meta-edc 1.1.8__py3-none-any.whl → 1.1.12__py3-none-any.whl

meta_analytics/notebooks/ven.ipynb

@@ -1,191 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%capture\n",
-    "import os\n",
-    "from pathlib import Path\n",
-    "import pandas as pd\n",
-    "from dj_notebook import activate\n",
-    "import numpy as np\n",
-    "from django_pandas.io import read_frame\n",
-    "\n",
-    "env_file = os.environ[\"META_ENV\"]\n",
-    "reports_folder = Path(os.environ[\"META_REPORTS_FOLDER\"])\n",
-    "analysis_folder = Path(os.environ[\"META_ANALYSIS_FOLDER\"])\n",
-    "pharmacy_folder = Path(os.environ[\"META_PHARMACY_FOLDER\"])\n",
-    "plus = activate(dotenv_file=env_file)\n",
-    "pd.set_option('future.no_silent_downcasting', True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from matplotlib import pyplot as plt\n",
-    "from matplotlib_venn import venn3, venn2\n",
-    "from meta_analytics.dataframes import get_screening_df\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def get_fbg_value(r):\n",
-    "    if not pd.isna(r[\"converted_fbg2_value\"]):\n",
-    "        return r[\"converted_fbg2_value\"]\n",
-    "    return r[\"converted_fbg_value\"]\n",
-    "\n",
-    "def get_ogtt_value(r):\n",
-    "    if not pd.isna(r[\"converted_ogtt2_value\"]):\n",
-    "        return r[\"converted_ogtt2_value\"]\n",
-    "    return r[\"converted_ogtt_value\"]\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from meta_analytics.dataframes import get_screening_df\n",
-    "\n",
-    "df_screening = get_screening_df()\n",
-    "df_screening[\"visit_code\"] = \"Enrol\"\n",
-    "df_screening[\"fbg_value\"] = df_screening.apply(get_fbg_value, axis=1)\n",
-    "df_screening[\"ogtt_value\"] = df_screening.apply(get_ogtt_value, axis=1)\n",
-    "df_screening[\"site_id\"] = df_screening.site.astype(int)\n",
-    "df_screening = df_screening.drop(columns=[\"site\"])\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_screening.query(\"\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "fbg = set(df_screening[df_screening.fbg_value>=7.0][[\"id\"]].id.to_list())\n",
-    "ogtt = set(df_screening[df_screening.ogtt_value>=11.1][[\"id\"]].id.to_list())\n",
-    "hba1c = set(df_screening[df_screening.hba1c_value>=6.5][[\"id\"]].id.to_list())\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\n",
-    "# plt.figure(figsize=(6, 6))\n",
-    "fig, ax = plt.subplots(figsize=(8, 8))\n",
-    "venn = venn3([fbg, ogtt, hba1c], set_labels=('FBG≥7.0 mmol/L', 'OGTT≥11.1 mmol/L', 'HBA1C≥6.5%'), ax=ax)\n",
-    "plt.title(\"Overlap in diabetes indicators for all screened patients (n=5552)\")\n",
-    "\n",
-    "region_ids = ['100', '010', '001']\n",
-    "for idx, region_id in enumerate(region_ids):\n",
-    "    patch = venn.get_patch_by_id(region_id)\n",
-    "    label = venn.set_labels[idx]\n",
-    "    if patch and label:\n",
-    "        label.set_color(patch.get_facecolor())\n",
-    "        label.set_fontweight('bold')\n",
-    "\n",
-    "# Show the plot\n",
-    "# plt.show()\n",
-    "plt.savefig(analysis_folder / \"meta3_venn.png\", bbox_inches='tight')\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\n",
-    "import matplotlib.pyplot as plt\n",
-    "from matplotlib_venn import venn2\n",
-    "from pathlib import Path\n",
-    "\n",
-    "# Define the output folder\n",
-    "analysis_folder = Path(\"analysis_output\")\n",
-    "analysis_folder.mkdir(parents=True, exist_ok=True)\n",
-    "\n",
-    "# Define the sets\n",
-    "set1 = set(['A', 'B', 'C', 'D'])\n",
-    "set2 = set(['C', 'D', 'E', 'F'])\n",
-    "\n",
-    "# Create the figure and axis\n",
-    "fig, ax = plt.subplots(figsize=(6, 6))\n",
-    "\n",
-    "# Draw the Venn diagram on the axis\n",
-    "venn2([set1, set2], set_labels=('Set 1', 'Set 2'), ax=ax)\n",
-    "\n",
-    "# Save the figure\n",
-    "fig.savefig(analysis_folder / \"meta3_venn.png\", bbox_inches='tight')\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "9",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 2
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.6"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

