meta-edc 1.0.6__py3-none-any.whl → 1.1.0__py3-none-any.whl

meta_subject/forms/blood_results/blood_results_rft_form.py

@@ -3,21 +3,78 @@ from django.utils.safestring import mark_safe
 from edc_action_item.forms import ActionItemCrfFormMixin
 from edc_crf.crf_form_validator import CrfFormValidator
 from edc_crf.modelform_mixins import CrfModelFormMixin
+from edc_egfr.form_validator_mixins import EgfrCkdEpiFormValidatorMixin
 from edc_lab_panel.panels import rft_panel
 from edc_lab_results.form_validator_mixins import BloodResultsFormValidatorMixin
-from edc_reportable import BmiFormValidatorMixin
+from edc_registration.models import RegisteredSubject
+from edc_utils import age
+from edc_visit_schedule.utils import is_baseline
+from edc_vitals.form_validators import BmiFormValidatorMixin
 
-from ...models import BloodResultsRft
+from meta_visit_schedule.constants import DAY1
+
+from ...models import BloodResultsRft, FollowupVitals, PhysicalExam, SubjectVisit
 
 
 class BloodResultsRftFormValidator(
-    BloodResultsFormValidatorMixin, BmiFormValidatorMixin, CrfFormValidator
+    BloodResultsFormValidatorMixin,
+    EgfrCkdEpiFormValidatorMixin,
+    BmiFormValidatorMixin,
+    CrfFormValidator,
 ):
     panel = rft_panel
 
     def clean(self):
         super().clean()
         self.validate_bmi()
+        if self.cleaned_data.get("creatinine_value") and self.cleaned_data.get(
+            "creatinine_units"
+        ):
+
+            if is_baseline(self.related_visit):
+                baseline_egfr_value = None
+            else:
+                baseline_visit = SubjectVisit.objects.get(
+                    subject_identifier=self.related_visit.subject_identifier,
+                    visit_code=DAY1,
+                    visit_code_sequence=0,
+                )
+                baseline_egfr_value = BloodResultsRft.objects.get(
+                    subject_visit=baseline_visit
+                ).egfr_value
+            rs = RegisteredSubject.objects.get(
+                subject_identifier=self.related_visit.subject_identifier
+            )
+            age_in_years = age(rs.dob, self.report_datetime).years
+
+            self.validate_egfr(
+                gender=rs.gender,
+                age_in_years=age_in_years,
+                ethnicity=rs.ethnicity,
+                weight_in_kgs=self.get_weight_in_kgs(),
+                baseline_egfr_value=baseline_egfr_value,
+            )
+
+    def get_weight_in_kgs(self) -> float | None:
+        if is_baseline(self.related_visit):
+            obj = (
+                PhysicalExam.objects.filter(
+                    subject_visit=self.related_visit, weight__isnull=False
+                )
+                .order_by("report_datetime")
+                .last()
+            )
+        else:
+            obj = (
+                FollowupVitals.objects.filter(
+                    subject_visit=self.related_visit, weight__isnull=False
+                )
+                .order_by("report_datetime")
+                .last()
+            )
+        if obj:
+            return obj.weight
+        return None
 
 
 class BloodResultsRftForm(ActionItemCrfFormMixin, CrfModelFormMixin, forms.ModelForm):

meta_subject/forms/study_medication_form.py

@@ -38,16 +38,18 @@ class StudyMedicationFormValidator(BaseStudyMedicationFormValidator):
 
     def validate_stock_codes_are_dispensed(self):
         if self.cleaned_data.get("stock_codes"):
-            pattern = re.compile("^([A-Z0-9]{6})(,[A-Z0-9]{6})*$")
+            # pattern = re.compile("^([A-Z0-9]{6})(,[A-Z0-9]{6})*$")
+            pattern = re.compile("^([A-Z0-9]{6})(\r\n[A-Z0-9]{6})*$")
             if not pattern.match(self.cleaned_data.get("stock_codes")):
                 raise forms.ValidationError(
                     {
                         "stock_codes": (
-                            "Invalid format. Enter one or more valid codes separated by comma"
+                            "Invalid format. Enter one or more valid codes. "
+                            "One code per line only. No commas, spaces, etc"
                         )
                     }
                 )
-            for stock_code in self.cleaned_data.get("stock_codes").split(","):
+            for stock_code in self.cleaned_data.get("stock_codes").split("\r\n"):
                 try:
                     Stock.objects.get(
                         code=stock_code,

