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| 0.9.0 | ||
| 0.9.1 |
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95 changes: 95 additions & 0 deletions
95
promort/clinical_annotations_manager/management/commands/get_gleason_data.py
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| # 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. | ||
|
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| from django.core.management.base import BaseCommand | ||
| from django.core.paginator import Paginator | ||
| from clinical_annotations_manager.models import GleasonElement | ||
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| from csv import DictWriter | ||
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| import logging | ||
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| logger = logging.getLogger('promort_commands') | ||
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| class Command(BaseCommand): | ||
| help = """ | ||
| Export existing Gleason items data to CSV. | ||
| No ROIs are exported, only metadata; to export ROIs use the extract_gleason_elements command. | ||
| """ | ||
|
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| 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)') | ||
|
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| def _dump_row(self, gleason_element, csv_writer): | ||
| try: | ||
| creation_start_date = gleason_element.creation_start_date.strftime('%Y-%m-%d %H:%M:%S') | ||
| except AttributeError: | ||
| creation_start_date = None | ||
| fr_ann = gleason_element.focus_region_annotation | ||
| csv_writer.writerow( | ||
| { | ||
| 'case_id': fr_ann.focus_region.core.slice.slide.case.id, | ||
| 'slide_id': fr_ann.focus_region.core.slice.slide.id, | ||
| 'rois_review_step_id': fr_ann.annotation_step.rois_review_step.label, | ||
| 'clinical_review_step_id': fr_ann.annotation_step.label, | ||
| 'reviewer': fr_ann.author.username, | ||
| 'focus_region_id': fr_ann.focus_region.id, | ||
| 'focus_region_label': fr_ann.focus_region.label, | ||
| 'core_id': fr_ann.focus_region.core.id, | ||
| 'core_label': fr_ann.focus_region.core.label, | ||
| 'gleason_element_id': gleason_element.id, | ||
| 'gleason_type': gleason_element.gleason_type, | ||
| 'creation_start_date': creation_start_date, | ||
| 'creation_date': gleason_element.creation_date.strftime('%Y-%m-%d %H:%M:%S') | ||
| } | ||
| ) | ||
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| def _dump_data(self, page_size, csv_writer): | ||
| if page_size > 0: | ||
| logger.info('Pagination enabled (%d records for page)', page_size) | ||
| ge_qs = GleasonElement.objects.get_queryset().order_by('creation_date') | ||
| paginator = Paginator(ge_qs, page_size) | ||
| for x in paginator.page_range: | ||
| logger.info(f'-- page {x} --') | ||
| page = paginator.page(x) | ||
| for ge in page.object_list: | ||
| self._dump_row(ge, csv_writer) | ||
| else: | ||
| logger.info('Loading full batch') | ||
| gleason_elements = GleasonElement.objects.all() | ||
| for ge in gleason_elements: | ||
| self._dump_row(ge, csv_writer) | ||
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| 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', 'gleason_element_id', 'gleason_type', | ||
| 'creation_start_date', 'creation_date'] | ||
| with open(out_file, 'w') as ofile: | ||
| writer = DictWriter(ofile, delimiter=',', fieldnames=header) | ||
| writer.writeheader() | ||
| self._dump_data(page_size, writer) | ||
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| def handle(self, *args, **opts): | ||
| logger.info('=== Starting export job ===') | ||
| self._export_data(opts['output'], opts['page_size']) | ||
| logger.info('=== Data saved to {0} ==='.format(opts['output'])) |
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33 changes: 33 additions & 0 deletions
33
promort/clinical_annotations_manager/migrations/0018_auto_20211128_1525.py
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| # Generated by Django 3.1.13 on 2021-11-28 15:25 | ||
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| from django.db import migrations | ||
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| class Migration(migrations.Migration): | ||
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| dependencies = [ | ||
| ('clinical_annotations_manager', '0017_auto_20210424_1321'), | ||
| ] | ||
|
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| operations = [ | ||
| migrations.RenameField( | ||
| model_name='coreannotation', | ||
| old_name='creation_start_date', | ||
| new_name='action_start_time', | ||
| ), | ||
| migrations.RenameField( | ||
| model_name='focusregionannotation', | ||
| old_name='creation_start_date', | ||
| new_name='action_start_time', | ||
| ), | ||
| migrations.RenameField( | ||
| model_name='gleasonelement', | ||
| old_name='creation_start_date', | ||
| new_name='action_start_time', | ||
| ), | ||
| migrations.RenameField( | ||
| model_name='sliceannotation', | ||
| old_name='creation_start_date', | ||
| new_name='action_start_time', | ||
| ), | ||
| ] |
33 changes: 33 additions & 0 deletions
33
promort/clinical_annotations_manager/migrations/0019_auto_20211201_0933.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| # Generated by Django 3.1.13 on 2021-12-01 09:33 | ||
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| from django.db import migrations, models | ||
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| class Migration(migrations.Migration): | ||
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| dependencies = [ | ||
| ('clinical_annotations_manager', '0018_auto_20211128_1525'), | ||
| ] | ||
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| operations = [ | ||
| migrations.AddField( | ||
| model_name='coreannotation', | ||
| name='action_complete_time', | ||
| field=models.DateTimeField(default=None, null=True), | ||
| ), | ||
| migrations.AddField( | ||
| model_name='focusregionannotation', | ||
| name='action_complete_time', | ||
| field=models.DateTimeField(default=None, null=True), | ||
| ), | ||
| migrations.AddField( | ||
| model_name='gleasonelement', | ||
| name='action_complete_time', | ||
| field=models.DateTimeField(default=None, null=True), | ||
| ), | ||
| migrations.AddField( | ||
| model_name='sliceannotation', | ||
| name='action_complete_time', | ||
| field=models.DateTimeField(default=None, null=True), | ||
| ), | ||
| ] |
30 changes: 30 additions & 0 deletions
30
promort/clinical_annotations_manager/migrations/0020_auto_20211206_1018.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| # Generated by Django 3.1.13 on 2021-12-06 10:18 | ||
|
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| from django.db import migrations | ||
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| def update_action_complete_time(apps, schema_editor): | ||
| GleasonElements = apps.get_model('clinical_annotations_manager', 'GleasonElement') | ||
| for g_element in GleasonElements.objects.all(): | ||
| g_element.action_complete_time = g_element.creation_date | ||
| g_element.creation_date = g_element.focus_region_annotation.creation_date | ||
| g_element.save() | ||
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| def reverse_action_complete_time(apps, schema_editor): | ||
| GleasonElements = apps.get_model('clinical_annotations_manager', 'GleasonElement') | ||
| for g_element in GleasonElements.objects.all(): | ||
| g_element.creation_date = g_element.action_complete_time | ||
| g_element.action_complete_time = None | ||
| g_element.save() | ||
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| class Migration(migrations.Migration): | ||
|
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| dependencies = [ | ||
| ('clinical_annotations_manager', '0019_auto_20211201_0933'), | ||
| ] | ||
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| operations = [ | ||
| migrations.RunPython(update_action_complete_time, reverse_action_complete_time), | ||
| ] |
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