meta-edc 0.3.33__py3-none-any.whl → 0.3.35__py3-none-any.whl

meta_subject/migrations/0107_auto_20220415_0043.py

@@ -1,5 +1,5 @@
 # Generated by Django 3.2.11 on 2022-04-14 21:43
-
+from django.core.exceptions import ObjectDoesNotExist
 from django.db import migrations
 from django.db.migrations import RunPython
 from edc_consent.utils import get_consent_model_name
@@ -10,28 +10,34 @@ from meta_pharmacy.constants import METFORMIN
 
 
 def func(apps, schema_editor):
-    medication = apps.get_model("edc_pharmacy.medication")._default_manager.get(name=METFORMIN)
-    site_model_cls = apps.get_model("sites.site")
-    subject_identifiers = [
-        tpl[0]
-        for tpl in apps.get_model("edc_pharmacy.rx")._default_manager.values_list(
-            "subject_identifier"
-        )
-    ]
-    for subject_consent in apps.get_model(get_consent_model_name())._default_manager.exclude(
-        subject_identifier__in=subject_identifiers
-    ):
-        site = site_model_cls.objects.get(id=subject_consent.site.id)
-        create_prescription(
-            subject_identifier=subject_consent.subject_identifier,
-            report_datetime=subject_consent.consent_datetime,
-            randomizer_name=get_meta_version(),
-            medications=[METFORMIN],
-            site_id=site.id,
+    try:
+        medication = apps.get_model("edc_pharmacy.medication")._default_manager.get(
+            name=METFORMIN
         )
-    for obj in apps.get_model("edc_pharmacy.rx")._default_manager.all():
-        obj.medications.clear()
-        obj.medications.add(medication)
+    except ObjectDoesNotExist:
+        pass
+    else:
+        site_model_cls = apps.get_model("sites.site")
+        subject_identifiers = [
+            tpl[0]
+            for tpl in apps.get_model("edc_pharmacy.rx")._default_manager.values_list(
+                "subject_identifier"
+            )
+        ]
+        for subject_consent in apps.get_model(
+            get_consent_model_name()
+        )._default_manager.exclude(subject_identifier__in=subject_identifiers):
+            site = site_model_cls.objects.get(id=subject_consent.site.id)
+            create_prescription(
+                subject_identifier=subject_consent.subject_identifier,
+                report_datetime=subject_consent.consent_datetime,
+                randomizer_name=get_meta_version(),
+                medications=[METFORMIN],
+                site_id=site.id,
+            )
+        for obj in apps.get_model("edc_pharmacy.rx")._default_manager.all():
+            obj.medications.clear()
+            obj.medications.add(medication)
 
 
 class Migration(migrations.Migration):

meta_subject/migrations/0126_auto_20220719_2142.py

@@ -4,11 +4,11 @@ from django.db import migrations
 
 
 def update_egfr_drop_action(apps, schema_editor):
-    action_item_model_cls = apps.get_model("edc_action_item.actionitem")
+    # action_item_model_cls = apps.get_model("edc_action_item.actionitem")
     crf_metadata_model_cls = apps.get_model("edc_metadata.crfmetadata")
-    action_item_model_cls.objects.filter(
-        reference_model="meta_subject.egfrnotification"
-    ).update(reference_model="meta_subject.egfrdropnotification")
+    # action_item_model_cls.objects.filter(
+    #     reference_model="meta_subject.egfrnotification"
+    # ).update(reference_model="meta_subject.egfrdropnotification")
     crf_metadata_model_cls.objects.filter(model="meta_subject.egfrnotification").update(
         model="meta_subject.egfrdropnotification"
     )

