Release v0.6.0

promort/VERSION

@@ -1 +1 @@
-0.5.4
+0.6.0

promort/clinical_annotations_manager/management/commands/get_cores_clinical_data.py

@@ -56,6 +56,10 @@ def _dump_data(self, page_size, csv_writer):
                 self._dump_row(ca, csv_writer)
 
     def _dump_row(self, core_annotation, csv_writer):
+        try:
+            creation_start_date = core_annotation.creation_start_date.strftime('%Y-%m-%d %H:%M:%S')
+        except AttributeError:
+            creation_start_date = None
         csv_writer.writerow(
             {
                 'case_id': core_annotation.core.slice.slide.case.id,
@@ -65,6 +69,7 @@ def _dump_row(self, core_annotation, csv_writer):
                 'reviewer': core_annotation.author.username,
                 'core_id': core_annotation.core.id,
                 'core_label': core_annotation.core.label,
+                'creation_start_date': creation_start_date,
                 'creation_date': core_annotation.creation_date.strftime('%Y-%m-%d %H:%M:%S'),
                 'primary_gleason': core_annotation.primary_gleason,
                 'secondary_gleason': core_annotation.secondary_gleason,
@@ -74,8 +79,8 @@ def _dump_row(self, core_annotation, csv_writer):
 
     def _export_data(self, out_file, page_size):
         header = ['case_id', 'slide_id', 'rois_review_step_id', 'clinical_review_step_id', 'reviewer',
-                  'core_id', 'core_label', 'creation_date', 'primary_gleason', 'secondary_gleason',
-                  'gleason_group_who_16']
+                  'core_id', 'core_label', 'creation_start_date', 'creation_date', 'primary_gleason',
+                  'secondary_gleason', 'gleason_group_who_16']
         with open(out_file, 'w') as ofile:
             writer = DictWriter(ofile, delimiter=',', fieldnames=header)
             writer.writeheader()

promort/clinical_annotations_manager/management/commands/get_focus_regions_clinical_data.py

@@ -55,6 +55,10 @@ def _dump_data(self, page_size, csv_writer):
                 self._dump_row(fra, csv_writer)
 
     def _dump_row(self, focus_region_annotation, csv_writer):
+        try:
+            creation_start_date = focus_region_annotation.creation_start_date.strftime('%Y-%m-%d %H:%M:%S')
+        except AttributeError:
+            creation_start_date = None
         csv_writer.writerow(
             {
                 'case_id': focus_region_annotation.focus_region.core.slice.slide.case.id,
@@ -66,6 +70,7 @@ def _dump_row(self, focus_region_annotation, csv_writer):
                 'focus_region_label': focus_region_annotation.focus_region.label,
                 'core_id': focus_region_annotation.focus_region.core.id,
                 'core_label': focus_region_annotation.focus_region.core.label,
+                'creation_start_date': creation_start_date,
                 'creation_date': focus_region_annotation.creation_date.strftime('%Y-%m-%d %H:%M:%S'),
                 'perineural_involvement': focus_region_annotation.perineural_involvement,
                 'intraductal_carcinoma': focus_region_annotation.intraductal_carcinoma,
@@ -83,9 +88,9 @@ def _dump_row(self, focus_region_annotation, csv_writer):
 
     def _export_data(self, out_file, page_size):
         header = ['case_id', 'slide_id', 'rois_review_step_id', 'clinical_review_step_id', 'reviewer',
-                  'focus_region_id', 'focus_region_label', 'core_id', 'core_label', 'creation_date',
-                  'perineural_involvement', 'intraductal_carcinoma', 'ductal_carcinoma', 'poorly_formed_glands',
-                  'cribriform_pattern', 'small_cell_signet_ring', 'hypernephroid_pattern',
+                  'focus_region_id', 'focus_region_label', 'core_id', 'core_label', 'creation_start_date',
+                  'creation_date', 'perineural_involvement', 'intraductal_carcinoma', 'ductal_carcinoma',
+                  'poorly_formed_glands', 'cribriform_pattern', 'small_cell_signet_ring', 'hypernephroid_pattern',
                   'mucinous', 'comedo_necrosis', 'total_gleason_4_area', 'gleason_4_percentage']
         with open(out_file, 'w') as ofile:
             writer = DictWriter(ofile, delimiter=',', fieldnames=header)

promort/clinical_annotations_manager/management/commands/get_slices_clinical_data.py

