endoreg-db 0.3.5__py3-none-any.whl → 0.3.6__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 (341) hide show
  1. endoreg_db/admin.py +3 -3
  2. endoreg_db/apps.py +6 -6
  3. endoreg_db/data/__init__.py +64 -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/patient_lab_sample_type/generic.yaml +5 -5
  70. endoreg_db/data/pdf_type/data.yaml +28 -28
  71. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -66
  72. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -33
  73. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -308
  74. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -88
  75. endoreg_db/data/profession/data.yaml +70 -70
  76. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -55
  77. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +26 -26
  78. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +19 -19
  79. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -15
  80. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -12
  81. endoreg_db/data/unit/concentration.yaml +92 -92
  82. endoreg_db/data/unit/data.yaml +17 -17
  83. endoreg_db/data/unit/length.yaml +30 -30
  84. endoreg_db/data/unit/misc.yaml +19 -19
  85. endoreg_db/data/unit/rate.yaml +5 -5
  86. endoreg_db/data/unit/time.yaml +12 -12
  87. endoreg_db/data/unit/volume.yaml +35 -35
  88. endoreg_db/data/unit/weight.yaml +37 -37
  89. endoreg_db/data/waste/data.yaml +11 -11
  90. endoreg_db/forms/__init__.py +2 -2
  91. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -23
  92. endoreg_db/forms/settings/__init__.py +8 -8
  93. endoreg_db/forms/unit.py +5 -5
  94. endoreg_db/management/commands/_load_model_template.py +40 -40
  95. endoreg_db/management/commands/delete_all.py +18 -18
  96. endoreg_db/management/commands/delete_legacy_images.py +19 -19
  97. endoreg_db/management/commands/delete_legacy_videos.py +16 -16
  98. endoreg_db/management/commands/extract_legacy_video_frames.py +18 -18
  99. endoreg_db/management/commands/fetch_legacy_image_dataset.py +32 -32
  100. endoreg_db/management/commands/fix_auth_permission.py +20 -20
  101. endoreg_db/management/commands/import_legacy_images.py +94 -94
  102. endoreg_db/management/commands/import_legacy_videos.py +76 -76
  103. endoreg_db/management/commands/load_active_model_data.py +44 -44
  104. endoreg_db/management/commands/load_ai_model_data.py +44 -44
  105. endoreg_db/management/commands/load_base_db_data.py +128 -128
  106. endoreg_db/management/commands/load_center_data.py +42 -42
  107. endoreg_db/management/commands/load_disease_classification_choices_data.py +40 -40
  108. endoreg_db/management/commands/load_disease_classification_data.py +40 -40
  109. endoreg_db/management/commands/load_disease_data.py +39 -39
  110. endoreg_db/management/commands/load_distribution_data.py +65 -65
  111. endoreg_db/management/commands/load_endoscope_type_data.py +44 -44
  112. endoreg_db/management/commands/load_endoscopy_processor_data.py +44 -44
  113. endoreg_db/management/commands/load_event_data.py +40 -40
  114. endoreg_db/management/commands/load_examination_data.py +74 -74
  115. endoreg_db/management/commands/load_g_play_data.py +112 -112
  116. endoreg_db/management/commands/load_gender_data.py +43 -43
  117. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +132 -132
  118. endoreg_db/management/commands/load_information_source.py +44 -44
  119. endoreg_db/management/commands/load_lab_value_data.py +49 -49
  120. endoreg_db/management/commands/load_label_data.py +66 -66
  121. endoreg_db/management/commands/load_medication_data.py +40 -40
  122. endoreg_db/management/commands/load_medication_indication_data.py +62 -62