meta_subject/migrations/0131_auto_20220722_0411.py

@@ -1,5 +1,5 @@
 # Generated by Django 3.2.11 on 2022-07-22 01:11
-
+from django.core.exceptions import ObjectDoesNotExist
 from django.db import migrations
 from edc_action_item.identifiers import ActionIdentifier
 from edc_constants.constants import CLOSED, HIGH_PRIORITY
@@ -13,28 +13,33 @@ def update_missing_action_items_for_missed_visits(apps, schema_editor):
     actionitem_model_cls = apps.get_model("edc_action_item.actionitem")
     subjectvisitmissed_model_cls = apps.get_model("meta_subject.subjectvisitmissed")
     subjectvisit_model_cls = apps.get_model("meta_subject.subjectvisit")
-    action_type = actiontype_model_cls.objects.get(name=MISSED_VISIT_ACTION)
-
-    total = subjectvisitmissed_model_cls.objects.filter(action_identifier__isnull=True).count()
-    for obj in tqdm(
-        subjectvisitmissed_model_cls.objects.filter(action_identifier__isnull=True),
-        total=total,
-    ):
-        subject_visit = subjectvisit_model_cls.objects.get(id=obj.subject_visit_id)
-        action_item = actionitem_model_cls.objects.create(
-            subject_identifier=subject_visit.subject_identifier,
-            action_identifier=ActionIdentifier(site_id=subject_visit.site_id).identifier,
-            report_datetime=subject_visit.report_datetime,
-            action_type=action_type,
-            reference_model="meta_subject.subjectvisitmissed",
-            linked_to_reference=True,
-            priority=HIGH_PRIORITY,
-            status=CLOSED,
-            auto_created=True,
-            site_id=subject_visit.site_id,
-        )
-        obj.action_identifier = action_item.action_identifier
-        obj.save_base(update_fields=["action_identifier"])
+    try:
+        action_type = actiontype_model_cls.objects.get(name=MISSED_VISIT_ACTION)
+    except ObjectDoesNotExist:
+        pass
+    else:
+        total = subjectvisitmissed_model_cls.objects.filter(
+            action_identifier__isnull=True
+        ).count()
+        for obj in tqdm(
+            subjectvisitmissed_model_cls.objects.filter(action_identifier__isnull=True),
+            total=total,
+        ):
+            subject_visit = subjectvisit_model_cls.objects.get(id=obj.subject_visit_id)
+            action_item = actionitem_model_cls.objects.create(
+                subject_identifier=subject_visit.subject_identifier,
+                action_identifier=ActionIdentifier(site_id=subject_visit.site_id).identifier,
+                report_datetime=subject_visit.report_datetime,
+                action_type=action_type,
+                reference_model="meta_subject.subjectvisitmissed",
+                linked_to_reference=True,
+                priority=HIGH_PRIORITY,
+                status=CLOSED,
+                auto_created=True,
+                site_id=subject_visit.site_id,
+            )
+            obj.action_identifier = action_item.action_identifier
+            obj.save_base(update_fields=["action_identifier"])
 
 
 class Migration(migrations.Migration):

