endoreg-db 0.6.2__tar.gz → 0.6.4__tar.gz

{endoreg_db-0.6.2 → endoreg_db-0.6.4}/.gitignore

@@ -16,6 +16,8 @@ __pycache__/
 _build
 .direnv
 
+*.sqlite3
+
 .devenv.flake.nix
 
 ###### Do not Remove ###### # Deprecated?

{endoreg_db-0.6.2 → endoreg_db-0.6.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: endoreg-db
-Version: 0.6.2
+Version: 0.6.4
 Summary: EndoReg Db Django App
 Project-URL: Homepage, https://info.coloreg.de
 Project-URL: Repository, https://github.com/wg-lux/endoreg-db

endoreg_db-0.6.4/changelogs/changelog-0.6.4.md

@@ -0,0 +1,54 @@
+@
+
+# Major Changes
+
+## Improve CLI
+
+added files:
+
+- dev/dev_settings.py
+- manage.py
+
+We can now run migrations and test commands directly from within the endoreg-db repository
+
+## Add Db Models
+
+- Risk, RiskType
+- Requirement, RequirementSet
+- RequirementValueType, RequirementOperator
+
+_Explanation:_
+Risk is a Model to define risks.
+Risks are grouped by risk_type (e.g. thrombosis, bleeding, perforation, etc). Risks within a group (e.g., "bleeding_low", "bleeding_high") are ordered by risk value (e.g., 1, 3; float, increasing meaning a higher risk). An unknown risk is indicated by 0. In future, protective factors might be reflected by negative risks
+
+Risk and RequirementSet have a Many2Many relationship which is defined in the risk model. In future, we will also implement something like an "Action" which will have a Many2Many relationship to RequirementSet (e.g., follow-up within 6 Months)
+
+RequirementSet and Requirement have a Many2Many relationship defined in the RequirementSet.
+
+RequirementSet has an "evaluate" function which expects fetches all linked Requirements and call
+
+Requirement references RequirementValueType (e.g. LabValue, PerformedIntervention, PlannedIntervention) as ForeignKey. This also determines the required inputs for the evaluate function.
+
+Requirement has an evaluate function taking kwargs. Depending on the RequirementValueType, specific kwargs must be available.
+
+Requirement references RequirementOperator as ForeignKey.
+
+A Requirement has may have a text, json, or numeric value (each stored in different fields)
+
+The RequirementOperator defines functions to evaluate a requirement by fetching the correct fields from the required objects (for lab values we need to fetch the associated patients lab values including the samples reference lab value and so on)
+
+# To-Do
+
+## Updates to contribution Guide
+
+- Django classes should have correct typing implementations for Foreign keys and Many2Many Relationships on both sides (for example take a look at models for: Risk / RiskType)
+
+- init files should declare an `__all__` variable
+
+- If development ends up causing many new migration files (since we tried around a bit and ran "makemigrations" a couple of times), we should delete the new migration files and create a single final migration step by running "makemigrations" again.
+
+- add unit type model to filter units by type (e.g. time related units etc.)
+
+- add action model (similar to requirement)
+
+- add actionType model (e.g., recommended, set_value, ...)

endoreg_db-0.6.4/dev/dev_settings.py

@@ -0,0 +1,25 @@
+import os
+from pathlib import Path
+
+DEBUG = True
+SECRET_KEY = "fake-key"
+INSTALLED_APPS = [
+    "tests",
+    "endoreg_db.apps.EndoregDbConfig",
+    "django.contrib.auth",
+    "django.contrib.contenttypes",
+    "django.contrib.sessions",
+    "django.contrib.staticfiles",
+]
+DEFAULT_AUTO_FIELD = "django.db.models.BigAutoField"
+
+BASE_DIR = Path(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+
+DATABASES = {
+    "default": {
+        "ENGINE": "django.db.backends.sqlite3",
+        "NAME": BASE_DIR / "dev_db.sqlite3",
+    },
+}
+
+TIME_ZONE = "Europe/Berlin"