@@ -56,6 +56,10 @@ def _dump_data(self, page_size, csv_writer):
                 self._dump_row(sa, csv_writer)
 
     def _dump_row(self, slice_annotation, csv_writer):
+        try:
+            creation_start_date = slice_annotation.creation_start_date.strftime('%Y-%m-%d %H:%M:%S')
+        except AttributeError:
+            creation_start_date = None
         csv_writer.writerow(
             {
                 'case_id': slice_annotation.slice.slide.case.id,
@@ -65,6 +69,7 @@ def _dump_row(self, slice_annotation, csv_writer):
                 'reviewer': slice_annotation.author.username,
                 'slice_id': slice_annotation.slice.id,
                 'slice_label': slice_annotation.slice.label,
+                'creation_start_date': creation_start_date,
                 'creation_date': slice_annotation.creation_date.strftime('%Y-%m-%d %H:%M:%S'),
                 'high_grade_pin': slice_annotation.high_grade_pin,
                 'pah': slice_annotation.pah,
@@ -78,8 +83,8 @@ def _dump_row(self, slice_annotation, csv_writer):
 
     def _export_data(self, out_file, page_size):
         header = ['case_id', 'slide_id', 'rois_review_step_id', 'clinical_review_step_id', 'reviewer',
-                  'slice_id', 'slice_label', 'creation_date', 'high_grade_pin', 'pah', 'chronic_inflammation',
-                  'acute_inflammation', 'periglandular_inflammation',
+                  'slice_id', 'slice_label', 'creation_start_date', 'creation_date', 'high_grade_pin', 'pah',
+                  'chronic_inflammation', 'acute_inflammation', 'periglandular_inflammation',
                   'intraglandular_inflammation', 'stromal_inflammation']
         with open(out_file, 'w') as ofile:
             writer = DictWriter(ofile, delimiter=',', fieldnames=header)

promort/clinical_annotations_manager/migrations/0016_auto_20201124_0832.py

@@ -0,0 +1,35 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.29 on 2020-11-24 08:32
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('clinical_annotations_manager', '0015_gleasonelement_creation_date'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='coreannotation',
+            name='creation_start_date',
+            field=models.DateTimeField(default=None, null=True),
+        ),
+        migrations.AddField(
+            model_name='focusregionannotation',
+            name='creation_start_date',
+            field=models.DateTimeField(default=None, null=True),
+        ),
+        migrations.AddField(
+            model_name='gleasonelement',
+            name='creation_start_date',
+            field=models.DateTimeField(default=None, null=True),
+        ),
+        migrations.AddField(
+            model_name='sliceannotation',
+            name='creation_start_date',
+            field=models.DateTimeField(default=None, null=True),
+        ),
+    ]

