], # e.g. ["intervention_types"]
-        "foreign_key_models": [] # e.g. [InterventionType]
-    }
-}
-
-class Command(BaseCommand):
-    help = """Load all .yaml files in the data/intervention directory
-    into the Intervention and InterventionType model"""
-
-    def add_arguments(self, parser):
-        parser.add_argument(
-            '--verbose',
-            action='store_true',
-            help='Display verbose output',
-        )
-
-    def handle(self, *args, **options):
-        verbose = options['verbose']
-        for model_name in IMPORT_MODELS:
-            _metadata = IMPORT_METADATA[model_name]
-            load_model_data_from_yaml(
-                self,
-                model_name,
-                _metadata,
-                verbose
+from django.conf import settings
+import os
+from django.core.management.base import BaseCommand
+from ...models import ActiveModel
+from ...utils import load_model_data_from_yaml
+from ...data import ACTIVE_MODEL_DATA_DIR
+
+SOURCE_DIR = ACTIVE_MODEL_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
+
+MODEL_0 = ActiveModel
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_0.__name__,
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": MODEL_0, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # e.g. [InterventionType]
+    }
+}
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output',
+        )
+
+    def handle(self, *args, **options):
+        verbose = options['verbose']
+        for model_name in IMPORT_MODELS:
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data_from_yaml(
+                self,
+                model_name,
+                _metadata,
+                verbose
             )

endoreg_db/management/commands/load_ai_model_data.py

@@ -1,45 +1,45 @@
-from django.conf import settings
-import os
-from django.core.management.base import BaseCommand
-from ...models import ModelType
-from ...utils import load_model_data_from_yaml
-from ...data import MODEL_TYPE_DATA_DIR
-
-SOURCE_DIR = MODEL_TYPE_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
-
-MODEL_0 = ModelType
-
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
-    MODEL_0.__name__,
-]
-
-IMPORT_METADATA = {
-    MODEL_0.__name__: {
-        "dir": SOURCE_DIR, # e.g. "interventions"
-        "model": MODEL_0, # e.g. Intervention
-        "foreign_keys": [], # e.g. ["intervention_types"]
-        "foreign_key_models": [] # e.g. [InterventionType]
-    }
-}
-
-class Command(BaseCommand):
-    help = """Load all .yaml files in the data/intervention directory
-    into the Intervention and InterventionType model"""
-
-    def add_arguments(self, parser):
-        parser.add_argument(
-            '--verbose',
-            action='store_true',
-            help='Display verbose output',
-        )
-
-    def handle(self, *args, **options):
-        verbose = options['verbose']
-        for model_name in IMPORT_MODELS:
-            _metadata = IMPORT_METADATA[model_name]
-            load_model_data_from_yaml(
-                self,
-                model_name,
-                _metadata,
-                verbose
+from django.conf import settings
+import os
+from django.core.management.base import BaseCommand
+from ...models import ModelType
+from ...utils import load_model_data_from_yaml
+from ...data import MODEL_TYPE_DATA_DIR
+
+SOURCE_DIR = MODEL_TYPE_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
+
+MODEL_0 = ModelType
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_0.__name__,
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": MODEL_0, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # e.g. [InterventionType]
+    }
+}
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output',
+        )
+
+    def handle(self, *args, **options):
+        verbose = options['verbose']
+        for model_name in IMPORT_MODELS:
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data_from_yaml(
+                self,
+                model_name,
+                _metadata,
+                verbose
             )

endoreg_db/management/commands/load_base_db_data.py

@@ -1,128 +1,132 @@
-from django.core.management import BaseCommand, call_command
-
-class Command(BaseCommand):
-    help = 'Run all data loading commands in the correct order'
-
-    def add_arguments(self, parser):
-        parser.add_argument(
-            '--verbose',
-            action='store_true',
-            help='Display verbose output for all commands',
-        )
-
-    def handle(self, *args, **options):
-        # verbose = options['verbose']
-        verbose = True
-
-        self.stdout.write(self.style.SUCCESS("Populating base db models with data..."))
-
-        # Run the load_profession_data command
-        self.stdout.write(self.style.SUCCESS("Running load_profession_data..."))
-        call_command('load_profession_data', verbose=verbose)
-
-        # run the load_gender_data command
-        self.stdout.write(self.style.SUCCESS("Running load_gender_data..."))
-        call_command('load_gender_data', verbose=verbose)
-
-        # Run the load_disease data command
-        self.stdout.write(self.style.SUCCESS("Running load_disease_data..."))
-        call_command('load_disease_data', verbose=verbose)
-
-        # Run the load_disease_classification data command
-        self.stdout.write(self.style.SUCCESS("Running load_disease_classification_data..."))
-        call_command('load_disease_classification_data', verbose=verbose)
-
-        # Run the load_disease_classification_choices data command
-        self.stdout.write(self.style.SUCCESS("Running load_disease_classification_choices_data..."))
-        call_command('load_disease_classification_choices_data', verbose=verbose)
-
-        # rund the load_user_groups command
-        self.stdout.write(self.style.SUCCESS("Running load_user_groups..."))