meta_subject/migrations/0221_auto_20250402_1913.py

@@ -0,0 +1,42 @@
+# Generated by Django 6.0 on 2025-04-02 16:13
+from django.apps import apps as django_apps
+from django.db import migrations
+from django.db.migrations import RunPython
+from edc_appointment.constants import MISSED_APPT
+from edc_pdutils.dataframes import get_crf
+from edc_utils import get_utcnow
+from tqdm import tqdm
+
+
+def update(apps, schema_editor):
+    """Correct missed appointments incorrectly set to
+    appt_timing=ONTIME_APPT.
+    """
+    appointment_model_cls = django_apps.get_model("edc_appointment.appointment")
+    df_missedvisit = get_crf(
+        "meta_subject.subjectvisitmissed",
+        subject_visit_model="meta_subject.subjectvisit",
+    )
+    df_subjects = df_missedvisit[df_missedvisit.appt_timing != MISSED_APPT][
+        ["subject_identifier", "visit_code_str", "visit_code_sequence"]
+    ].copy()
+    for tpl in tqdm(df_subjects.itertuples(), total=len(df_subjects)):
+        obj = appointment_model_cls.objects.get(
+            subject_identifier=tpl.subject_identifier,
+            visit_code=tpl.visit_code_str,
+            visit_code_sequence=tpl.visit_code_sequence,
+        )
+        obj.appt_timing = MISSED_APPT
+        obj.modified = get_utcnow()
+        obj.user_modified = "erikvw"
+
+        obj.save(update_fields=["appt_timing", "user_modified", "modified"])
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_subject", "0220_historicalbloodresultsgludummy_bloodresultsgludummy"),
+    ]
+
+    operations = [RunPython(update)]

meta_subject/migrations/0222_alter_historicalstudymedication_stock_codes_and_more.py

@@ -0,0 +1,46 @@
+# Generated by Django 6.0 on 2025-04-15 22:06
+
+import django.core.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_subject", "0221_auto_20250402_1913"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="historicalstudymedication",
+            name="stock_codes",
+            field=models.TextField(
+                blank=True,
+                help_text="Enter the medication bottle barcode or barcodes. Type one code per line",
+                max_length=30,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        message="Enter one or more valid codes, one code per line",
+                        regex="^([A-Z0-9]{6})(\r\n[A-Z0-9]{6})*$",
+                    )
+                ],
+            ),
+        ),
+        migrations.AlterField(
+            model_name="studymedication",
+            name="stock_codes",
+            field=models.TextField(
+                blank=True,
+                help_text="Enter the medication bottle barcode or barcodes. Type one code per line",
+                max_length=30,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        message="Enter one or more valid codes, one code per line",
+                        regex="^([A-Z0-9]{6})(\r\n[A-Z0-9]{6})*$",
+                    )
+                ],
+            ),
+        ),
+    ]

meta_subject/migrations/0223_bloodresultsfbc_errors_bloodresultsgludummy_errors_and_more.py

@@ -0,0 +1,83 @@
+# Generated by Django 5.2.3 on 2025-06-25 20:55
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_subject", "0222_alter_historicalstudymedication_stock_codes_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="bloodresultsfbc",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsgludummy",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultshba1c",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsins",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultslft",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultslipids",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsrft",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsfbc",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsgludummy",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultshba1c",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsins",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultslft",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultslipids",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsrft",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+    ]

meta_subject/migrations/0224_bloodresultsfbc_abnormal_summary_and_more.py

@@ -0,0 +1,153 @@
+# Generated by Django 5.2.3 on 2025-06-25 23:57
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_subject", "0223_bloodresultsfbc_errors_bloodresultsgludummy_errors_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="bloodresultsfbc",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsfbc",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsgludummy",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsgludummy",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultshba1c",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultshba1c",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsins",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsins",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultslft",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultslft",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultslipids",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultslipids",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsrft",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsrft",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsfbc",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsfbc",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsgludummy",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsgludummy",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultshba1c",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultshba1c",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsins",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsins",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultslft",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultslft",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultslipids",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultslipids",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsrft",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsrft",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+    ]