promort/clinical_annotations_manager/models.py

@@ -30,6 +30,7 @@ class SliceAnnotation(models.Model):
                               related_name='clinical_annotations')
     annotation_step = models.ForeignKey(ClinicalAnnotationStep, on_delete=models.PROTECT,
                                         blank=False, related_name='slice_annotations')
+    creation_start_date = models.DateTimeField(null=True, default=None)
     creation_date = models.DateTimeField(default=timezone.now)
     high_grade_pin = models.BooleanField(blank=False, null=False, default=False)
     pah = models.BooleanField(blank=False, null=False, default=False)
@@ -84,6 +85,7 @@ class CoreAnnotation(models.Model):
                              related_name='clinical_annotations')
     annotation_step = models.ForeignKey(ClinicalAnnotationStep, on_delete=models.PROTECT,
                                         blank=False, related_name='core_annotations')
+    creation_start_date = models.DateTimeField(null=True, default=None)
     creation_date = models.DateTimeField(default=timezone.now)
     primary_gleason = models.IntegerField(blank=False)
     secondary_gleason = models.IntegerField(blank=False)
@@ -130,6 +132,7 @@ class FocusRegionAnnotation(models.Model):
                                      blank=False, related_name='clinical_annotations')
     annotation_step = models.ForeignKey(ClinicalAnnotationStep, on_delete=models.PROTECT,
                                         blank=False, related_name='focus_region_annotations')
+    creation_start_date = models.DateTimeField(null=True, default=None)
     creation_date = models.DateTimeField(default=timezone.now)
     # cancerous region fields
     perineural_involvement = models.BooleanField(blank=False, null=False, default=False)
@@ -187,6 +190,7 @@ class GleasonElement(models.Model):
     cellular_density_helper_json = models.TextField(blank=True, null=True)
     cellular_density = models.IntegerField(blank=True, null=True)
     cells_count = models.IntegerField(blank=True, null=True)
+    creation_start_date = models.DateTimeField(null=True, default=None)
     creation_date = models.DateTimeField(default=timezone.now)
 
     def get_gleason_type_label(self):

promort/clinical_annotations_manager/serializers.py

@@ -41,7 +41,7 @@ class SliceAnnotationSerializer(serializers.ModelSerializer):
 
     class Meta:
         model = SliceAnnotation
-        fields = ('id', 'author', 'slice', 'annotation_step', 'creation_date', 'high_grade_pin',
+        fields = ('id', 'author', 'slice', 'annotation_step', 'creation_start_date', 'creation_date', 'high_grade_pin',
                   'pah', 'chronic_inflammation', 'acute_inflammation', 'periglandular_inflammation',
                   'intraglandular_inflammation', 'stromal_inflammation', 'gleason_4_percentage')
         read_only_fields = ('id', 'creation_date', 'gleason_4_percentage')
@@ -73,7 +73,7 @@ class CoreAnnotationSerializer(serializers.ModelSerializer):
 
     class Meta:
         model = CoreAnnotation
-        fields = ('id', 'author', 'core', 'annotation_step', 'creation_date', 'primary_gleason',
+        fields = ('id', 'author', 'core', 'annotation_step', 'creation_start_date', 'creation_date', 'primary_gleason',
                   'secondary_gleason', 'gleason_score', 'gleason_4_percentage', 'gleason_group')
         read_only_fields = ('id', 'creation_date', 'gleason_score', 'gleason_4_percentage')
         write_only_fields = ('annotation_step',)
@@ -105,7 +105,7 @@ class Meta:
         model = GleasonElement
         fields = ('id', 'gleason_type', 'gleason_label', 'json_path', 'area',
                   'cellular_density_helper_json', 'cellular_density', 'cells_count',
-                  'creation_date')
+                  'creation_date', 'creation_start_date')
         read_only_fields = ('gleason_label',)
 
     @staticmethod
@@ -140,11 +140,11 @@ class FocusRegionAnnotationSerializer(serializers.ModelSerializer):
 
     class Meta:
         model = FocusRegionAnnotation
-        fields = ('id', 'author', 'focus_region', 'annotation_step', 'creation_date', 'perineural_involvement',
-                  'intraductal_carcinoma', 'ductal_carcinoma', 'poorly_formed_glands', 'cribriform_pattern',
-                  'small_cell_signet_ring', 'hypernephroid_pattern', 'mucinous', 'comedo_necrosis',
-                  'inflammation', 'pah', 'atrophic_lesions', 'adenosis', 'cellular_density_helper_json',
-                  'cellular_density', 'cells_count', 'gleason_elements')
+        fields = ('id', 'author', 'focus_region', 'annotation_step', 'creation_start_date', 'creation_date',
+                  'perineural_involvement', 'intraductal_carcinoma', 'ductal_carcinoma', 'poorly_formed_glands',
+                  'cribriform_pattern', 'small_cell_signet_ring', 'hypernephroid_pattern', 'mucinous',
+                  'comedo_necrosis', 'inflammation', 'pah', 'atrophic_lesions', 'adenosis',
+                  'cellular_density_helper_json', 'cellular_density', 'cells_count', 'gleason_elements')
         read_only_fields = ('creation_date',)
         write_only_fields = ('id', 'annotation_step', 'gleason_elements', 'author')
 