-        call_command('load_user_groups', verbose=verbose)
-
-        # run the load_report_reader_flag command
-        self.stdout.write(self.style.SUCCESS("Running load_report_reader_flag..."))
-        call_command('load_report_reader_flag', verbose=verbose)
-
-        # Run the load_pdf_type_data command
-        self.stdout.write(self.style.SUCCESS("Running load_pdf_type_data..."))
-        call_command('load_pdf_type_data', verbose=verbose)
-
-        # Run the load_endoscopy_processor_data command
-        self.stdout.write(self.style.SUCCESS("Running load_endoscopy_processor_data..."))
-        call_command('load_endoscopy_processor_data', verbose=verbose)
-
-        # Run the load_endoscope_type_data command
-        self.stdout.write(self.style.SUCCESS("Running load_endoscope_type_data..."))
-        call_command('load_endoscope_type_data', verbose=verbose)
-
-        # Run the load_unit_data command
-        self.stdout.write(self.style.SUCCESS("Running load_unit_data..."))
-        call_command('load_unit_data', verbose=verbose)
-
-        # Run the load_lab_value_data command
-        self.stdout.write(self.style.SUCCESS("Running load_lab_value_data..."))
-        call_command("load_lab_value_data", verbose=verbose)
-
-        # Run the load_information_source command
-        self.stdout.write(self.style.SUCCESS("Running load_information_source..."))
-        call_command('load_information_source', verbose=verbose)
-
-        # Run the load_center_data command
-        self.stdout.write(self.style.SUCCESS("Running load_center_data..."))
-        call_command('load_center_data', verbose=verbose)
-
-        # Run the load_examination_data command
-        self.stdout.write(self.style.SUCCESS("Running load_examination_data..."))
-        call_command('load_examination_data', verbose=verbose)
-
-        # Run the load_label_data command
-        self.stdout.write(self.style.SUCCESS("Running load_label_data..."))
-        call_command('load_label_data', verbose=verbose)
-
-        # Run the load_ai_model_data command
-        self.stdout.write(self.style.SUCCESS("Running load_ai_model_data..."))
-        call_command('load_ai_model_data', verbose=verbose)
-
-        # Run the load_event_data command
-        self.stdout.write(self.style.SUCCESS("Running load_event_data..."))
-        call_command('load_event_data', verbose=verbose)
-
-        # run the load_medication_data command
-        self.stdout.write(self.style.SUCCESS("Running load_medication_data..."))
-        call_command('load_medication_data', verbose=verbose)
-
-        # Run the load_medication_indication_type_data command
-        self.stdout.write(self.style.SUCCESS("Running load_medication_indication_type_data..."))
-        call_command('load_medication_indication_type_data', verbose=verbose)
-
-        # Run the load_medication_intake_time_data command
-        self.stdout.write(self.style.SUCCESS("Running load_medication_intake_time_data..."))
-        call_command('load_medication_intake_time_data', verbose=verbose)
-
-        # Run the load_medication_schedule_data command
-        self.stdout.write(self.style.SUCCESS("Running load_medication_schedule_data..."))
-        call_command('load_medication_schedule_data', verbose=verbose)
-
-        # Run the load_medication_indication_data command
-        self.stdout.write(self.style.SUCCESS("Running load_medication_indication_data..."))
-        call_command('load_medication_indication_data', verbose=verbose)
-
-        # Run the load_green_endoscopy_wuerzburg_data command
-        self.stdout.write(self.style.SUCCESS("Running load_green_endoscopy_wuerzburg_data..."))
-        call_command('load_green_endoscopy_wuerzburg_data', verbose=verbose)
-
-        # Load G-Play Data
-        # run the load_distribution_data command
-        self.stdout.write(self.style.SUCCESS("Running load_distribution_data..."))
-        call_command('load_distribution_data', verbose=verbose)
-        # Run the load_g_play_data command
-        self.stdout.write(self.style.SUCCESS("Running load_g_play_data..."))
-        call_command('load_g_play_data', verbose=verbose)
-
-        # Necessary? Migrate? FIXME
-        # # Run the load_active_model_data command
-        # self.stdout.write(self.style.SUCCESS("Running load_active_model_data..."))
-        # call_command('load_active_model_data', verbose=verbose)
-        
-        self.stdout.write(self.style.SUCCESS("All data loading commands executed successfully."))
+from django.core.management import BaseCommand, call_command
+
+class Command(BaseCommand):
+    help = 'Run all data loading commands in the correct order'
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output for all commands',
+        )
+
+    def handle(self, *args, **options):
+        # verbose = options['verbose']
+        verbose = True
+
+        self.stdout.write(self.style.SUCCESS("Populating base db models with data..."))
+
+        # Run the load_network_data command
+        self.stdout.write(self.style.SUCCESS("Running load_network_data..."))
+        call_command('load_network_data', verbose=verbose)
+
+        # Run the load_profession_data command
+        self.stdout.write(self.style.SUCCESS("Running load_profession_data..."))
+        call_command('load_profession_data', verbose=verbose)
+
+        # run the load_gender_data command
+        self.stdout.write(self.style.SUCCESS("Running load_gender_data..."))
