endoreg-db 0.3.6__py3-none-any.whl → 0.3.7__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (347) hide show
  1. endoreg_db/admin.py +3 -3
  2. endoreg_db/apps.py +6 -6
  3. endoreg_db/data/__init__.py +67 -64
  4. endoreg_db/data/active_model/data.yaml +2 -2
  5. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -167
  6. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +7 -7
  7. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +8 -8
  8. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +22 -22
  9. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +18 -18
  10. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +18 -18
  11. endoreg_db/data/case_template/rule/19_create_patient.yaml +16 -16
  12. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -35
  13. endoreg_db/data/case_template/rule_value_type/base_types.yaml +58 -58
  14. endoreg_db/data/case_template/template/base.yaml +7 -7
  15. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +2 -2
  16. endoreg_db/data/case_template/tmp/_rule_value +13 -13
  17. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -21
  18. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +9 -9
  19. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +6 -6
  20. endoreg_db/data/center/data.yaml +59 -59
  21. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -144
  22. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -48
  23. endoreg_db/data/disease/cardiovascular.yaml +37 -37
  24. endoreg_db/data/disease/hepatology.yaml +4 -4
  25. endoreg_db/data/disease/misc.yaml +5 -5
  26. endoreg_db/data/disease/renal.yaml +4 -4
  27. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +5 -5
  28. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +5 -5
  29. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +40 -40
  30. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +19 -19
  31. endoreg_db/data/distribution/date/patient.yaml +6 -6
  32. endoreg_db/data/distribution/single_categorical/patient.yaml +6 -6
  33. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -132
  34. endoreg_db/data/endoscope_type/data.yaml +10 -10
  35. endoreg_db/data/endoscopy_processor/data.yaml +45 -45
  36. endoreg_db/data/event/cardiology.yaml +27 -27
  37. endoreg_db/data/event/neurology.yaml +13 -13
  38. endoreg_db/data/event/surgery.yaml +12 -12
  39. endoreg_db/data/event/thrombembolism.yaml +19 -19
  40. endoreg_db/data/examination/examinations/data.yaml +65 -65
  41. endoreg_db/data/examination/time/data.yaml +47 -47
  42. endoreg_db/data/examination/time-type/data.yaml +7 -7
  43. endoreg_db/data/examination/type/data.yaml +5 -5
  44. endoreg_db/data/gender/data.yaml +18 -18
  45. endoreg_db/data/information_source/data.yaml +30 -30
  46. endoreg_db/data/information_source/medication.yaml +5 -5
  47. endoreg_db/data/lab_value/cardiac_enzymes.yaml +30 -30
  48. endoreg_db/data/lab_value/coagulation.yaml +48 -48
  49. endoreg_db/data/lab_value/electrolytes.yaml +189 -189
  50. endoreg_db/data/lab_value/gastrointestinal_function.yaml +121 -121
  51. endoreg_db/data/lab_value/hematology.yaml +169 -169
  52. endoreg_db/data/lab_value/hormones.yaml +53 -53
  53. endoreg_db/data/lab_value/lipids.yaml +44 -44
  54. endoreg_db/data/lab_value/misc.yaml +30 -30
  55. endoreg_db/data/lab_value/renal_function.yaml +10 -10
  56. endoreg_db/data/label/label/data.yaml +62 -62
  57. endoreg_db/data/label/label-set/data.yaml +17 -17
  58. endoreg_db/data/label/label-type/data.yaml +6 -6
  59. endoreg_db/data/medication/anticoagulation.yaml +64 -64
  60. endoreg_db/data/medication/tah.yaml +69 -69
  61. endoreg_db/data/medication_indication/anticoagulation.yaml +120 -120
  62. endoreg_db/data/medication_indication_type/data.yaml +10 -10
  63. endoreg_db/data/medication_indication_type/thrombembolism.yaml +40 -40
  64. endoreg_db/data/medication_intake_time/base.yaml +30 -30
  65. endoreg_db/data/medication_schedule/apixaban.yaml +94 -94
  66. endoreg_db/data/medication_schedule/ass.yaml +12 -12
  67. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -26
  68. endoreg_db/data/model_type/data.yaml +6 -6
  69. endoreg_db/data/network_device/data.yaml +17 -0
  70. endoreg_db/data/network_device_type/data.yaml +8 -0
  71. endoreg_db/data/patient_lab_sample_type/generic.yaml +5 -5
  72. endoreg_db/data/pdf_type/data.yaml +28 -28
  73. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -66