meta_analytics/notebooks/vitals.ipynb

@@ -1,263 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%capture\n",
-    "import os\n",
-    "import pandas as pd\n",
-    "from dj_notebook import activate\n",
-    "from pathlib import Path\n",
-    "env_file = os.environ[\"META_ENV\"]\n",
-    "analysis_folder = Path(os.environ[\"META_ANALYSIS_FOLDER\"])\n",
-    "reports_folder = Path(os.environ[\"META_ANALYSIS_FOLDER\"])\n",
-    "plus = activate(dotenv_file=env_file)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from edc_pdutils.dataframes import get_crf\n",
-    "from edc_appointment.analytics import get_appointment_df\n",
-    "from edc_appointment.constants import MISSED_APPT\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_visit = get_crf(\"meta_subject.glucosefbg\", subject_visit_model=\"meta_subject.subjectvisit\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_missedvisit = get_crf(\"meta_subject.subjectvisitmissed\", subject_visit_model=\"meta_subject.subjectvisit\")\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_missedvisit[df_missedvisit.appt_timing!=MISSED_APPT]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "dffbg = get_crf(\"meta_subject.glucosefbg\", subject_visit_model=\"meta_subject.subjectvisit\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "dffbg[dffbg.fbg_value<=3.0][[\"subject_identifier\", \"visit_code\", \"fbg_value\"]]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "dfglu = get_crf(\"meta_subject.glucose\", subject_visit_model=\"meta_subject.subjectvisit\")\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "9",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "dfglu.fbg_value.describe()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "10",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_appt = get_appointment_df()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "11",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_appt"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "12",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "dffbg.visit_code.value_counts()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "13",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "dfglu.visit_code.value_counts()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "14",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df = df_appt.merge(dffbg[[\"subject_identifier\", \"visit_code\", \"fbg_value\"]], on=[\"subject_identifier\", \"visit_code\"], how=\"left\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "15",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df[df.visit_code==1005.0].appt_status.value_counts()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "16",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df[(df.visit_code==1005.0) & (df.fbg_value.isna())].appt_status.value_counts()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "17",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from datetime import datetime\n",
-    "\n",
-    "df[(df.visit_code==1005.0) & (df.fbg_value.isna()) & (df.appt_datetime<=pd.to_datetime(datetime(2024,3,4)))].appt_status.value_counts()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "18",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "missed_subjects = [\n",
-    "    \"105-60-0164-5\",\n",
-    "    \"105-20-0384-3\",\n",
-    "    \"105-60-0196-7\",\n",
-    "    \"105-60-0157-9\",\n",
-    "    \"105-40-0324-7\",\n",
-    "    \"105-30-0118-4\",\n",
-    "]\n",
-    "\n",
-    "df[(df.visit_code==1005.0) & (df.fbg_value.isna()) & (df.appt_datetime<=pd.to_datetime(datetime(2024,3,4)))].subject_identifier"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "19",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df[(df.visit_code==1005.0) & (df.fbg_value.isna()) & (df.appt_datetime<=pd.to_datetime(datetime(2024,3,4))) & (df.appt_timing) ][[\"subject_identifier\", \"appt_timing\", \"appt_status\", \"visit_code\"]]\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "20",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_appt[df_appt.subject_identifier==\"105-60-0157-9\"]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "21",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 2
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.6"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