+        call_command('load_gender_data', verbose=verbose)
+
+        # Run the load_disease data command
+        self.stdout.write(self.style.SUCCESS("Running load_disease_data..."))
+        call_command('load_disease_data', verbose=verbose)
+
+        # Run the load_disease_classification data command
+        self.stdout.write(self.style.SUCCESS("Running load_disease_classification_data..."))
+        call_command('load_disease_classification_data', verbose=verbose)
+
+        # Run the load_disease_classification_choices data command
+        self.stdout.write(self.style.SUCCESS("Running load_disease_classification_choices_data..."))
+        call_command('load_disease_classification_choices_data', verbose=verbose)
+
+        # rund the load_user_groups command
+        self.stdout.write(self.style.SUCCESS("Running load_user_groups..."))
+        call_command('load_user_groups', verbose=verbose)
+
+        # run the load_report_reader_flag command
+        self.stdout.write(self.style.SUCCESS("Running load_report_reader_flag..."))
+        call_command('load_report_reader_flag', verbose=verbose)
+
+        # Run the load_pdf_type_data command
+        self.stdout.write(self.style.SUCCESS("Running load_pdf_type_data..."))
+        call_command('load_pdf_type_data', verbose=verbose)
+
+        # Run the load_endoscopy_processor_data command
+        self.stdout.write(self.style.SUCCESS("Running load_endoscopy_processor_data..."))
+        call_command('load_endoscopy_processor_data', verbose=verbose)
+
+        # Run the load_endoscope_type_data command
+        self.stdout.write(self.style.SUCCESS("Running load_endoscope_type_data..."))
+        call_command('load_endoscope_type_data', verbose=verbose)
+
+        # Run the load_unit_data command
+        self.stdout.write(self.style.SUCCESS("Running load_unit_data..."))
+        call_command('load_unit_data', verbose=verbose)
+
+        # Run the load_lab_value_data command
+        self.stdout.write(self.style.SUCCESS("Running load_lab_value_data..."))
+        call_command("load_lab_value_data", verbose=verbose)
+
+        # Run the load_information_source command
+        self.stdout.write(self.style.SUCCESS("Running load_information_source..."))
+        call_command('load_information_source', verbose=verbose)
+
+        # Run the load_center_data command
+        self.stdout.write(self.style.SUCCESS("Running load_center_data..."))
+        call_command('load_center_data', verbose=verbose)
+
+        # Run the load_examination_data command
+        self.stdout.write(self.style.SUCCESS("Running load_examination_data..."))
+        call_command('load_examination_data', verbose=verbose)
+
+        # Run the load_label_data command
+        self.stdout.write(self.style.SUCCESS("Running load_label_data..."))
+        call_command('load_label_data', verbose=verbose)
+
+        # Run the load_ai_model_data command
+        self.stdout.write(self.style.SUCCESS("Running load_ai_model_data..."))
+        call_command('load_ai_model_data', verbose=verbose)
+
+        # Run the load_event_data command
+        self.stdout.write(self.style.SUCCESS("Running load_event_data..."))
+        call_command('load_event_data', verbose=verbose)
+
+        # run the load_medication_data command
+        self.stdout.write(self.style.SUCCESS("Running load_medication_data..."))
+        call_command('load_medication_data', verbose=verbose)
+
+        # Run the load_medication_indication_type_data command
+        self.stdout.write(self.style.SUCCESS("Running load_medication_indication_type_data..."))
+        call_command('load_medication_indication_type_data', verbose=verbose)
+
+        # Run the load_medication_intake_time_data command
+        self.stdout.write(self.style.SUCCESS("Running load_medication_intake_time_data..."))
+        call_command('load_medication_intake_time_data', verbose=verbose)
+
+        # Run the load_medication_schedule_data command
+        self.stdout.write(self.style.SUCCESS("Running load_medication_schedule_data..."))
+        call_command('load_medication_schedule_data', verbose=verbose)
+
+        # Run the load_medication_indication_data command
+        self.stdout.write(self.style.SUCCESS("Running load_medication_indication_data..."))
+        call_command('load_medication_indication_data', verbose=verbose)
+
+        # Run the load_green_endoscopy_wuerzburg_data command
+        self.stdout.write(self.style.SUCCESS("Running load_green_endoscopy_wuerzburg_data..."))
+        call_command('load_green_endoscopy_wuerzburg_data', verbose=verbose)
+
+        # Load G-Play Data
+        # run the load_distribution_data command
+        self.stdout.write(self.style.SUCCESS("Running load_distribution_data..."))
+        call_command('load_distribution_data', verbose=verbose)
+        # Run the load_g_play_data command
+        self.stdout.write(self.style.SUCCESS("Running load_g_play_data..."))
+        call_command('load_g_play_data', verbose=verbose)
+
+        # Necessary? Migrate? FIXME
+        # # Run the load_active_model_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_active_model_data..."))
+        # call_command('load_active_model_data', verbose=verbose)
+        
+        self.stdout.write(self.style.SUCCESS("All data loading commands executed successfully."))