  123. endoreg_db/management/commands/load_medication_indication_type_data.py +40 -40
  124. endoreg_db/management/commands/load_medication_intake_time_data.py +40 -40
  125. endoreg_db/management/commands/load_medication_schedule_data.py +54 -54
  126. endoreg_db/management/commands/load_pdf_type_data.py +60 -60
  127. endoreg_db/management/commands/load_profession_data.py +43 -43
  128. endoreg_db/management/commands/load_report_reader_flag.py +45 -45
  129. endoreg_db/management/commands/load_unit_data.py +45 -45
  130. endoreg_db/management/commands/load_user_groups.py +28 -28
  131. endoreg_db/management/commands/register_ai_model.py +65 -65
  132. endoreg_db/management/commands/reset_celery_schedule.py +9 -9
  133. endoreg_db/migrations/0001_initial.py +582 -582
  134. endoreg_db/migrations/0002_rawvideofile.py +26 -26
  135. endoreg_db/migrations/0003_rawvideofile_frames_required.py +18 -18
  136. endoreg_db/migrations/0004_rename_hash_rawvideofile_video_hash.py +18 -18
  137. endoreg_db/migrations/0005_ffmpegmeta_remove_videoimportmeta_center_and_more.py +56 -56
  138. endoreg_db/migrations/0006_rawvideofile_center_alter_videometa_processor.py +25 -25
  139. endoreg_db/migrations/0007_rawvideofile_processor.py +19 -19
  140. endoreg_db/migrations/0008_rename_frames_required_rawvideofile_state_frames_required.py +18 -18
  141. endoreg_db/migrations/0009_sensitivemeta_rawvideofile_sensitive_meta.py +31 -31
  142. endoreg_db/migrations/0010_rename_endoscope_serial_number_sensitivemeta_endoscope_sn.py +18 -18
  143. endoreg_db/migrations/0011_rawvideofile_state_sensitive_data_retrieved.py +18 -18
  144. endoreg_db/migrations/0012_rawvideofile_prediction_dir_and_more.py +109 -109
  145. endoreg_db/migrations/0013_rawpdffile.py +31 -31
  146. endoreg_db/migrations/0014_pdftype_alter_rawpdffile_file_pdfmeta.py +38 -38
  147. endoreg_db/migrations/0015_rename_report_processed_rawpdffile_state_report_processed_and_more.py +31 -31
  148. endoreg_db/migrations/0016_rawpdffile_state_report_processing_required.py +18 -18
  149. endoreg_db/migrations/0017_firstname_lastname_center_first_names_and_more.py +37 -37
  150. endoreg_db/migrations/0018_reportreaderflag_reportreaderconfig.py +37 -37
  151. endoreg_db/migrations/0019_pdftype_cut_off_above_lines_and_more.py +42 -42
  152. endoreg_db/migrations/0020_rename_endoscopy_info_line_pdftype_endoscope_info_line.py +18 -18
  153. endoreg_db/migrations/0021_alter_pdftype_endoscope_info_line.py +19 -19
  154. endoreg_db/migrations/0022_alter_pdftype_endoscope_info_line.py +19 -19
  155. endoreg_db/migrations/0023_ttoquestionnaire_alter_pdftype_endoscope_info_line.py +59 -59
  156. endoreg_db/migrations/0024_remove_ttoquestionnaire_infections_and_more.py +27 -27
  157. endoreg_db/migrations/0025_event_alter_rawpdffile_file_patientevent.py +42 -42
  158. endoreg_db/migrations/0026_disease_diseaseclassification_and_more.py +166 -166
  159. endoreg_db/migrations/0027_labvalue_abbreviation_labvalue_default_normal_range_and_more.py +38 -38
  160. endoreg_db/migrations/0028_alter_unit_abbreviation.py +18 -18
  161. endoreg_db/migrations/0029_medicationintaketime_and_more.py +75 -75
  162. endoreg_db/migrations/0030_medicationindicationtype_and_more.py +101 -101
  163. endoreg_db/migrations/0031_rename_adapt_to_liver_function_medication_adapt_to_age_and_more.py +38 -38
  164. endoreg_db/migrations/0032_alter_medicationschedule_therapy_duration_d.py +18 -18
  165. endoreg_db/migrations/0033_medicationindication_sources.py +18 -18
  166. endoreg_db/migrations/0034_alter_rawpdffile_file.py +20 -20
  167. endoreg_db/migrations/0035_alter_medicationindication_sources.py +18 -18