meta_subject/tests/tests/test_egfr.py

@@ -205,8 +205,8 @@ class TestEgfr(MetaTestCaseMixin, TestCase):
         data.update(creatinine_value=152.0, creatinine_units=MICROMOLES_PER_LITER)
         obj_1000 = BloodResultsRft.objects.create(**data)
         obj_1000.refresh_from_db()
-        self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value, 3), Decimal("49.030"))
-        self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value, 2), Decimal("49.03"))
+        self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value, 3), Decimal("49.019"))
+        self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value, 2), Decimal("49.02"))
         self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value, 1), Decimal("49.0"))
         self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value), Decimal("49"))
 
@@ -228,7 +228,7 @@ class TestEgfr(MetaTestCaseMixin, TestCase):
         data.update(creatinine_value=150.8, creatinine_units=MICROMOLES_PER_LITER)
         obj_2000 = BloodResultsRft.objects.create(**data)
         obj_2000.refresh_from_db()
-        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value, 3), Decimal("49.503"))
-        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value, 2), Decimal("49.50"))
+        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value, 3), Decimal("49.492"))
+        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value, 2), Decimal("49.49"))
         self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value, 1), Decimal("49.5"))
-        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value), Decimal("50"))
+        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value), Decimal("49"))

meta_analytics/dataframes/enrolled/__init__.py

@@ -1 +0,0 @@
-from .get_glucose_df import get_glucose_df

meta_analytics/dataframes/enrolled/get_glucose_df.py

@@ -1,122 +0,0 @@
-import numpy as np
-import pandas as pd
-from django_pandas.io import read_frame
-from edc_pdutils.dataframes import get_eos, get_subject_consent, get_subject_visit
-
-from meta_subject.models import Glucose, GlucoseFbg
-
-
-def get_glucose_df() -> pd.DataFrame:
-    qs_glucose_fbg = GlucoseFbg.objects.all()
-    df_glucose_fbg = read_frame(qs_glucose_fbg)
-    df_glucose_fbg.rename(
-        columns={"fbg_fasting": "fasting", "subject_visit": "subject_visit_id"},
-        inplace=True,
-    )
-
-    df_glucose_fbg.loc[(df_glucose_fbg["fasting"] == "fasting"), "fasting"] = "Yes"
-    df_glucose_fbg.loc[(df_glucose_fbg["fasting"] == "non_fasting"), "fasting"] = "No"
-    df_glucose_fbg["fasting_hrs"] = np.nan
-    df_glucose_fbg["fasting_hrs"] = df_glucose_fbg["fasting_duration_delta"].apply(
-        lambda x: x.total_seconds() / 3600
-    )
-    df_glucose_fbg["fasting_hrs"] = df_glucose_fbg["fasting_hrs"].apply(
-        lambda x: 8.05 if not x else x
-    )
-    # df_glucose_fbg = df_glucose_fbg.loc[df_glucose_fbg["fasting_hrs"] >= 8.0]
-    # df_glucose_fbg.reset_index(drop=True, inplace=True)
-    df_glucose_fbg.loc[
-        :,
-        ["ogtt_value", "ogtt_units", "ogtt_datetime"],
-    ] = [np.nan, None, pd.NaT]
-    df_glucose_fbg["source"] = "meta_subject.glucosefbg"
-
-    qs_glucose = Glucose.objects.all()
-    df_glucose = read_frame(qs_glucose)
-    df_glucose.rename(columns={"subject_visit": "subject_visit_id"}, inplace=True)
-    df_glucose.loc[(df_glucose["fasting"] == "fasting"), "fasting"] = "Yes"
-    df_glucose.loc[(df_glucose["fasting"] == "non_fasting"), "fasting"] = "No"
