meta-edc 0.3.32__py3-none-any.whl → 0.3.34__py3-none-any.whl

meta_subject/migrations/0132_auto_20220722_1825.py

@@ -1,5 +1,5 @@
 # Generated by Django 3.2.11 on 2022-07-22 15:25
-
+from django.core.exceptions import ObjectDoesNotExist
 from django.db import migrations
 from tqdm import tqdm
 
@@ -9,11 +9,15 @@ from meta_pharmacy.constants import METFORMIN
 def update_rx_missing_medication(apps, schema_editor):
     medication_model_cls = apps.get_model("edc_pharmacy.medication")
     rx_model_cls = apps.get_model("edc_pharmacy.rx")
-    medication = medication_model_cls.objects.get(name=METFORMIN)
-    total = rx_model_cls.objects.filter(medications__isnull=True).count()
-    for obj in tqdm(rx_model_cls.objects.filter(medications__isnull=True), total=total):
-        if not obj.medications.all().exists():
-            obj.medications.add(medication)
+    try:
+        medication = medication_model_cls.objects.get(name=METFORMIN)
+    except ObjectDoesNotExist:
+        pass
+    else:
+        total = rx_model_cls.objects.filter(medications__isnull=True).count()
+        for obj in tqdm(rx_model_cls.objects.filter(medications__isnull=True), total=total):
+            if not obj.medications.all().exists():
+                obj.medications.add(medication)
 
 
 class Migration(migrations.Migration):

meta_subject/migrations/0135_auto_20220722_2212.py

@@ -9,42 +9,46 @@ from tqdm import tqdm
 def update_revised_egrf(apps, schema_editor):
     bloodresultrft_model_cls = apps.get_model("meta_subject.bloodresultsrft")
     subjectvisit_model_cls = apps.get_model("meta_subject.subjectvisit")
-    subjectscreening_model_cls = apps.get_model("meta_screening.subjectscreening")
-    total = bloodresultrft_model_cls.objects.all().count()
-    for obj in tqdm(bloodresultrft_model_cls.objects.all(), total=total):
-        subject_visit = subjectvisit_model_cls.objects.get(id=obj.subject_visit_id)
-        subject_screening = subjectscreening_model_cls.objects.get(
-            subject_identifier=subject_visit.subject_identifier
-        )
-        try:
-            baseline_obj = bloodresultrft_model_cls.objects.get(
-                subject_visit__subject_identifier=subject_visit.subject_identifier,
-                subject_visit__visit_code=DAY1,
-                subject_visit__visit_code_sequence=0,
-            )
-        except ObjectDoesNotExist:
-            pass
-        else:
-            obj.old_egfr_value = obj.egfr_value
-            obj.old_egfr_drop_value = obj.egfr_drop_value
-            obj.egfr_value = EgfrCkdEpi(
-                gender=subject_screening.gender,
-                ethnicity=subject_screening.ethnicity,
-                age_in_years=subject_screening.age_in_years,
-                creatinine_value=obj.creatinine_value,
-                creatinine_units=obj.creatinine_units,
-            ).value
-            obj.egfr_drop_value = egfr_percent_change(
-                float(obj.egfr_value), float(baseline_obj.egfr_value)
-            )
-            obj.save_base(
-                update_fields=[
-                    "egfr_value",
-                    "egfr_drop_value",
-                    "old_egfr_value",
-                    "old_egfr_drop_value",
-                ]
+    try:
+        subjectscreening_model_cls = apps.get_model("meta_screening.subjectscreening")
+    except LookupError:
+        pass
+    else:
+        total = bloodresultrft_model_cls.objects.all().count()
+        for obj in tqdm(bloodresultrft_model_cls.objects.all(), total=total):
+            subject_visit = subjectvisit_model_cls.objects.get(id=obj.subject_visit_id)
+            subject_screening = subjectscreening_model_cls.objects.get(
+                subject_identifier=subject_visit.subject_identifier
             )
+            try:
+                baseline_obj = bloodresultrft_model_cls.objects.get(
+                    subject_visit__subject_identifier=subject_visit.subject_identifier,
+                    subject_visit__visit_code=DAY1,
+                    subject_visit__visit_code_sequence=0,
+                )
+            except ObjectDoesNotExist:
+                pass
+            else:
+                obj.old_egfr_value = obj.egfr_value
+                obj.old_egfr_drop_value = obj.egfr_drop_value
+                obj.egfr_value = EgfrCkdEpi(
+                    gender=subject_screening.gender,
+                    ethnicity=subject_screening.ethnicity,
+                    age_in_years=subject_screening.age_in_years,
+                    creatinine_value=obj.creatinine_value,
+                    creatinine_units=obj.creatinine_units,
+                ).value
+                obj.egfr_drop_value = egfr_percent_change(
+                    float(obj.egfr_value), float(baseline_obj.egfr_value)
+                )
+                obj.save_base(
+                    update_fields=[
+                        "egfr_value",
+                        "egfr_drop_value",
+                        "old_egfr_value",
+                        "old_egfr_drop_value",
+                    ]
+                )
 