  168. endoreg_db/migrations/0036_alter_rawpdffile_file.py +20 -20
  169. endoreg_db/migrations/0037_alter_medicationindication_sources.py +18 -18
  170. endoreg_db/migrations/0038_emissionfactor_material_product_productgroup_and_more.py +164 -164
  171. endoreg_db/migrations/0039_referenceproduct_name.py +19 -19
  172. endoreg_db/migrations/0040_quizanswertype_quizquestiontype_quizquestion_and_more.py +50 -50
  173. endoreg_db/migrations/0041_gender_patientmedication_medication_indication_and_more.py +40 -40
  174. endoreg_db/migrations/0042_casetemplateruletype_casetemplaterulevalue_and_more.py +74 -74
  175. endoreg_db/migrations/0043_casetemplatetype_name_de_casetemplatetype_name_en.py +23 -23
  176. endoreg_db/migrations/0044_casetemplateruletype_name_de_and_more.py +23 -23
  177. endoreg_db/migrations/0045_casetemplaterulevalue_value_type.py +19 -19
  178. endoreg_db/migrations/0046_casetemplaterulevalue_target_field.py +18 -18
  179. endoreg_db/migrations/0047_casetemplaterule_target_model.py +18 -18
  180. endoreg_db/migrations/0048_remove_casetemplaterule_chained_rules_and_more.py +22 -22
  181. endoreg_db/migrations/0049_remove_casetemplaterule_rule_values.py +17 -17
  182. endoreg_db/migrations/0050_casetemplaterule_rule_values.py +18 -18
  183. endoreg_db/migrations/0051_remove_casetemplaterule_calling_rules_and_more.py +27 -27
  184. endoreg_db/migrations/0052_rename_case_template_type_casetemplate_template_type.py +18 -18
  185. endoreg_db/migrations/0053_patientlabsampletype_patientlabsample_and_more.py +38 -38
  186. endoreg_db/migrations/0054_multiplecategoricalvaluedistribution_and_more.py +69 -69
  187. endoreg_db/migrations/0055_remove_casetemplaterule_rule_values_and_more.py +59 -59
  188. endoreg_db/migrations/0056_datevaluedistribution_and_more.py +32 -32
  189. endoreg_db/migrations/0057_remove_datevaluedistribution_max_date_and_more.py +72 -72
  190. endoreg_db/migrations/0058_datevaluedistribution_description_and_more.py +28 -28
  191. endoreg_db/migrations/0059_casetemplaterule_rule_values.py +18 -18
  192. endoreg_db/migrations/0060_labvalue__default_date_value_distribution_and_more.py +44 -44
  193. endoreg_db/migrations/0061_remove_patientlabvalue_date_patientlabvalue_datetime.py +24 -24
  194. endoreg_db/migrations/0062_labvalue_numeric_precision.py +18 -18
  195. endoreg_db/migrations/0063_alter_labvalue_numeric_precision.py +18 -18
  196. endoreg_db/migrations/0064_casetemplaterule_extra_parameters_and_more.py +23 -23
  197. endoreg_db/migrations/0065_rename__date_value_distribution_casetemplaterule_date_value_distribution_and_more.py +58 -58
  198. endoreg_db/migrations/0066_alter_patientlabvalue_patient_and_more.py +29 -29
  199. endoreg_db/migrations/0067_alter_medicationindication_indication_type.py +19 -19
  200. endoreg_db/models/__init__.py +74 -74
  201. endoreg_db/models/ai_model/__init__.py +3 -3
  202. endoreg_db/models/ai_model/active_model.py +9 -9
  203. endoreg_db/models/ai_model/model_meta.py +24 -24
  204. endoreg_db/models/ai_model/model_type.py +25 -25
  205. endoreg_db/models/ai_model/utils.py +8 -8
  206. endoreg_db/models/annotation/__init__.py +1 -1
  207. endoreg_db/models/annotation/binary_classification_annotation_task.py +80 -80
  208. endoreg_db/models/annotation/image_classification.py +26 -26
  209. endoreg_db/models/case_template/__init__.py +5 -5
  210. endoreg_db/models/case_template/case_template.py +81 -81
  211. endoreg_db/models/case_template/case_template_rule.py +276 -276
  212. endoreg_db/models/case_template/case_template_rule_value.py +73 -73
  213. endoreg_db/models/case_template/case_template_type.py +27 -27
  214. endoreg_db/models/center/__init__.py +4 -4