  74. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -33
  75. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -308
  76. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -88
  77. endoreg_db/data/profession/data.yaml +70 -70
  78. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -55
  79. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +26 -26
  80. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +19 -19
  81. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -15
  82. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -12
  83. endoreg_db/data/unit/concentration.yaml +92 -92
  84. endoreg_db/data/unit/data.yaml +17 -17
  85. endoreg_db/data/unit/length.yaml +30 -30
  86. endoreg_db/data/unit/misc.yaml +19 -19
  87. endoreg_db/data/unit/rate.yaml +5 -5
  88. endoreg_db/data/unit/time.yaml +12 -12
  89. endoreg_db/data/unit/volume.yaml +35 -35
  90. endoreg_db/data/unit/weight.yaml +37 -37
  91. endoreg_db/data/waste/data.yaml +11 -11
  92. endoreg_db/forms/__init__.py +2 -2
  93. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -23
  94. endoreg_db/forms/settings/__init__.py +8 -8
  95. endoreg_db/forms/unit.py +5 -5
  96. endoreg_db/management/commands/_load_model_template.py +40 -40
  97. endoreg_db/management/commands/delete_all.py +18 -18
  98. endoreg_db/management/commands/delete_legacy_images.py +19 -19
  99. endoreg_db/management/commands/delete_legacy_videos.py +16 -16
  100. endoreg_db/management/commands/extract_legacy_video_frames.py +18 -18
  101. endoreg_db/management/commands/fetch_legacy_image_dataset.py +32 -32
  102. endoreg_db/management/commands/fix_auth_permission.py +20 -20
  103. endoreg_db/management/commands/import_legacy_images.py +94 -94
  104. endoreg_db/management/commands/import_legacy_videos.py +76 -76
  105. endoreg_db/management/commands/load_active_model_data.py +44 -44
  106. endoreg_db/management/commands/load_ai_model_data.py +44 -44
  107. endoreg_db/management/commands/load_base_db_data.py +132 -128
  108. endoreg_db/management/commands/load_center_data.py +42 -42
  109. endoreg_db/management/commands/load_disease_classification_choices_data.py +40 -40
  110. endoreg_db/management/commands/load_disease_classification_data.py +40 -40
  111. endoreg_db/management/commands/load_disease_data.py +39 -39
  112. endoreg_db/management/commands/load_distribution_data.py +65 -65
  113. endoreg_db/management/commands/load_endoscope_type_data.py +44 -44
  114. endoreg_db/management/commands/load_endoscopy_processor_data.py +44 -44
  115. endoreg_db/management/commands/load_event_data.py +40 -40
  116. endoreg_db/management/commands/load_examination_data.py +74 -74
  117. endoreg_db/management/commands/load_g_play_data.py +112 -112
  118. endoreg_db/management/commands/load_gender_data.py +43 -43
  119. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +132 -132
  120. endoreg_db/management/commands/load_information_source.py +44 -44
  121. endoreg_db/management/commands/load_lab_value_data.py +49 -49
  122. endoreg_db/management/commands/load_label_data.py +66 -66
  123. endoreg_db/management/commands/load_medication_data.py +40 -40
  124. endoreg_db/management/commands/load_medication_indication_data.py +62 -62
  125. endoreg_db/management/commands/load_medication_indication_type_data.py +40 -40
  126. endoreg_db/management/commands/load_medication_intake_time_data.py +40 -40
  127. endoreg_db/management/commands/load_medication_schedule_data.py +54 -54
  128. endoreg_db/management/commands/load_network_data.py +49 -0
  129. endoreg_db/management/commands/load_pdf_type_data.py +60 -60
  130. endoreg_db/management/commands/load_profession_data.py +43 -43
  131. endoreg_db/management/commands/load_report_reader_flag.py +45 -45
  132. endoreg_db/management/commands/load_unit_data.py +45 -45
  133. endoreg_db/management/commands/load_user_groups.py +28 -28
  134. endoreg_db/management/commands/register_ai_model.py +65 -65
  135. endoreg_db/management/commands/reset_celery_schedule.py +9 -9
  136. endoreg_db/migrations/0001_initial.py +582 -582
  137. endoreg_db/migrations/0002_rawvideofile.py +26 -26
  138. endoreg_db/migrations/0003_rawvideofile_frames_required.py +18 -18
  139. endoreg_db/migrations/0004_rename_hash_rawvideofile_video_hash.py +18 -18
  140. endoreg_db/migrations/0005_ffmpegmeta_remove_videoimportmeta_center_and_more.py +56 -56