meta_analytics/tests/test_endpoints_by_date.py

@@ -1,94 +0,0 @@
-from datetime import datetime
-
-import numpy as np
-import pandas as pd
-from dateutil.relativedelta import relativedelta
-from django.test import TestCase
-from edc_constants.constants import YES
-
-from meta_analytics.dataframes import EndpointByDate
-
-
-class TestEndpointsByDate(TestCase):
-    def test_case_one(self):
-        def d(m: int, w: int | None = None):
-            if w:
-                return datetime.now() - relativedelta(months=m, weeks=w)
-            return datetime.now() - relativedelta(months=m)
-
-        def append_to(subject_df, endpoint_df):
-            if endpoint_df.empty:
-                endpoint_df = subject_df.copy()
-            elif subject_df.empty:
-                pass
-            else:
-                endpoint_df = pd.concat([endpoint_df, subject_df])
-                endpoint_df = self.endpoint_df.sort_values(
-                    by=["subject_identifier", "visit_code"]
-                )
-                endpoint_df.reset_index(drop=True, inplace=True)
-
-        subject_identifier = "101-1"
-        data = {
-            "subject_identifier": [subject_identifier] * 10,
-            "visit_code": [
-                1000.0,
-                1005.0,
-                1010.0,
-                1030.0,
-                1060.0,
-                1090.0,
-                1120.0,
-                1115.0,
-                1118.0,
-                1210.0,
-            ],
-            "fasting": [YES] * 10,
-            "fbg_datetime": [
-                d(0),
-                d(0, 2),
-                d(1),
-                d(3),
-                d(6),
-                d(9),
-                d(12),
-                d(15),
-                d(18),
-                d(21),
-            ],
-            "fbg_value": [np.nan, 6.9, 6.9, 7.1, 7.1, 6.4, 7.0, np.nan, 8.1, np.nan],
-            "ogtt_value": [
-                np.nan,
-                np.nan,
-                np.nan,
-                np.nan,
-                np.nan,
-                np.nan,
-                np.nan,
-                np.nan,
-                7.9,
-                np.nan,
-            ],
-        }
-
-        fbgs = [np.nan, 6.9, 6.9, 7.1, 7.1, 6.4, 7.0, np.nan, 8.1, np.nan]
-        ogtts = [np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, 7.9, np.nan]
-
-        fbgs = [np.nan, 6.9, 6.9, 7.1, 7.1, 6.4, 7.0, 8.1, np.nan, np.nan]
-        ogtts = [np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, 7.9, np.nan, np.nan]
-
-        data.update(fbg_values=fbgs, ogtt_values=ogtts)
-        subject_df = pd.DataFrame(data)
-        subject_df["fasting"] = subject_df.apply(
-            lambda r: np.nan if pd.isna(r.fbg_value) else r.fbg_value, axis=1
-        )
-        subject_df["fbg_datetime"] = subject_df.apply(
-            lambda r: np.nan if pd.isna(r.fbg_value) else r.fbg_datetime, axis=1
-        )
-
-        endpoint_df = pd.DataFrame()
-        for index, row in subject_df.iterrows():
-            cls = EndpointByDate(index, row, fbg_threshhold=7.0, ogtt_threshhold=11.1)
-            append_to(cls.subject_df, endpoint_df)
-
-        endpoint_df

meta_consent/tests/holidays.csv

@@ -1,15 +0,0 @@
-2019-01-01,New Year's Day,tanzania
-2019-01-12,Zanzibar Revolution Day,tanzania
-2019-04-07,The Sheikh Abeid Amani Karume Day,tanzania
-2019-04-17,Easter Monday,tanzania
-2019-04-26,Union Day,tanzania
-2019-05-01,Labour Day,tanzania
-2019-06-26,Eid al-Fitr,tanzania
-2019-07-07,Saba Saba Day,tanzania
-2019-07-14,Good Friday,tanzania
-2019-08-08,Nane Nane Day,tanzania
-2019-10-14,Nyerere Day,tanzania
-2019-12-01,Mawlid Day,tanzania
-2019-12-09,Independence Day,tanzania
-2019-12-25,Christmas Day,tanzania
-2019-12-26,Boxing Day,tanzania