{endoreg_db-0.6.2 → endoreg_db-0.6.4}/devenv.nix

@@ -40,6 +40,7 @@ in
     hello.exec = "${pkgs.uv}/bin/uv run python hello.py";
     runtests.package = pkgs.zsh;
     runtests.exec = "${pkgs.uv}/bin/uv run python runtests.py";
+    pyshell.exec = "${pkgs.uv}/bin/uv run python manage.py shell";
   };
 
   tasks = {

endoreg_db-0.6.4/devlog/bleeding-risk.md

@@ -0,0 +1,72 @@
+Quelle: https://register.awmf.org/assets/guidelines/021-022l_S2k_KF_Qualitaetsanforderungen-gastrointestinale-Endoskopie_2025-01.pdf
+
+## 4.2 Endoskopische Prozeduren bei erhöhtem Blutungsrisiko
+
+### 4.2.1 Laborchemie vor Endoskopie
+
+Empfehlung 2.13:
+
+- Ein Routinescreening vor Endoskopie mit niedrigem Blutungsrisiko (INR, PTT, Blutungszeit) sollte in Abwesenheit einer klinischen Anamnese für ein Blutungsereignis, einer Risikoerkrankung oder eines klinischen Verdachtes nicht vorgenommen werden.
+- Ebenso sollte keine Routinetestung bzgl Anämie, Nieren-, Leberfunktionsstörung oder anderer Serumparameter ohne eine klinische Anamnese erfolgen
+
+Empfehlung 2.14:
+
+- Zur Labordiagnostik vor Eingriffen mit hohem Blutungsrisiko kann aufgrund mangelnder Evidenz keine eindeutige Empfehlung abgegeben werden
+
+Empfehlung 2.15:
+
+- Gerrinungsdiagnostik soll bei Vorliegen von anamnestischen Faktoren und Vorerkrankungen erfolgen die auf ein erhöhtes Blutungsrisiko hinweisen sofern hier nicht bereits Befunde vorliegen
+- Beinhaltet: 
+  - Pos. Blutungsanamnese nach stattgehabten Eingriffen
+  - Internistische Vorerkrankungen mit erhöhtem Blutungsrisiko 
+    - Vaskulär Hämorrhagische Diathesen (M. Osler, Ehlers Danlos Syndrom, Marfan Syndrom)
+    - Angeborene Thrombozytopathien
+    - Angeborene plasmatische Gerinnungsstörungen (von-Willebrand-Syndrom, Faktor VIII o. IX Mangel
+    - Erworbene Thrombozytenfunktionsstörungen / plasmatische Gerinnungsstörungen bspw. bei 
+      - Lebererkrankung
+      - Nierenerkrankung
+      - prolongierter biliärer Obstruktion
+      - prolongierter Antibiotikaeinnahme
+      - malnutrition
+      - myeloproliferative Erkrankungen
+    - Medikamentenanamnese 
+      - "ob die Einnahme von Thrombozytenaggregationshemmern oder oralen Antikoagulatien gerinnungsphysiologische Untersuchungen indiziert ist im Einzelfall zu Entscheiden.
+
+### 4.2.2 Blutungsrisiko endoskopischer Eingriffe
+
+Empfehlung 2.16 / Tabelle 14:
+
+Um eine (Nutzen-)Risiko Abwägung für den Patienten treffen zu können, soll eine Einschätzung des Blutungsrisikos des jeweiligen endoskopischen Eingriffes in Eingriffe mit niedrigem Blutungsrisiko und Eingriffe mit hohem Blutungsrisiko erfolgen.
+
+Niedriges Blutungsrisiko
+
+- Diagnostische Endoskopie mit / ohne Biopsie 
+  - Gastroskopie
+  - Kolonoskopie
+  - Ballnenteroskopie
+  - Kapsel
+- ERCP ohne EST mit /ohne Stent
+- EUS ohne Feinnadelpunktion
+- Enterale Stentimplantation ohne Dilatation
+- APC von GI Blutungen
+
+Hohes Blutungsrisiko
+
+- Polypektomie
+- EMR/ESD/POEM
+- ERCP mit EST oder Ballondilatation
+- EUS mit Feinnadelpunktion oder EUS gesteuerte interventionelle Therapie
+- Ballondilatation/Bougierung
+- Varizentherapie (Ligatur, Sklerosierung)
+- PEG
+- Diagnostische Laparoskopie mit Organbiopsie
+- PTC / PTCD
+- Radiofrequenzablation
+
+### 4.2.3 Medikation mit Thrombozytenaggregationshemmern, Heparinen, (direkten) oralen Antikoagulatien
+
+Empfehlung 2.17
+
+Bei geplanten endoskopischen Eingriffen unter Medikation mit Thrombozytenaggregationshemmern und/oder oralen Antikoagulantien soll das individuelle Blutungsrisiko des Patienten unter Berücksichtigung des endoskopischen Eingriffes und der bestehenden Medikation gegen das individuelle Risiko für eine thrombembolische Komplikation durch ein Pausieren der Medikation abgewogen werden. Dies gilt auch für die Wiederaufnahme der Medikation. Im Einzelfall sollte das Vorgehen mit den Ärzten abgestimmt werden, die die Indikation für diese Medikation gestellt haben.
+
+Starke Empfehlung, Empfehlung, starker Konsens