 
 class Migration(migrations.Migration):

meta_subject/migrations/0150_auto_20220914_0039.py

@@ -5,18 +5,22 @@ from tqdm import tqdm
 
 def update_rs_missing_ethnicity(apps, schema_editor):
     register_subject_model_cls = apps.get_model("edc_registration.registeredsubject")
-    subject_screening_model_cls = apps.get_model("meta_screening.subjectscreening")
     subject_consent_model_cls = apps.get_model("meta_consent.subjectconsent")
-    total = subject_consent_model_cls.objects.all().count()
-    for subject_consent in tqdm(subject_consent_model_cls.objects.all(), total=total):
-        subject_screening = subject_screening_model_cls.objects.get(
-            subject_identifier=subject_consent.subject_identifier
-        )
-        register_subject = register_subject_model_cls.objects.get(
-            subject_identifier=subject_consent.subject_identifier
-        )
-        register_subject.ethnicity = subject_screening.ethnicity
-        register_subject.save(update_fields=["ethnicity"])
+    try:
+        subject_screening_model_cls = apps.get_model("meta_screening.subjectscreening")
+    except LookupError:
+        pass
+    else:
+        total = subject_consent_model_cls.objects.all().count()
+        for subject_consent in tqdm(subject_consent_model_cls.objects.all(), total=total):
+            subject_screening = subject_screening_model_cls.objects.get(
+                subject_identifier=subject_consent.subject_identifier
+            )
+            register_subject = register_subject_model_cls.objects.get(
+                subject_identifier=subject_consent.subject_identifier
+            )
+            register_subject.ethnicity = subject_screening.ethnicity
+            register_subject.save(update_fields=["ethnicity"])
 
 
 class Migration(migrations.Migration):