promort/rois_manager/management/commands/get_cores_data.py

@@ -56,6 +56,10 @@ def _dump_data(self, page_size, csv_writer):
                 self._dump_row(c, csv_writer)
 
     def _dump_row(self, core, csv_writer):
+        try:
+            creation_start_date = core.creation_start_date.strftime('%Y-%m-%d %H:%M:%S')
+        except AttributeError:
+            creation_start_date = None
         csv_writer.writerow(
             {
                 'case_id': core.slice.slide.case.id,
@@ -64,6 +68,7 @@ def _dump_row(self, core, csv_writer):
                 'parent_slice_id': core.slice.id,
                 'core_label': core.label,
                 'core_id': core.id,
+                'creation_start_date': creation_start_date,
                 'creation_date': core.creation_date.strftime('%Y-%m-%d %H:%M:%S'),
                 'reviewer': core.author.username,
                 'length': core.length,
@@ -76,8 +81,8 @@ def _dump_row(self, core, csv_writer):
         )
 
     def _export_data(self, out_file, page_size):
-        header = ['case_id', 'slide_id', 'roi_review_step_id', 'parent_slice_id',
-                  'core_label', 'core_id', 'creation_date', 'reviewer', 'length', 'area', 'tumor_length',
+        header = ['case_id', 'slide_id', 'roi_review_step_id', 'parent_slice_id', 'core_label', 'core_id',
+                  'creation_start_date', 'creation_date', 'reviewer', 'length', 'area', 'tumor_length',
                   'positive_core', 'normal_tissue_percentage', 'total_tumor_area']
         with open(out_file, 'w') as ofile:
             writer = DictWriter(ofile, delimiter=',', fieldnames=header)

promort/rois_manager/management/commands/get_focus_regions_data.py

@@ -56,6 +56,10 @@ def _dump_data(self, page_size, csv_writer):
                 self._dump_row(fr, csv_writer)
 
     def _dump_row(self, focus_region, csv_writer):
+        try:
+            creation_start_date = focus_region.creation_start_date.strftime('%Y-%m-%d %H:%M:%S')
+        except AttributeError:
+            creation_start_date = None
         csv_writer.writerow(
             {
                 'case_id': focus_region.core.slice.slide.case.id,
@@ -65,6 +69,7 @@ def _dump_row(self, focus_region, csv_writer):
                 'parent_core_label': focus_region.core.label,
                 'focus_region_label': focus_region.label,
                 'focus_region_id': focus_region.id,
+                'creation_start_date': creation_start_date,
                 'creation_date': focus_region.creation_date.strftime('%Y-%m-%d %H:%M:%S'),
                 'reviewer': focus_region.author.username,
                 'length': focus_region.length,
@@ -84,7 +89,7 @@ def _get_region_tissue_status(self, focus_region):
 
     def _export_data(self, out_file, page_size):
         header = ['case_id', 'slide_id', 'rois_review_step_id', 'parent_core_id', 'parent_core_label',
-                  'focus_region_label', 'focus_region_id', 'creation_date', 'reviewer', 'length',
+                  'focus_region_label', 'focus_region_id', 'creation_start_date', 'creation_date', 'reviewer', 'length',
                   'area', 'tissue_status', 'core_coverage_percentage']
         with open(out_file, 'w') as ofile:
             writer = DictWriter(ofile, delimiter=',', fieldnames=header)