{endoreg_db-0.6.2 → endoreg_db-0.6.4}/endoreg_db/data/__init__.py

@@ -17,6 +17,9 @@ REPORT_READER_FLAG_DATA_DIR = DATA_DIR / "report_reader_flag"
 EVENT_DATA_DIR = DATA_DIR / "event"
 GENDER_DATA_DIR = DATA_DIR / "gender"
 ORGAN_DATA_DIR = DATA_DIR / "organ"
+NAMES_FIRST_DATA_DIR = DATA_DIR / "names_first"
+NAMES_LAST_DATA_DIR = DATA_DIR / "names_last"
+
 
 # Contraindication
 CONTRAINDICATION_DATA_DIR = DATA_DIR / "contraindication"
@@ -102,6 +105,17 @@ LABEL_DATA_DIR = DATA_DIR / "ai_model_label"
 VIDEO_SEGMENTATION_LABEL_DATA_DIR = DATA_DIR / "ai_model_video_segmentation_label"
 VIDEO_SEGMENTATION_LABELSET_DATA_DIR = DATA_DIR / "ai_model_video_segmentation_labelset"
 
+# RISK
+RISK_DATA_DIR = DATA_DIR / "risk"
+RISK_TYPE_DATA_DIR = DATA_DIR / "risk_type"
+
+# REQUIREMENT
+REQUIREMENT_DATA_DIR = DATA_DIR / "requirement"
+REQUIREMENT_OPERATOR_DATA_DIR = DATA_DIR / "requirement_operator"
+REQUIREMENT_SET_DATA_DIR = DATA_DIR / "requirement_set"
+REQUIREMENT_SET_TYPE_DATA_DIR = DATA_DIR / "requirement_set_type"
+REQUIREMENT_TYPE_DATA_DIR = DATA_DIR / "requirement_type"
+
 # To Do
 LAB_VALUE_DATA_DIR = DATA_DIR / "lab_value"
 PATIENT_LAB_SAMPLE_TYPE_DATA_DIR = DATA_DIR / "patient_lab_sample_type"

{endoreg_db-0.6.2 → endoreg_db-0.6.4}/endoreg_db/data/disease_classification/chronic_kidney_disease.yaml

@@ -1,6 +1,6 @@
 - model: endoreg_db.disease_classification
   fields:
-    name: "chronic_kideny_disease_kdigo"
+    name: "chronic_kidney_disease_kdigo"
     name_de: "Chronische Nierenerkrankung (KDIGO)"
     name_en: "Chronic Kidney Disease (KDIGO)"
-    disease: "chronic_kidney_disease"
+    disease: "chronic_kidney_disease"

{endoreg_db-0.6.2 → endoreg_db-0.6.4}/endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml

@@ -3,39 +3,39 @@
     name: "ckd_kdigo_1"
     name_de: "Chronische Nierenerkrankung (KDIGO) (Stadium 1)"
     name_en: "Chronic Kidney Disease (KDIGO) (Stage 1)"
-    disease_classification: "chronic_kideny_disease_kdigo"
+    disease_classification: "chronic_kidney_disease_kdigo"
 
 - model: endoreg_db.disease_classification_choice
   fields:
     name: "ckd_kdigo_2"
     name_de: "Chronische Nierenerkrankung (KDIGO) (Stadium 2)"
     name_en: "Chronic Kidney Disease (KDIGO) (Stage 2)"
-    disease_classification: "chronic_kideny_disease_kdigo"
+    disease_classification: "chronic_kidney_disease_kdigo"
 
 - model: endoreg_db.disease_classification_choice
   fields:
     name: "ckd_kdigo_3a"
     name_de: "Chronische Nierenerkrankung (KDIGO) (Stadium 3a)"
     name_en: "Chronic Kidney Disease (KDIGO) (Stage 3a)"
-    disease_classification: "chronic_kideny_disease_kdigo"
+    disease_classification: "chronic_kidney_disease_kdigo"
 
 - model: endoreg_db.disease_classification_choice
   fields:
     name: "ckd_kdigo_3b"
     name_de: "Chronische Nierenerkrankung (KDIGO) (Stadium 3b)"
     name_en: "Chronic Kidney Disease (KDIGO) (Stage 3b)"
-    disease_classification: "chronic_kideny_disease_kdigo"
+    disease_classification: "chronic_kidney_disease_kdigo"
 