meta_consent/tests/tests/test_form_validators.py

@@ -1,110 +0,0 @@
-from zoneinfo import ZoneInfo
-
-from dateutil.relativedelta import relativedelta
-from django import forms
-from django.test import TestCase
-from edc_consent.constants import HOSPITAL_NUMBER
-from edc_constants.constants import FEMALE
-from edc_utils.date import get_utcnow
-
-from meta_consent.form_validators import SubjectConsentFormValidator
-from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
-
-
-class TestFormValidators(MetaTestCaseMixin, TestCase):
-    def setUp(self):
-        super().setUp()
-        self.eligibility_datetime = get_utcnow() - relativedelta(days=1)  # yesterday
-        self.subject_screening = self.get_subject_screening(
-            report_datetime=get_utcnow(), eligibility_datetime=self.eligibility_datetime
-        )
-        self.screening_identifier = self.subject_screening.screening_identifier
-
-    @staticmethod
-    def get_now():
-        return get_utcnow().astimezone(ZoneInfo("Africa/Dar_es_Salaam"))
-
-    def test_ok(self):
-        consent_datetime = self.get_now()
-        cleaned_data = dict(
-            screening_identifier=self.screening_identifier,
-            gender=FEMALE,
-            dob=self.subject_screening.report_datetime.date() - relativedelta(years=25),
-            consent_datetime=consent_datetime,
-            identity_type=HOSPITAL_NUMBER,
-            identity=self.subject_screening.hospital_identifier,
-            confirm_identity=self.subject_screening.hospital_identifier,
-        )
-        validator = SubjectConsentFormValidator(
-            cleaned_data=cleaned_data,
-        )
-        validator.clean()
-
-    def test_consent_before_eligibility_datetime(self):
-        consent_datetime = self.subject_screening.eligibility_datetime - relativedelta(
-            minutes=1
-        )
-        consent_datetime = consent_datetime.astimezone(ZoneInfo("Africa/Dar_es_Salaam"))
-        cleaned_data = dict(
-            screening_identifier=self.screening_identifier,
-            gender=FEMALE,
-            dob=self.subject_screening.report_datetime.date() - relativedelta(years=25),
-            consent_datetime=consent_datetime,
-            identity_type=HOSPITAL_NUMBER,
-            identity=self.subject_screening.hospital_identifier,
-            confirm_identity=self.subject_screening.hospital_identifier,
-        )
-        validator = SubjectConsentFormValidator(
-            cleaned_data=cleaned_data,
-        )
-        self.assertRaises(forms.ValidationError, validator.validate)
-        with self.assertRaises(forms.ValidationError) as cm:
-            validator.validate()
-        self.assertIn("consent_datetime", str(cm.exception))
-
-    def test_consent_after_eligibility_datetime(self):
-        consent_datetime = self.subject_screening.eligibility_datetime + relativedelta(
-            minutes=1
-        )
-        consent_datetime = consent_datetime.astimezone(ZoneInfo("Africa/Dar_es_Salaam"))
-        cleaned_data = dict(
-            screening_identifier=self.screening_identifier,
-            gender=FEMALE,
-            dob=self.subject_screening.report_datetime.date() - relativedelta(years=25),
-            consent_datetime=consent_datetime,
-            identity_type=HOSPITAL_NUMBER,
-            identity=self.subject_screening.hospital_identifier,
-            confirm_identity=self.subject_screening.hospital_identifier,
-        )
-        validator = SubjectConsentFormValidator(
-            cleaned_data=cleaned_data,
-        )
-        try:
-            validator.clean()
-        except forms.ValidationError:
-            self.fail("ValidationError unexpectedly raised")
-
-    def test_mismatch_between_screening_age_and_calculated_consent_age_raises(self):
-        consent_datetime = self.get_now()
-        data = dict(
-            screening_identifier=self.screening_identifier,
-            gender=FEMALE,
-            dob=self.subject_screening.report_datetime.date()
-            - relativedelta(years=self.subject_screening.age_in_years + 1),
-            consent_datetime=consent_datetime,
-            identity_type=HOSPITAL_NUMBER,
-            identity=self.subject_screening.hospital_identifier,
-            confirm_identity=self.subject_screening.hospital_identifier,
-        )
-        form_validator = SubjectConsentFormValidator(
-            cleaned_data=data,
-        )
-        with self.assertRaises(forms.ValidationError) as cm:
-            form_validator.validate()
-        self.assertIn("dob", cm.exception.error_dict)
-        self.assertIn(
-            "Age mismatch. "
-            "The date of birth entered does not match the age at screening. "
-            "Expected 25. Got 26.",
-            str(cm.exception.error_dict.get("dob")),
-        )

meta_consent/tests/tests/test_subject_consent.py

@@ -1,10 +0,0 @@
-from django.test import TestCase
-
-from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
-
-
-class TestSubjectConsent(MetaTestCaseMixin, TestCase):
-    def test_(self):
-        subject_screening = self.get_subject_screening()
-        subject_consent = self.get_subject_consent(subject_screening)
-        self.assertIsNotNone(subject_consent.subject_identifier)