  215. endoreg_db/models/center/center.py +24 -24
  216. endoreg_db/models/center/center_product.py +33 -33
  217. endoreg_db/models/center/center_resource.py +18 -18
  218. endoreg_db/models/center/center_waste.py +10 -10
  219. endoreg_db/models/data_file/__init__.py +5 -5
  220. endoreg_db/models/data_file/base_classes/__init__.py +2 -2
  221. endoreg_db/models/data_file/base_classes/abstract_frame.py +50 -50
  222. endoreg_db/models/data_file/base_classes/abstract_video.py +200 -200
  223. endoreg_db/models/data_file/frame.py +45 -45
  224. endoreg_db/models/data_file/import_classes/__init__.py +31 -31
  225. endoreg_db/models/data_file/import_classes/processing_functions/__init__.py +34 -34
  226. endoreg_db/models/data_file/import_classes/processing_functions/pdf.py +28 -28
  227. endoreg_db/models/data_file/import_classes/processing_functions/video.py +260 -260
  228. endoreg_db/models/data_file/import_classes/raw_pdf.py +188 -188
  229. endoreg_db/models/data_file/import_classes/raw_video.py +343 -343
  230. endoreg_db/models/data_file/metadata/__init__.py +3 -3
  231. endoreg_db/models/data_file/metadata/pdf_meta.py +70 -70
  232. endoreg_db/models/data_file/metadata/sensitive_meta.py +31 -31
  233. endoreg_db/models/data_file/metadata/video_meta.py +132 -132
  234. endoreg_db/models/data_file/report_file.py +89 -89
  235. endoreg_db/models/data_file/video/__init__.py +6 -6
  236. endoreg_db/models/data_file/video/import_meta.py +25 -25
  237. endoreg_db/models/data_file/video/video.py +25 -25
  238. endoreg_db/models/data_file/video_segment.py +107 -107
  239. endoreg_db/models/disease.py +55 -55
  240. endoreg_db/models/emission/emission_factor.py +19 -19
  241. endoreg_db/models/event.py +21 -21
  242. endoreg_db/models/examination/__init__.py +3 -3
  243. endoreg_db/models/examination/examination.py +26 -26
  244. endoreg_db/models/examination/examination_time.py +27 -27
  245. endoreg_db/models/examination/examination_time_type.py +24 -24
  246. endoreg_db/models/examination/examination_type.py +18 -18
  247. endoreg_db/models/hardware/__init__.py +1 -1
  248. endoreg_db/models/hardware/endoscope.py +44 -44
  249. endoreg_db/models/hardware/endoscopy_processor.py +143 -143
  250. endoreg_db/models/information_source.py +29 -29
  251. endoreg_db/models/label/label.py +84 -84
  252. endoreg_db/models/laboratory/lab_value.py +102 -102
  253. endoreg_db/models/legacy_data/__init__.py +3 -3
  254. endoreg_db/models/legacy_data/image.py +34 -34
  255. endoreg_db/models/medication/medication.py +148 -148
  256. endoreg_db/models/other/__init__.py +4 -4
  257. endoreg_db/models/other/distribution.py +215 -215
  258. endoreg_db/models/other/material.py +16 -16
  259. endoreg_db/models/other/resource.py +17 -17
  260. endoreg_db/models/other/transport_route.py +20 -20
  261. endoreg_db/models/other/waste.py +20 -20
  262. endoreg_db/models/patient_examination/__init__.py +35 -35
  263. endoreg_db/models/permissions/__init__.py +44 -44
  264. endoreg_db/models/persons/__init__.py +6 -6
  265. endoreg_db/models/persons/examiner/__init__.py +1 -1
  266. endoreg_db/models/persons/examiner/examiner.py +15 -15
  267. endoreg_db/models/persons/examiner/examiner_type.py +1 -1
  268. endoreg_db/models/persons/first_name.py +17 -17
  269. endoreg_db/models/persons/gender.py +22 -22
  270. endoreg_db/models/persons/last_name.py +19 -19
  271. endoreg_db/models/persons/patient/__init__.py +7 -7
  272. endoreg_db/models/persons/patient/case/case.py +30 -30
  273. endoreg_db/models/persons/patient/patient.py +216 -216
  274. endoreg_db/models/persons/patient/patient_disease.py +16 -16