  141. endoreg_db/migrations/0006_rawvideofile_center_alter_videometa_processor.py +25 -25
  142. endoreg_db/migrations/0007_rawvideofile_processor.py +19 -19
  143. endoreg_db/migrations/0008_rename_frames_required_rawvideofile_state_frames_required.py +18 -18
  144. endoreg_db/migrations/0009_sensitivemeta_rawvideofile_sensitive_meta.py +31 -31
  145. endoreg_db/migrations/0010_rename_endoscope_serial_number_sensitivemeta_endoscope_sn.py +18 -18
  146. endoreg_db/migrations/0011_rawvideofile_state_sensitive_data_retrieved.py +18 -18
  147. endoreg_db/migrations/0012_rawvideofile_prediction_dir_and_more.py +109 -109
  148. endoreg_db/migrations/0013_rawpdffile.py +31 -31
  149. endoreg_db/migrations/0014_pdftype_alter_rawpdffile_file_pdfmeta.py +38 -38
  150. endoreg_db/migrations/0015_rename_report_processed_rawpdffile_state_report_processed_and_more.py +31 -31
  151. endoreg_db/migrations/0016_rawpdffile_state_report_processing_required.py +18 -18
  152. endoreg_db/migrations/0017_firstname_lastname_center_first_names_and_more.py +37 -37
  153. endoreg_db/migrations/0018_reportreaderflag_reportreaderconfig.py +37 -37
  154. endoreg_db/migrations/0019_pdftype_cut_off_above_lines_and_more.py +42 -42
  155. endoreg_db/migrations/0020_rename_endoscopy_info_line_pdftype_endoscope_info_line.py +18 -18
  156. endoreg_db/migrations/0021_alter_pdftype_endoscope_info_line.py +19 -19
  157. endoreg_db/migrations/0022_alter_pdftype_endoscope_info_line.py +19 -19
  158. endoreg_db/migrations/0023_ttoquestionnaire_alter_pdftype_endoscope_info_line.py +59 -59
  159. endoreg_db/migrations/0024_remove_ttoquestionnaire_infections_and_more.py +27 -27
  160. endoreg_db/migrations/0025_event_alter_rawpdffile_file_patientevent.py +42 -42
  161. endoreg_db/migrations/0026_disease_diseaseclassification_and_more.py +166 -166
  162. endoreg_db/migrations/0027_labvalue_abbreviation_labvalue_default_normal_range_and_more.py +38 -38
  163. endoreg_db/migrations/0028_alter_unit_abbreviation.py +18 -18
  164. endoreg_db/migrations/0029_medicationintaketime_and_more.py +75 -75
  165. endoreg_db/migrations/0030_medicationindicationtype_and_more.py +101 -101
  166. endoreg_db/migrations/0031_rename_adapt_to_liver_function_medication_adapt_to_age_and_more.py +38 -38
  167. endoreg_db/migrations/0032_alter_medicationschedule_therapy_duration_d.py +18 -18
  168. endoreg_db/migrations/0033_medicationindication_sources.py +18 -18
  169. endoreg_db/migrations/0034_alter_rawpdffile_file.py +20 -20
  170. endoreg_db/migrations/0035_alter_medicationindication_sources.py +18 -18
  171. endoreg_db/migrations/0036_alter_rawpdffile_file.py +20 -20
  172. endoreg_db/migrations/0037_alter_medicationindication_sources.py +18 -18
  173. endoreg_db/migrations/0038_emissionfactor_material_product_productgroup_and_more.py +164 -164
  174. endoreg_db/migrations/0039_referenceproduct_name.py +19 -19
  175. endoreg_db/migrations/0040_quizanswertype_quizquestiontype_quizquestion_and_more.py +50 -50
  176. endoreg_db/migrations/0041_gender_patientmedication_medication_indication_and_more.py +40 -40
  177. endoreg_db/migrations/0042_casetemplateruletype_casetemplaterulevalue_and_more.py +74 -74
  178. endoreg_db/migrations/0043_casetemplatetype_name_de_casetemplatetype_name_en.py +23 -23
  179. endoreg_db/migrations/0044_casetemplateruletype_name_de_and_more.py +23 -23
  180. endoreg_db/migrations/0045_casetemplaterulevalue_value_type.py +19 -19
  181. endoreg_db/migrations/0046_casetemplaterulevalue_target_field.py +18 -18
  182. endoreg_db/migrations/0047_casetemplaterule_target_model.py +18 -18
  183. endoreg_db/migrations/0048_remove_casetemplaterule_chained_rules_and_more.py +22 -22
  184. endoreg_db/migrations/0049_remove_casetemplaterule_rule_values.py +17 -17
  185. endoreg_db/migrations/0050_casetemplaterule_rule_values.py +18 -18
  186. endoreg_db/migrations/0051_remove_casetemplaterule_calling_rules_and_more.py +27 -27
  187. endoreg_db/migrations/0052_rename_case_template_type_casetemplate_template_type.py +18 -18
  188. endoreg_db/migrations/0053_patientlabsampletype_patientlabsample_and_more.py +38 -38
  189. endoreg_db/migrations/0054_multiplecategoricalvaluedistribution_and_more.py +69 -69
  190. endoreg_db/migrations/0055_remove_casetemplaterule_rule_values_and_more.py +59 -59
  191. endoreg_db/migrations/0056_datevaluedistribution_and_more.py +32 -32
