feat: extract Gleason subregions data

promort/clinical_annotations_manager/management/commands/get_gleason_subregions_data.py

@@ -0,0 +1,114 @@
+#  Copyright (c) 2021, CRS4
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a copy of
+#  this software and associated documentation files (the "Software"), to deal in
+#  the Software without restriction, including without limitation the rights to
+#  use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+#  the Software, and to permit persons to whom the Software is furnished to do so,
+#  subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included in all
+#  copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+#  FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+#  COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+#  IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+#  CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+from django.core.management.base import BaseCommand
+from django.core.paginator import Paginator
+from clinical_annotations_manager.models import GleasonPatternSubregion
+
+from csv import DictWriter
+
+import logging, json
+
+logger = logging.getLogger("promort_commands")
+
+
+class Command(BaseCommand):
+    help = """
+    Export existing Gleason Pattern subregions data to a CSV
+    """
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "--output_file",
+            dest="output",
+            type=str,
+            required=True,
+            help="path of the output CSV file",
+        )
+        parser.add_argument(
+            "--page_size",
+            dest="page_size",
+            type=int,
+            default=0,
+            help="the number of records retrieved for each page (this will enable pagination)",
+        )
+
+    def _dump_row(self, gleason_subregion, csv_writer):
+        gp = gleason_subregion.gleason_pattern
+        csv_writer.writerow(
+            {
+                "case_id": gp.annotation_step.slide.case.id,
+                "slide_id": gp.annotation_step.slide.id,
+                "clinical_review_step_id": gp.annotation_step.label,
+                "reviewer": gp.author.username,
+                "focus_region_id": gp.focus_region.id,
+                "gleason_pattern_id": gp.id,
+                "gleason_pattern_label": gp.label,
+                "creation_date": gleason_subregion.creation_date.strftime(
+                    "%Y-%m-%d %H:%M:%S"
+                ),
+                "subregion_id": gleason_subregion.id,
+                "subregion_label": gleason_subregion.label,
+                "type": json.loads(gleason_subregion.details_json)["type"],
+                "area": gleason_subregion.area,
+            }
+        )
+
+    def _dump_data(self, page_size, csv_writer):
+        if page_size > 0:
+            logger.info(f"Pagination enabled ({page_size} records for page)")
+            g_el_qs = GleasonPatternSubregion.objects.get_queryset().order_by(
+                "creation_date"
+            )
+            paginator = Paginator(g_el_qs, page_size)
+            for x in paginator.page_range:
+                logger.info(f"-- page {x} --")
+                page = paginator.page(x)
+                for g_el in page.object_list:
+                    self._dump_row(g_el, csv_writer)
+        else:
+            logger.info("Loading full batch")
+            gleason_patterns = GleasonPatternSubregion.objects.all()
+            for g_el in gleason_patterns:
+                self._dump_row(g_el, csv_writer)
+
+    def _export_data(self, out_file, page_size):
+        header = [
+            "case_id",
+            "slide_id",
+            "clinical_review_step_id",
+            "reviewer",
+            "focus_region_id",
+            "gleason_pattern_id",
+            "gleason_pattern_label",
+            "creation_date",
+            "subregion_id",
+            "subregion_label",
+            "type",
+            "area",
+        ]
+        with open(out_file, "w") as ofile:
+            writer = DictWriter(ofile, delimiter=",", fieldnames=header)
+            writer.writeheader()
+            self._dump_data(page_size, writer)
+
+    def handle(self, *args, **opts):
+        logger.info("=== Starting export job ===")
+        self._export_data(opts["output"], opts["page_size"])
+        logger.info(f"=== Data saved to {opts['output']}===")