-    df_glucose["fasting_hrs"] = np.nan
-    df_glucose["fasting_hrs"] = df_glucose[df_glucose["fasting"] == "Yes"][
-        "fasting_duration_delta"
-    ].apply(lambda x: x.total_seconds() / 3600)
-    df_glucose["fasting_hrs"] = df_glucose["fasting_hrs"].apply(lambda x: 8.05 if not x else x)
-    # df_glucose = df_glucose.loc[df_glucose["fasting_hrs"] >= 8.0]
-    # df_glucose.reset_index(drop=True, inplace=True)
-    df_glucose["source"] = "meta_subject.glucose"
-
-    keep_cols = [
-        "subject_visit_id",
-        "fasting",
-        "fasting_hrs",
-        "fbg_value",
-        "fbg_units",
-        "fbg_datetime",
-        "ogtt_value",
-        "ogtt_units",
-        "ogtt_datetime",
-        "source",
-        "revision",
-        "report_datetime",
-    ]
-    df_glucose = df_glucose[keep_cols]
-    df_glucose_fbg = df_glucose_fbg[keep_cols]
-    # df = pd.concat([df_glucose_fbg, df_glucose])
-    df = pd.merge(
-        df_glucose,
-        df_glucose_fbg,
-        on="subject_visit_id",
-        how="outer",
-        indicator=True,
-        suffixes=("", "_2"),
-    )
-
-    for suffix in ["", "_2"]:
-        cols = [f"fasting_hrs{suffix}", f"fbg_value{suffix}", f"ogtt_value{suffix}"]
-        df[cols] = df[cols].apply(pd.to_numeric)
-        cols = [f"fbg_datetime{suffix}", f"ogtt_datetime{suffix}"]
-        df[cols] = df[cols].apply(pd.to_datetime)
-        df.loc[
-            (df[f"fbg_units{suffix}"] != "mmol/L (millimoles/L)")
-            & (df[f"fbg_value{suffix}"] >= 0),
-            f"fbg_units{suffix}",
-        ] = "mmol/L (millimoles/L)"
-        df.loc[
-            (df[f"ogtt_units{suffix}"] != "mmol/L (millimoles/L)")
-            & (df[f"ogtt_value{suffix}"] >= 0),
-            f"ogtt_units{suffix}",
-        ] = "mmol/L (millimoles/L)"
-        # remove values if not fasted
-        # df.loc[(df[f"fasting{suffix}"] != YES), f"fbg_value{suffix}"] = np.nan
-        # df.loc[(df[f"fasting{suffix}"] != YES), f"ogtt_value{suffix}"] = np.nan
-
-    # reconcile all to single column
-    df.loc[(df["fbg_value"].isna()) & (df["fbg_value_2"].notna()), "fbg_value"] = df[
-        "fbg_value_2"
-    ]
-    df.loc[(df["ogtt_value"].isna()) & (df["ogtt_value_2"].notna()), "ogtt_value"] = df[
-        "ogtt_value_2"
-    ]
-    cols = [col for col in list(df.columns) if col.endswith("_2")]
-    df.drop(columns=cols, inplace=True)
-    cols = [col for col in list(df.columns) if col.endswith("_3")]
-    df.drop(columns=cols, inplace=True)
-
-    df_subject_visit = get_subject_visit("meta_subject.subjectvisit")
-    df_consent = get_subject_consent("meta_consent.subjectconsent")
-    df_eos = get_eos("meta_prn.endofstudy")
-
-    df = pd.merge(df_subject_visit, df, on="subject_visit_id", how="left")
-    df = pd.merge(df, df_consent, on="subject_identifier", how="left")
-    df = pd.merge(df, df_eos, on="subject_identifier", how="left")
-
-    df["visit_days"] = df["baseline_datetime"].rsub(df["visit_datetime"]).dt.days
-    df["fgb_days"] = df["baseline_datetime"].rsub(df["fbg_datetime"]).dt.days
-    df["ogtt_days"] = df["baseline_datetime"].rsub(df["ogtt_datetime"]).dt.days
-    df["visit_days"] = pd.to_numeric(df["visit_days"], downcast="integer")
-    df["fgb_days"] = pd.to_numeric(df["fgb_days"], downcast="integer")
-    df["ogtt_days"] = pd.to_numeric(df["ogtt_days"], downcast="integer")
-
-    df = df.sort_values(by=["subject_identifier", "visit_code"])
-    df.reset_index(drop=True, inplace=True)
-    return df