  192. endoreg_db/migrations/0057_remove_datevaluedistribution_max_date_and_more.py +72 -72
  193. endoreg_db/migrations/0058_datevaluedistribution_description_and_more.py +28 -28
  194. endoreg_db/migrations/0059_casetemplaterule_rule_values.py +18 -18
  195. endoreg_db/migrations/0060_labvalue__default_date_value_distribution_and_more.py +44 -44
  196. endoreg_db/migrations/0061_remove_patientlabvalue_date_patientlabvalue_datetime.py +24 -24
  197. endoreg_db/migrations/0062_labvalue_numeric_precision.py +18 -18
  198. endoreg_db/migrations/0063_alter_labvalue_numeric_precision.py +18 -18
  199. endoreg_db/migrations/0064_casetemplaterule_extra_parameters_and_more.py +23 -23
  200. endoreg_db/migrations/0065_rename__date_value_distribution_casetemplaterule_date_value_distribution_and_more.py +58 -58
  201. endoreg_db/migrations/0066_alter_patientlabvalue_patient_and_more.py +29 -29
  202. endoreg_db/migrations/0067_alter_medicationindication_indication_type.py +19 -19
  203. endoreg_db/models/__init__.py +75 -74
  204. endoreg_db/models/ai_model/__init__.py +3 -3
  205. endoreg_db/models/ai_model/active_model.py +9 -9
  206. endoreg_db/models/ai_model/model_meta.py +24 -24
  207. endoreg_db/models/ai_model/model_type.py +25 -25
  208. endoreg_db/models/ai_model/utils.py +8 -8
  209. endoreg_db/models/annotation/__init__.py +1 -1
  210. endoreg_db/models/annotation/binary_classification_annotation_task.py +80 -80
  211. endoreg_db/models/annotation/image_classification.py +26 -26
  212. endoreg_db/models/case_template/__init__.py +5 -5
  213. endoreg_db/models/case_template/case_template.py +81 -81
  214. endoreg_db/models/case_template/case_template_rule.py +276 -276
  215. endoreg_db/models/case_template/case_template_rule_value.py +73 -73
  216. endoreg_db/models/case_template/case_template_type.py +27 -27
  217. endoreg_db/models/center/__init__.py +4 -4
  218. endoreg_db/models/center/center.py +24 -24
  219. endoreg_db/models/center/center_product.py +33 -33
  220. endoreg_db/models/center/center_resource.py +18 -18
  221. endoreg_db/models/center/center_waste.py +10 -10
  222. endoreg_db/models/data_file/__init__.py +5 -5
  223. endoreg_db/models/data_file/base_classes/__init__.py +2 -2
  224. endoreg_db/models/data_file/base_classes/abstract_frame.py +50 -50
  225. endoreg_db/models/data_file/base_classes/abstract_video.py +200 -200
  226. endoreg_db/models/data_file/frame.py +45 -45
  227. endoreg_db/models/data_file/import_classes/__init__.py +31 -31
  228. endoreg_db/models/data_file/import_classes/processing_functions/__init__.py +34 -34
  229. endoreg_db/models/data_file/import_classes/processing_functions/pdf.py +28 -28
  230. endoreg_db/models/data_file/import_classes/processing_functions/video.py +260 -260
  231. endoreg_db/models/data_file/import_classes/raw_pdf.py +188 -188
  232. endoreg_db/models/data_file/import_classes/raw_video.py +343 -343
  233. endoreg_db/models/data_file/metadata/__init__.py +3 -3
  234. endoreg_db/models/data_file/metadata/pdf_meta.py +70 -70
  235. endoreg_db/models/data_file/metadata/sensitive_meta.py +31 -31
  236. endoreg_db/models/data_file/metadata/video_meta.py +132 -132
  237. endoreg_db/models/data_file/report_file.py +89 -89
  238. endoreg_db/models/data_file/video/__init__.py +6 -6
  239. endoreg_db/models/data_file/video/import_meta.py +25 -25
  240. endoreg_db/models/data_file/video/video.py +25 -25
  241. endoreg_db/models/data_file/video_segment.py +107 -107
  242. endoreg_db/models/disease.py +55 -55
  243. endoreg_db/models/emission/emission_factor.py +19 -19
  244. endoreg_db/models/event.py +21 -21
  245. endoreg_db/models/examination/__init__.py +3 -3
  246. endoreg_db/models/examination/examination.py +26 -26
  247. endoreg_db/models/examination/examination_time.py +27 -27
  248. endoreg_db/models/examination/examination_time_type.py +24 -24
  249. endoreg_db/models/examination/examination_type.py +18 -18
  250. endoreg_db/models/hardware/__init__.py +1 -1
  251. endoreg_db/models/hardware/endoscope.py +44 -44
  252. endoreg_db/models/hardware/endoscopy_processor.py +143 -143
  253. endoreg_db/models/information_source.py +29 -29
  254. endoreg_db/models/label/label.py +84 -84
  255. endoreg_db/models/laboratory/lab_value.py +102 -102
  256. endoreg_db/models/legacy_data/__init__.py +3 -3
  257. endoreg_db/models/legacy_data/image.py +34 -34
  258. endoreg_db/models/medication/medication.py +148 -148