promort/rois_manager/management/commands/get_slices_data.py

@@ -56,13 +56,18 @@ def _dump_data(self, page_size, csv_writer):
                 self._dump_row(s, csv_writer)
 
     def _dump_row(self, slice, csv_writer):
+        try:
+            creation_start_date = slice.creation_start_date.strftime('%Y-%m-%d %H:%M:%S')
+        except AttributeError:
+            creation_start_date = None
         csv_writer.writerow(
             {
                 'case_id': slice.slide.case.id,
                 'slide_id': slice.slide.id,
                 'roi_review_step_id': slice.annotation_step.label,
                 'slice_label': slice.label,
                 'slice_id': slice.id,
+                'creation_start_date': creation_start_date,
                 'creation_date': slice.creation_date.strftime('%Y-%m-%d %H:%M:%S'),
                 'reviewer': slice.author.username,
                 'positive_slice': slice.is_positive(),
@@ -72,8 +77,8 @@ def _dump_row(self, slice, csv_writer):
         )
 
     def _export_data(self, out_file, page_size):
-        header = ['case_id', 'slide_id', 'roi_review_step_id', 'slice_label', 'slice_id', 'creation_date',
-                  'reviewer', 'positive_slice', 'positive_cores', 'total_cores']
+        header = ['case_id', 'slide_id', 'roi_review_step_id', 'slice_label', 'slice_id', 'creation_start_date',
+                  'creation_date', 'reviewer', 'positive_slice', 'positive_cores', 'total_cores']
         with open(out_file, 'w') as ofile:
             writer = DictWriter(ofile, delimiter=',', fieldnames=header)
             writer.writeheader()

promort/rois_manager/migrations/0019_auto_20201123_0925.py

@@ -0,0 +1,30 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.29 on 2020-11-23 09:25
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('rois_manager', '0018_remove_focusregion_cancerous_region'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='core',
+            name='craetion_start_date',
+            field=models.DateTimeField(default=None, null=True),
+        ),
+        migrations.AddField(
+            model_name='focusregion',
+            name='creation_start_date',
+            field=models.DateTimeField(default=None, null=True),
+        ),
+        migrations.AddField(
+            model_name='slice',
+            name='creation_start_date',
+            field=models.DateTimeField(default=None, null=True),
+        ),
+    ]

promort/rois_manager/migrations/0020_auto_20201123_1615.py

@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.29 on 2020-11-23 16:15
+from __future__ import unicode_literals
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('rois_manager', '0019_auto_20201123_0925'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='core',
+            old_name='craetion_start_date',
+            new_name='creation_start_date',
+        ),
+    ]

promort/rois_manager/models.py

@@ -29,6 +29,7 @@ class Slice(models.Model):
     author = models.ForeignKey(User, on_delete=models.PROTECT, blank=False)
     annotation_step = models.ForeignKey(ROIsAnnotationStep, on_delete=models.PROTECT,
                                         blank=False, related_name='slices')
+    creation_start_date = models.DateTimeField(null=True, default=None)
     creation_date = models.DateTimeField(auto_now_add=True)
     roi_json = models.TextField(blank=False)
     total_cores = models.IntegerField(blank=False, default=0)
@@ -62,6 +63,7 @@ class Core(models.Model):
                               blank=False, related_name='cores')
     author = models.ForeignKey(User, on_delete=models.PROTECT,
                                blank=False)
+    creation_start_date = models.DateTimeField(null=True, default=None)
     creation_date = models.DateTimeField(auto_now_add=True)
     roi_json = models.TextField(blank=False)
     length = models.FloatField(blank=False, default=0.0)
@@ -101,6 +103,7 @@ class FocusRegion(models.Model):
                              blank=False, related_name='focus_regions')
     author = models.ForeignKey(User, on_delete=models.PROTECT,
                                blank=False)
+    creation_start_date = models.DateTimeField(null=True, default=None)
     creation_date = models.DateTimeField(auto_now_add=True)
     roi_json = models.TextField(blank=False)
     length = models.FloatField(blank=False, default=0.0)