meta_analytics/notebooks/meta_endpoints.ipynb

@@ -1,201 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "28e21930-b943-4a08-a79a-ff2712ae9215",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%capture\n",
-    "import os\n",
-    "import pandas as pd\n",
-    "import numpy as np\n",
-    "from datetime import datetime\n",
-    "from django_pandas.io import read_frame\n",
-    "from pathlib import Path\n",
-    "\n",
-    "\n",
-    "from dj_notebook import activate\n",
-    "\n",
-    "# pd.options.mode.copy_on_write = True\n",
-    "# pd.options.mode.chained_assignment = \"raise\"\n",
-    "env_file = os.environ[\"META_ENV\"]\n",
-    "report_folder = os.environ[\"META_DOCUMENTS_FOLDER\"]\n",
-    "report_folder = Path(report_folder)\n",
-    "\n",
-    "plus = activate(dotenv_file=env_file)\n",
-    "\n",
-    "# output is suppressed ut normally would spew out all the edc loading messages"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "52d4bb98-18a5-4528-be8d-e8370b1b5d1e",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from edc_constants.constants import YES\n",
-    "from edc_pdutils.dataframes import get_crf\n",
-    "\n",
-    "from meta_subject.models import Glucose, GlucoseFbg\n",
-    "from meta_analytics.dataframes import GlucoseEndpointsByDate"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7df19192-923c-4848-85e2-72b9d2489673",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "cls = GlucoseEndpointsByDate()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1eea8cf7-f52c-46d0-b49c-b875e11f9ae0",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "cls.run()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7a4b0246-b082-460c-8f9a-dee8d0fc1d63",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "len(cls.endpoint_df[\"subject_identifier\"].unique())"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "df519e75-d536-435e-8c1e-d4087b99d174",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "cls.summarize()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "526b5f1a-cc77-4182-b9b4-c17c297344f6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# table meta_subject.glucose\n",
-    "fname = f\"meta-subject-glucose-{datetime.now().strftime(\"%Y-%m-%d-%H%M\")}.csv\"\n",
-    "get_crf(\"meta_subject.glucose\", subject_visit_model=\"meta_subject.subjectvisit\", drop_columns=[\"consent_model\"]).to_csv(report_folder / fname, sep=\"|\", encoding=\"utf8\", index=False)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b914aef9-5a27-4474-8359-2d8e0509720b",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# table meta_subject.glucosefbg\n",
-    "fname = f\"meta-subject-glucosefbg-{datetime.now().strftime(\"%Y-%m-%d-%H%M\")}.csv\"\n",
-    "get_crf(\"meta_subject.glucosefbg\", subject_visit_model=\"meta_subject.subjectvisit\", drop_columns=[\"consent_model\"]).to_csv(report_folder / fname, sep=\"|\", encoding=\"utf8\", index=False)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "66064ddd-51b6-4474-9664-42ecd471e9ce",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# all glucose merged\n",
-    "fname = f\"glucose-merged-{datetime.now().strftime(\"%Y-%m-%d-%H%M\")}.csv\"\n",
-    "cls.df.to_csv(report_folder / fname, sep=\"|\", encoding=\"utf8\", index=False)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "a8a9da26-84f0-4cc3-a33b-83bf1c292380",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# pivot of glucose readings for subjects who have reached\n",
-    "# an ednpoint\n",
-    "fname = f\"glucose-pivot-{datetime.now().strftime(\"%Y-%m-%d-%H%M\")}.csv\"\n",
-    "df_pivot = cls.endpoint_df.sort_values(by=[\"subject_identifier\"]).set_index(\"subject_identifier\").pivot_table(columns=[\"visit_code\"], values=[\"fbg_value\",\"ogtt_value\"], index=[\"subject_identifier\"])\n",
-    "df_pivot.sort_values(('visit_code'), axis=1).sort_values(\"subject_identifier\").to_csv(report_folder / fname, sep=\"|\", encoding=\"utf8\", index=True)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "f97dcfa7-4575-43c1-8614-9f51eb4adff5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# all subjects with endpoint data\n",
-    "fname = f\"endpoint_df-{datetime.now().strftime(\"%Y-%m-%d-%H%M\")}.csv\"\n",
-    "cls.endpoint_df.to_csv(report_folder / fname, sep=\"|\", encoding=\"utf8\", index=False)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b394252c-443c-49a9-9f32-77a686d00067",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# len(cls.endpoint_only_df)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "82634927-c2bf-4745-9fdf-841a1fec008b",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# len(cls.endpoint_only_df[\"subject_identifier\"].unique())"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "dc597ae7-d66e-4e1f-9f69-b35dd2d28ec4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# subject_identifier = \"105-10-0064-2\"\n",
-    "# cls.df[cls.df[\"subject_identifier\"]==subject_identifier][[\"visit_code\", \"fbg_datetime\", \"fasting\", \"fbg_value\", \"ogtt_value\"]]"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.2"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}