  259. endoreg_db/models/network/__init__.py +2 -0
  260. endoreg_db/models/network/network_device.py +27 -0
  261. endoreg_db/models/network/network_device_type.py +23 -0
  262. endoreg_db/models/other/__init__.py +4 -4
  263. endoreg_db/models/other/distribution.py +215 -215
  264. endoreg_db/models/other/material.py +16 -16
  265. endoreg_db/models/other/resource.py +17 -17
  266. endoreg_db/models/other/transport_route.py +20 -20
  267. endoreg_db/models/other/waste.py +20 -20
  268. endoreg_db/models/patient_examination/__init__.py +35 -35
  269. endoreg_db/models/permissions/__init__.py +44 -44
  270. endoreg_db/models/persons/__init__.py +6 -6
  271. endoreg_db/models/persons/examiner/__init__.py +1 -1
  272. endoreg_db/models/persons/examiner/examiner.py +15 -15
  273. endoreg_db/models/persons/examiner/examiner_type.py +1 -1
  274. endoreg_db/models/persons/first_name.py +17 -17
  275. endoreg_db/models/persons/gender.py +22 -22
  276. endoreg_db/models/persons/last_name.py +19 -19
  277. endoreg_db/models/persons/patient/__init__.py +7 -7
  278. endoreg_db/models/persons/patient/case/case.py +30 -30
  279. endoreg_db/models/persons/patient/patient.py +216 -216
  280. endoreg_db/models/persons/patient/patient_disease.py +16 -16
  281. endoreg_db/models/persons/patient/patient_event.py +22 -22
  282. endoreg_db/models/persons/patient/patient_lab_sample.py +106 -106
  283. endoreg_db/models/persons/patient/patient_lab_value.py +176 -176
  284. endoreg_db/models/persons/patient/patient_medication.py +43 -43
  285. endoreg_db/models/persons/patient/patient_medication_schedule.py +27 -27
  286. endoreg_db/models/persons/person.py +31 -31
  287. endoreg_db/models/persons/portal_user_information.py +27 -27
  288. endoreg_db/models/prediction/__init__.py +1 -1
  289. endoreg_db/models/prediction/image_classification.py +37 -37
  290. endoreg_db/models/prediction/video_prediction_meta.py +244 -244
  291. endoreg_db/models/product/__init__.py +4 -4
  292. endoreg_db/models/product/product.py +97 -97
  293. endoreg_db/models/product/product_group.py +19 -19
  294. endoreg_db/models/product/product_material.py +24 -24
  295. endoreg_db/models/product/product_weight.py +26 -26
  296. endoreg_db/models/product/reference_product.py +99 -99
  297. endoreg_db/models/questionnaires/__init__.py +114 -114
  298. endoreg_db/models/quiz/__init__.py +1 -1
  299. endoreg_db/models/quiz/quiz_answer.py +41 -41
  300. endoreg_db/models/quiz/quiz_question.py +54 -54
  301. endoreg_db/models/report_reader/__init__.py +1 -1
  302. endoreg_db/models/report_reader/report_reader_config.py +53 -53
  303. endoreg_db/models/report_reader/report_reader_flag.py +19 -19
  304. endoreg_db/models/rules/__init__.py +4 -4
  305. endoreg_db/models/rules/rule.py +23 -23
  306. endoreg_db/models/rules/rule_applicator.py +224 -224
  307. endoreg_db/models/rules/rule_attribute_dtype.py +18 -18
  308. endoreg_db/models/rules/rule_type.py +21 -21
  309. endoreg_db/models/rules/ruleset.py +19 -19
  310. endoreg_db/models/unit.py +21 -21
  311. endoreg_db/queries/__init__.py +4 -4
  312. endoreg_db/queries/annotations/__init__.py +2 -2
  313. endoreg_db/queries/annotations/legacy.py +159 -159
  314. endoreg_db/queries/get/__init__.py +5 -5
  315. endoreg_db/queries/get/center.py +42 -42
  316. endoreg_db/queries/get/model.py +13 -13
  317. endoreg_db/queries/get/patient.py +14 -14
  318. endoreg_db/queries/get/patient_examination.py +20 -20
  319. endoreg_db/queries/get/report_file.py +33 -33
  320. endoreg_db/queries/get/video.py +31 -31
  321. endoreg_db/serializers/__init__.py +9 -9
  322. endoreg_db/serializers/ai_model.py +18 -18
  323. endoreg_db/serializers/annotation.py +17 -17
  324. endoreg_db/serializers/center.py +11 -11
  325. endoreg_db/serializers/examination.py +32 -32
  326. endoreg_db/serializers/frame.py +13 -13
  327. endoreg_db/serializers/hardware.py +20 -20
  328. endoreg_db/serializers/label.py +22 -22
  329. endoreg_db/serializers/patient.py +10 -10
  330. endoreg_db/serializers/prediction.py +15 -15
  331. endoreg_db/serializers/report_file.py +7 -7
  332. endoreg_db/serializers/video.py +27 -27
  333. endoreg_db/tests.py +3 -3
  334. endoreg_db/utils/cropping.py +28 -28
  335. endoreg_db/utils/dataloader.py +92 -92
  336. endoreg_db/utils/file_operations.py +30 -30
  337. endoreg_db/utils/hashs.py +33 -33