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

@@ -1,286 +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": "b0ebcb02-9d70-43b2-8614-b97ce6fc5aac",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "kb_subjects = [\n",
-    "    \"105-10-0156-6\",\n",
-    "    \"105-10-0020-4\",\n",
-    "    \"105-10-0061-8\",\n",
-    "    \"105-10-0009-7\",\n",
-    "    \"105-10-0074-1\",\n",
-    "    \"105-10-0136-8\",\n",
-    "    \"105-10-0162-4\",\n",
-    "    \"105-10-0054-3\",\n",
-    "    \"105-10-0080-8\",\n",
-    "    \"105-10-0097-2\",\n",
-    "    \"105-20-0159-9\",\n",
-    "    \"105-20-0236-5\",\n",
-    "    \"105-20-0009-6\",\n",
-    "    \"105-20-0197-9\",\n",
-    "    \"105-20-0354-6\",\n",
-    "    \"105-20-0067-4\",\n",
-    "    \"105-20-0015-3\",\n",
-    "    \"105-30-0044-2\",\n",
-    "    \"105-30-0037-6\",\n",
-    "    \"105-30-0147-3\",\n",
-    "    \"105-30-0052-5\",\n",
-    "    \"105-40-0034-2\",\n",
-    "    \"105-40-0246-2\",\n",
-    "    \"105-40-0160-5\",\n",
-    "    \"105-40-0153-0\",\n",
-    "    \"105-40-0054-0\",\n",
-    "    \"105-40-0390-8\",\n",
-    "    \"105-40-0389-0\",\n",
-    "    \"105-40-0379-1\",\n",
-    "    \"105-40-0036-7\",\n",
-    "    \"105-40-0024-3\",\n",
-    "    \"105-40-0233-0\",\n",
-    "    \"105-40-0202-5\",\n",
-    "    \"105-40-0028-4\",\n",
-    "    \"105-40-0010-2\",\n",
-    "    \"105-40-0029-2\",\n",
-    "    \"105-40-0215-7\",\n",
-    "    \"105-40-0274-4\",\n",
-    "    \"105-40-0124-1\",\n",
-    "    \"105-40-0186-0\",\n",
-    "    \"105-40-0219-9\",\n",
-    "    \"105-40-0336-1\",\n",
-    "    \"105-40-0304-9\",\n",
-    "    \"105-40-0214-0\",\n",
-    "    \"105-40-0111-8\",\n",
-    "    \"105-40-0361-9\",\n",
-    "    \"105-40-0121-7\",\n",
-    "    \"105-40-0158-9\",\n",
-    "    \"105-40-0048-2\",\n",
-    "    \"105-40-0273-6\",\n",
-    "    \"105-40-0333-8\",\n",
-    "    \"105-40-0298-3\",\n",
-    "    \"105-40-0021-9\",\n",
-    "    \"105-40-0494-8\",\n",
-    "    \"105-40-0171-2\",\n",
-    "    \"105-40-0303-1\",\n",
-    "    \"105-40-0109-2\",\n",
-    "    \"105-60-0173-6\",\n",
-    "    \"105-60-0104-1\",\n",
-    "    \"105-60-0144-7\",\n",
-    "    \"105-60-0163-7\",\n",
-    "    \"105-60-0121-5\",\n",
-    "    \"105-60-0198-3\",\n",
-    "    \"105-60-0145-4\",\n",
-    "    \"105-60-0155-3\",\n",
-    "    \"105-60-0146-2\",\n",
-    "    \"105-60-0076-1\",\n",
-    "    \"105-60-0172-8\",\n",
-    "    \"105-60-0024-1\",\n",
-    "    \"105-60-0201-5\",\n",
-    "    \"105-60-0029-0\",\n",
-    "    \"105-60-0166-0\",\n",
-    "    \"105-60-0212-2\",\n",
-    "    \"105-60-0106-6\",\n",
-    "]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5bee69bb-30db-4b51-9e81-b391ccb63c42",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "kb_extras = [s for s in cls.endpoint_only_df[\"subject_identifier\"] if s not in kb_subjects]\n",
-    "ew_extras = [s for s in kb_subjects if s not in list(cls.endpoint_only_df[\"subject_identifier\"])]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b3856dc1-cd6e-4886-a89b-e73c064b5f56",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "kb_extras"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "ecb272b1-341b-4488-90dd-25ce98087dcc",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "ew_extras"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "df519e75-d536-435e-8c1e-d4087b99d174",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "526b5f1a-cc77-4182-b9b4-c17c297344f6",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b914aef9-5a27-4474-8359-2d8e0509720b",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "66064ddd-51b6-4474-9664-42ecd471e9ce",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "a8a9da26-84f0-4cc3-a33b-83bf1c292380",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "f97dcfa7-4575-43c1-8614-9f51eb4adff5",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b394252c-443c-49a9-9f32-77a686d00067",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "82634927-c2bf-4745-9fdf-841a1fec008b",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "dc597ae7-d66e-4e1f-9f69-b35dd2d28ec4",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "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",
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