  275. endoreg_db/models/persons/patient/patient_event.py +22 -22
  276. endoreg_db/models/persons/patient/patient_lab_sample.py +106 -106
  277. endoreg_db/models/persons/patient/patient_lab_value.py +176 -176
  278. endoreg_db/models/persons/patient/patient_medication.py +43 -43
  279. endoreg_db/models/persons/patient/patient_medication_schedule.py +27 -27
  280. endoreg_db/models/persons/person.py +31 -31
  281. endoreg_db/models/persons/portal_user_information.py +27 -27
  282. endoreg_db/models/prediction/__init__.py +1 -1
  283. endoreg_db/models/prediction/image_classification.py +37 -37
  284. endoreg_db/models/prediction/video_prediction_meta.py +244 -244
  285. endoreg_db/models/product/__init__.py +4 -4
  286. endoreg_db/models/product/product.py +97 -97
  287. endoreg_db/models/product/product_group.py +19 -19
  288. endoreg_db/models/product/product_material.py +24 -24
  289. endoreg_db/models/product/product_weight.py +26 -26
  290. endoreg_db/models/product/reference_product.py +99 -99
  291. endoreg_db/models/questionnaires/__init__.py +114 -114
  292. endoreg_db/models/quiz/__init__.py +1 -1
  293. endoreg_db/models/quiz/quiz_answer.py +41 -41
  294. endoreg_db/models/quiz/quiz_question.py +54 -54
  295. endoreg_db/models/report_reader/__init__.py +1 -1
  296. endoreg_db/models/report_reader/report_reader_config.py +53 -53
  297. endoreg_db/models/report_reader/report_reader_flag.py +19 -19
  298. endoreg_db/models/rules/__init__.py +4 -4
  299. endoreg_db/models/rules/rule.py +23 -23
  300. endoreg_db/models/rules/rule_applicator.py +224 -224
  301. endoreg_db/models/rules/rule_attribute_dtype.py +18 -18
  302. endoreg_db/models/rules/rule_type.py +21 -21
  303. endoreg_db/models/rules/ruleset.py +19 -19
  304. endoreg_db/models/unit.py +21 -21
  305. endoreg_db/queries/__init__.py +4 -4
  306. endoreg_db/queries/annotations/__init__.py +2 -2
  307. endoreg_db/queries/annotations/legacy.py +159 -159
  308. endoreg_db/queries/get/__init__.py +5 -5
  309. endoreg_db/queries/get/center.py +42 -42
  310. endoreg_db/queries/get/model.py +13 -13
  311. endoreg_db/queries/get/patient.py +14 -14
  312. endoreg_db/queries/get/patient_examination.py +20 -20
  313. endoreg_db/queries/get/report_file.py +33 -33
  314. endoreg_db/queries/get/video.py +31 -31
  315. endoreg_db/serializers/__init__.py +9 -9
  316. endoreg_db/serializers/ai_model.py +18 -18
  317. endoreg_db/serializers/annotation.py +17 -17
  318. endoreg_db/serializers/center.py +11 -11
  319. endoreg_db/serializers/examination.py +32 -32
  320. endoreg_db/serializers/frame.py +13 -13
  321. endoreg_db/serializers/hardware.py +20 -20
  322. endoreg_db/serializers/label.py +22 -22
  323. endoreg_db/serializers/patient.py +10 -10
  324. endoreg_db/serializers/prediction.py +15 -15
  325. endoreg_db/serializers/report_file.py +7 -7
  326. endoreg_db/serializers/video.py +27 -27
  327. endoreg_db/tests.py +3 -3
  328. endoreg_db/utils/cropping.py +28 -28
  329. endoreg_db/utils/dataloader.py +92 -92
  330. endoreg_db/utils/file_operations.py +30 -30
  331. endoreg_db/utils/hashs.py +33 -33
  332. endoreg_db/utils/legacy_ocr.py +201 -201
  333. endoreg_db/utils/ocr.py +197 -197
  334. endoreg_db/utils/uuid.py +4 -4
  335. endoreg_db/utils/video_metadata.py +87 -87
  336. endoreg_db/views.py +3 -3
  337. {endoreg_db-0.3.5.dist-info → endoreg_db-0.3.6.dist-info}/LICENSE +674 -674
  338. {endoreg_db-0.3.5.dist-info → endoreg_db-0.3.6.dist-info}/METADATA +2 -2
  339. endoreg_db-0.3.6.dist-info/RECORD +357 -0
  340. {endoreg_db-0.3.5.dist-info → endoreg_db-0.3.6.dist-info}/WHEEL +1 -1
  341. endoreg_db-0.3.5.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