  338. endoreg_db/utils/legacy_ocr.py +201 -201
  339. endoreg_db/utils/ocr.py +197 -197
  340. endoreg_db/utils/uuid.py +4 -4
  341. endoreg_db/utils/video_metadata.py +87 -87
  342. endoreg_db/views.py +3 -3
  343. {endoreg_db-0.3.6.dist-info → endoreg_db-0.3.7.dist-info}/LICENSE +674 -674
  344. {endoreg_db-0.3.6.dist-info → endoreg_db-0.3.7.dist-info}/METADATA +2 -2
  345. endoreg_db-0.3.7.dist-info/RECORD +363 -0
  346. {endoreg_db-0.3.6.dist-info → endoreg_db-0.3.7.dist-info}/WHEEL +1 -1
  347. endoreg_db-0.3.6.dist-info/RECORD +0 -357
@@ -1,92 +1,92 @@
1
- import os
2
- import yaml
3
- from django.core.exceptions import ObjectDoesNotExist
4
-
5
- def load_model_data_from_yaml(command, model_name, metadata, verbose):
6
- """
7
- Load model data from YAML files.
8
-
9
- Args:
10
- command: Command object for stdout writing.
11
- model_name: Name of the model being loaded.
12
- metadata: Metadata including directory and foreign key information.
13
- verbose: Boolean indicating whether to print verbose output.
14
- """
15
- if verbose:
16
- command.stdout.write(f"Start loading {model_name}")
17
- model = metadata["model"]
18
- dir_path = metadata["dir"]
19
- foreign_keys = metadata["foreign_keys"]
20
- foreign_key_models = metadata["foreign_key_models"]
21
-
22
- _files = [f for f in os.listdir(dir_path) if f.endswith('.yaml')]
23
- # sort
24
- _files.sort()
25
- for file in _files:
26
- with open(os.path.join(dir_path, file), 'r') as file:
27
- yaml_data = yaml.safe_load(file)
28
-
29
- load_data_with_foreign_keys(command, model, yaml_data, foreign_keys, foreign_key_models, verbose)
30
-
31
- def load_data_with_foreign_keys(command, model, yaml_data, foreign_keys, foreign_key_models, verbose):
32
- """
33
- Load data handling foreign keys and many-to-many relationships.
34
-
35
- Args:
36
- command: Command object for stdout writing.
37
- model: The Django model for the data.
38
- yaml_data: Data loaded from YAML.
39
- foreign_keys: List of foreign keys.
40
- foreign_key_models: Corresponding models for the foreign keys.
41
- verbose: Boolean indicating whether to print verbose output.
42
- """
43
- for entry in yaml_data:
44
- fields = entry.get('fields', {})
45
- name = fields.pop('name', None)
46
- m2m_relationships = {} # Store many-to-many relationships
47
- print(entry)
48
-
49
- # Handle foreign keys and many-to-many relationships
50
- for fk_field, fk_model in zip(foreign_keys, foreign_key_models):
51
- print(fk_field, fk_model)
52
- target_keys = fields.pop(fk_field, None)
53
-
54
- # Ensure the foreign key exists
55
- if target_keys is None:
56
- if verbose:
57
- command.stdout.write(command.style.WARNING(f"Foreign key {fk_field} not found in fields"))
58
- continue # Skip if no foreign key provided
59
-
60
- # Process many-to-many fields or foreign keys
61
- if isinstance(target_keys, list): # Assume many-to-many relationship
62
- related_objects = []
63
- for key in target_keys:
64
- obj, created = fk_model.objects.get_or_create(name=key)
65
- if created and verbose:
66
- command.stdout.write(command.style.SUCCESS(f"Created {fk_model.__name__} {key}"))
67
- related_objects.append(obj)
68
- m2m_relationships[fk_field] = related_objects
69
- else: # Single foreign key relationship
70
- try:
71
- if model == "endoreg_db.case_template_rule":
72
- print(fk_model, target_keys)
73
- obj = fk_model.objects.get_by_natural_key(target_keys)
74
- except ObjectDoesNotExist:
75
- if verbose:
76
- command.stdout.write(command.style.WARNING(f"{fk_model.__name__} with key {target_keys} not found"))
77
- continue
78
- fields[fk_field] = obj
79
-
80
- # Create or update the main object
81
- if name is None:
82
- obj, created = model.objects.get_or_create(**fields)
83
- else:
84
- obj, created = model.objects.update_or_create(defaults=fields, name=name)
85
- if created and verbose:
86
- command.stdout.write(command.style.SUCCESS(f'Created {model.__name__} {name}'))
87
- elif verbose:
88
- command.stdout.write(command.style.WARNING(f'Skipped {model.__name__} {name}, already exists'))
89
-
90
- # Set many-to-many relationships
91
- for field_name, related_objs in m2m_relationships.items():
92
- getattr(obj, field_name).set(related_objs)
1
+ import os
2
+ import yaml
3
+ from django.core.exceptions import ObjectDoesNotExist
4
+
5
+ def load_model_data_from_yaml(command, model_name, metadata, verbose):
6
+ """
7
+ Load model data from YAML files.