 - model: endoreg_db.disease_classification_choice
   fields:
     name: "ckd_kdigo_4"
     name_de: "Chronische Nierenerkrankung (KDIGO) (Stadium 4)"
     name_en: "Chronic Kidney Disease (KDIGO) (Stage 4)"
-    disease_classification: "chronic_kideny_disease_kdigo"
+    disease_classification: "chronic_kidney_disease_kdigo"
 
 - model: endoreg_db.disease_classification_choice
   fields:
     name: "ckd_kdigo_5"
     name_de: "Chronische Nierenerkrankung (KDIGO) (Stadium 5)"
     name_en: "Chronic Kidney Disease (KDIGO) (Stage 5)"
-    disease_classification: "chronic_kideny_disease_kdigo"
+    disease_classification: "chronic_kidney_disease_kdigo"

{endoreg_db-0.6.2 → endoreg_db-0.6.4}/endoreg_db/data/distribution/numeric/data.yaml

@@ -10,5 +10,5 @@
   fields:
     name: "uniform_high_x1.5"
     distribution_type: "uniform"
-    min_descriptor: "max_x_1"
+    min_descriptor: "min_x_1"
     max_descriptor: "max_x_1.5"

{endoreg_db-0.6.2 → endoreg_db-0.6.4}/endoreg_db/data/examination/examinations/data.yaml

@@ -3,18 +3,14 @@
     name: "colonoscopy"
     name_de: "Koloskopie"
     name_en: "Colonoscopy"
-    examination_types: [
-      "endoscopy"
-    ]
+    examination_types: ["endoscopy"]
 
 - model: report.Examination
   fields:
     name: "gastroscopy"
     name_de: "Gastroskopie"
     name_en: "Gastroscopy"
-    examination_types: [
-      "endoscopy"
-    ]
+    examination_types: ["endoscopy"]
 
 # endosonography_upper_gi
 - model: report.Examination
@@ -22,18 +18,14 @@
     name: "endosonography_upper_gi"
     name_de: "Endosonographie oberer GI-Trakt"
     name_en: "Endosonography Upper GI Tract"
-    examination_types: [
-      "endoscopy"
-    ]
+    examination_types: ["endoscopy"]
 
 - model: report.Examination
   fields:
     name: "endosonography_lower_gi"
     name_de: "Endosonographie unterer GI-Trakt"
     name_en: "Endosonography Lower GI Tract"
-    examination_types: [
-      "endoscopy"
-    ]
+    examination_types: ["endoscopy"]
 
 # ERCP
 - model: report.Examination
@@ -41,9 +33,7 @@
     name: "ercp"
     name_de: "ERCP"
     name_en: "ERCP"
-    examination_types: [
-      "endoscopy"
-    ]
+    examination_types: ["endoscopy"]
 
 # small bowel endoscopy
 - model: report.Examination
@@ -51,9 +41,7 @@
     name: "small_bowel_endoscopy"
     name_de: "Dünndarmendoskopie"
     name_en: "Small Bowel Endoscopy"
-    examination_types: [
-      "endoscopy"
-    ]
+    examination_types: ["endoscopy"]
 
 # capsule endoscopy
 - model: report.Examination
@@ -61,6 +49,19 @@
     name: "capsule_endoscopy"
     name_de: "Kapselendoskopie"
     name_en: "Capsule Endoscopy"
-    examination_types: [
-      "endoscopy"
-    ]
+    examination_types: ["endoscopy"]
+
+- model: report.Examination
+  fields:
+    name: "percutaneous_transhepatic_biliary_drainage"
+    name_de: "Perkutane transhepatische Gallengangdrainage"
+    name_en: "Percutaneous Transhepatic Biliary Drainage"
+    examination_types: ["endoscopy", "sonography", "xray"]
+
+# percutaneous_transhepatic_cholangiography
+- model: report.Examination
+  fields:
+    name: "percutaneous_transhepatic_cholangiography"
+    name_de: "Perkutane transhepatische Cholangiographie"
+    name_en: "Percutaneous Transhepatic Cholangiography"
+    examination_types: ["endoscopy", "sonography", "xray"]

endoreg_db-0.6.4/endoreg_db/data/examination/type/data.yaml

@@ -0,0 +1,17 @@
+- model: report.ExaminationType
+  fields:
+    name: "endoscopy"
+    name_de: "Endoskopie"
+    name_en: "Endoscopy"
+
+- model: report.ExaminationType
+  fields:
+    name: "sonography"
+    name_de: "Sonographie"
+    name_en: "Sonography"
+
+- model: report.ExaminationType
+  fields:
+    name: "xray"
+    name_de: "Röntgen"
+    name_en: "X-ray"