8
+
9
+ Args:
10
+ command: Command object for stdout writing.
11
+ model_name: Name of the model being loaded.
12
+ metadata: Metadata including directory and foreign key information.
13
+ verbose: Boolean indicating whether to print verbose output.
14
+ """
15
+ if verbose:
16
+ command.stdout.write(f"Start loading {model_name}")
17
+ model = metadata["model"]
18
+ dir_path = metadata["dir"]
19
+ foreign_keys = metadata["foreign_keys"]
20
+ foreign_key_models = metadata["foreign_key_models"]
21
+
22
+ _files = [f for f in os.listdir(dir_path) if f.endswith('.yaml')]
23
+ # sort
24
+ _files.sort()
25
+ for file in _files:
26
+ with open(os.path.join(dir_path, file), 'r') as file:
27
+ yaml_data = yaml.safe_load(file)
28
+
29
+ load_data_with_foreign_keys(command, model, yaml_data, foreign_keys, foreign_key_models, verbose)
30
+
31
+ def load_data_with_foreign_keys(command, model, yaml_data, foreign_keys, foreign_key_models, verbose):
32
+ """
33
+ Load data handling foreign keys and many-to-many relationships.
34
+
35
+ Args:
36
+ command: Command object for stdout writing.
37
+ model: The Django model for the data.
38
+ yaml_data: Data loaded from YAML.
39
+ foreign_keys: List of foreign keys.
40
+ foreign_key_models: Corresponding models for the foreign keys.
41
+ verbose: Boolean indicating whether to print verbose output.
42
+ """
43
+ for entry in yaml_data:
44
+ fields = entry.get('fields', {})
45
+ name = fields.pop('name', None)
46
+ m2m_relationships = {} # Store many-to-many relationships
47
+ print(entry)
48
+
49
+ # Handle foreign keys and many-to-many relationships
50
+ for fk_field, fk_model in zip(foreign_keys, foreign_key_models):
51
+ print(fk_field, fk_model)
52
+ target_keys = fields.pop(fk_field, None)
53
+
54
+ # Ensure the foreign key exists
55
+ if target_keys is None:
56
+ if verbose:
57
+ command.stdout.write(command.style.WARNING(f"Foreign key {fk_field} not found in fields"))
58
+ continue # Skip if no foreign key provided
59
+
60
+ # Process many-to-many fields or foreign keys
61
+ if isinstance(target_keys, list): # Assume many-to-many relationship
62
+ related_objects = []
63
+ for key in target_keys:
64
+ obj, created = fk_model.objects.get_or_create(name=key)
65
+ if created and verbose:
66
+ command.stdout.write(command.style.SUCCESS(f"Created {fk_model.__name__} {key}"))
67
+ related_objects.append(obj)
68
+ m2m_relationships[fk_field] = related_objects
69
+ else: # Single foreign key relationship
70
+ try:
71
+ if model == "endoreg_db.case_template_rule":
72
+ print(fk_model, target_keys)
73
+ obj = fk_model.objects.get_by_natural_key(target_keys)
74
+ except ObjectDoesNotExist:
75
+ if verbose:
76
+ command.stdout.write(command.style.WARNING(f"{fk_model.__name__} with key {target_keys} not found"))
77
+ continue
78
+ fields[fk_field] = obj
79
+
80
+ # Create or update the main object
81
+ if name is None:
82
+ obj, created = model.objects.get_or_create(**fields)
83
+ else:
84
+ obj, created = model.objects.update_or_create(defaults=fields, name=name)
85
+ if created and verbose:
86
+ command.stdout.write(command.style.SUCCESS(f'Created {model.__name__} {name}'))
87
+ elif verbose:
88
+ command.stdout.write(command.style.WARNING(f'Skipped {model.__name__} {name}, already exists'))
89
+
90
+ # Set many-to-many relationships
91
+ for field_name, related_objs in m2m_relationships.items():
92
+ getattr(obj, field_name).set(related_objs)
@@ -1,30 +1,30 @@
1
- import shutil
2
- from pathlib import Path
3
- from endoreg_db.utils.uuid import get_uuid
4
-
5
- def get_uuid_filename(file:Path) -> tuple[str, str]:
6
- """
7
- Returns a new filename with a uuid
8
- """
9
- # Get the file extension
10
- file_extension = file.suffix
11
- # Generate a new file name
12
- uuid = get_uuid()
13
- new_file_name = f"{uuid}{file_extension}"
14
- return new_file_name, uuid
15
-
16
- def rename_file_uuid(old_file:Path):
17
- """
18
- Rename a file by assigning a uuid while preserving file extension. Returns new filepath and uuid
19
- """
20
- # Get the file extension
21
- file_extension = old_file.suffix
22
- # Generate a new file name
23
- uuid = get_uuid()
24
- new_file_name = f"{uuid}{file_extension}"
25
-
26
- # Rename the file
27
- new_file = old_file.with_name(new_file_name)
28
- shutil.move(old_file.resolve().as_posix(), new_file.resolve().as_posix())
29
-
30
- return new_file, uuid
1
+ import shutil
2
+ from pathlib import Path
3
+ from endoreg_db.utils.uuid import get_uuid
4
+
5
+ def get_uuid_filename(file:Path) -> tuple[str, str]:
6
+ """
7
+ Returns a new filename with a uuid
8
+ """
9
+ # Get the file extension
10
+ file_extension = file.suffix
11
+ # Generate a new file name
12
+ uuid = get_uuid()
13
+ new_file_name = f"{uuid}{file_extension}"
14
+ return new_file_name, uuid
15
+
16
+ def rename_file_uuid(old_file:Path):
17
+ """
18
+ Rename a file by assigning a uuid while preserving file extension. Returns new filepath and uuid
19
+ """
20
+ # Get the file extension
21
+ file_extension = old_file.suffix
22
+ # Generate a new file name
23
+ uuid = get_uuid()
24
+ new_file_name = f"{uuid}{file_extension}"
25
+
26
+ # Rename the file
27
+ new_file = old_file.with_name(new_file_name)
28
+ shutil.move(old_file.resolve().as_posix(), new_file.resolve().as_posix())
29
+
30
+ return new_file, uuid
endoreg_db/utils/hashs.py CHANGED
@@ -1,34 +1,34 @@
1
- import hashlib
2
- from pathlib import Path
3
-
4
- def get_video_hash(video_path):
5
- """
6
- Get the hash of a video file.
7
- """
8
- # Open the video file in read-binary mode:
9
- with open(video_path, 'rb') as f:
10
- # Create the hash object, passing in the video contents for hashing:
11
- hash_object = hashlib.sha256(f.read())
12
- # Get the hexadecimal representation of the hash
13
- video_hash = hash_object.hexdigest()
14
- assert len(video_hash) <= 255, "Hash length exceeds 255 characters"
15
-
16
- return video_hash
17
-
18
- def get_pdf_hash(pdf_path:Path):
19
- """
20
- Get the hash of a pdf file.
21
- """
22
- pdf_hash = None
23
-
24
- # Open the file in binary mode and read its contents
25
- with open(pdf_path, 'rb') as f:
26
- pdf_contents = f.read()
27
- # Create a hash object using SHA-256 algorithm
28
-
29
- hash_object = hashlib.sha256(pdf_contents, usedforsecurity=False)
30
- # Get the hexadecimal representation of the hash
31
- pdf_hash = hash_object.hexdigest()
32
- assert len(pdf_hash) <= 255, "Hash length exceeds 255 characters"
33
-
1
+ import hashlib
2
+ from pathlib import Path
3
+
4
+ def get_video_hash(video_path):
5
+ """
6
+ Get the hash of a video file.
7
+ """
8
+ # Open the video file in read-binary mode:
9
+ with open(video_path, 'rb') as f:
10
+ # Create the hash object, passing in the video contents for hashing:
11
+ hash_object = hashlib.sha256(f.read())
12
+ # Get the hexadecimal representation of the hash
13
+ video_hash = hash_object.hexdigest()
14
+ assert len(video_hash) <= 255, "Hash length exceeds 255 characters"
15
+
16
+ return video_hash
17
+
18
+ def get_pdf_hash(pdf_path:Path):
19
+ """
20
+ Get the hash of a pdf file.
21
+ """
22
+ pdf_hash = None
23
+
24
+ # Open the file in binary mode and read its contents
25
+ with open(pdf_path, 'rb') as f:
26
+ pdf_contents = f.read()
27
+ # Create a hash object using SHA-256 algorithm
28
+
29
+ hash_object = hashlib.sha256(pdf_contents, usedforsecurity=False)
30
+ # Get the hexadecimal representation of the hash
31
+ pdf_hash = hash_object.hexdigest()
32
+ assert len(pdf_hash) <= 255, "Hash length exceeds 255 characters"
33
+
34
34
  return pdf_hash