meta-edc 0.3.7__py3-none-any.whl → 0.3.50__py3-none-any.whl

{meta_edc-0.3.7.dist-info → meta_edc-0.3.50.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{meta_edc-0.3.7.dist-info → meta_edc-0.3.50.dist-info}/top_level.txt

@@ -1,4 +1,5 @@
 meta_ae
+meta_analytics
 meta_auth
 meta_consent
 meta_dashboard

meta_pharmacy/admin/__init__.py

@@ -0,0 +1,2 @@
+from .rx_admin import RxAdmin
+from .substitutions_admin import SubstitutionsAdmin

meta_pharmacy/admin/rx_admin.py

@@ -0,0 +1,75 @@
+from django.contrib import admin
+from django_audit_fields.admin import audit_fieldset_tuple
+from edc_model_admin.dashboard import ModelAdminSubjectDashboardMixin
+from edc_pharmacy.admin.list_filters import MedicationsListFilter
+
+from ..admin_site import meta_pharmacy_admin
+from ..forms import RxForm
+from ..models import Rx
+
+
+@admin.register(Rx, site=meta_pharmacy_admin)
+class RxAdmin(ModelAdminSubjectDashboardMixin, admin.ModelAdmin):
+    """Admin class for proxy model of edc_pharmacy.Rx"""
+
+    show_object_tools = True
+
+    form = RxForm
+
+    fieldsets = (
+        (
+            None,
+            {
+                "fields": (
+                    "subject_identifier",
+                    "report_datetime",
+                    "rx_name",
+                    "rx_date",
+                    "medications",
+                    "clinician_initials",
+                    "notes",
+                )
+            },
+        ),
+        (
+            "Randomization",
+            {
+                "fields": ("rando_sid", "randomizer_name", "weight_in_kgs"),
+            },
+        ),
+        audit_fieldset_tuple,
+    )
+
+    filter_horizontal = ("medications",)
+
+    list_display = (
+        "subject_identifier",
+        "dashboard",
+        "rx_medications",
+        "rando_sid",
+        "rx_date",
+        "weight_in_kgs",
+        "rx_name",
+    )
+
+    list_filter = ("report_datetime", MedicationsListFilter, "site")
+
+    search_fields = (
+        "id",
+        "subject_identifier",
+        "rando_sid",
+        "registered_subject__initials",
+        "medications__name",
+        "site__id",
+        "rx_name",
+    )
+
+    readonly_fields = (
+        "rando_sid",
+        "weight_in_kgs",
+        "rx_name",
+    )
+
+    @admin.display
+    def rx_medications(self, obj):
+        return ", ".join([obj.display_name for obj in obj.medications.all()])

meta_pharmacy/admin/substitutions_admin.py

@@ -0,0 +1,67 @@
+from django.contrib import admin
+from django_audit_fields.admin import audit_fieldset_tuple
+from edc_model_admin.dashboard import ModelAdminSubjectDashboardMixin
+from edc_model_admin.history import SimpleHistoryAdmin
+from edc_model_admin.list_filters import ReportDateListFilter
+from edc_sites.admin import SiteModelAdminMixin
+
+from ..admin_site import meta_pharmacy_admin
+from ..forms import SubstitutionsForm
+from ..models import Substitutions
+
+
+@admin.register(Substitutions, site=meta_pharmacy_admin)
+class SubstitutionsAdmin(
+    SiteModelAdminMixin,
+    ModelAdminSubjectDashboardMixin,
+    SimpleHistoryAdmin,
+):
+    """Admin class for meta_pharmacy.Substitutions"""
+
+    form = SubstitutionsForm
+
+    autocomplete_fields = ["rx"]
+
+    add_instructions = "This form is used to record any substitions made for IMP refills"
+
+    fieldsets = (
+        (
+            None,
+            {"fields": ("report_datetime",)},
+        ),
+        ("Original label on bottle", {"fields": ("sid", "visit_no")}),
+        (
+            "Substitution / Changed label",
+            {
+                "description": "The label on this bottle has been changed to the following",
+                "fields": ("dispensed_sid", "updated_visit_no"),
+            },
+        ),
+        (
+            "Subject",
+            {
+                "fields": ("rx",),
+            },
+        ),
+        audit_fieldset_tuple,
+    )
+
+    list_display = (
+        "sid",
+        "dispensed_sid",
+        "arm_match",
+        "subject_identifier",
+        "report_date",
+    )
+
+    radio_fields = {"arm_match": admin.VERTICAL}
+
+    list_filter = ("arm_match", ReportDateListFilter)
+
+    search_fields = ["subject_identifier", "sid", "dispensed_sid"]
+
+    @admin.display(description="Report date", ordering="report_datetime")
+    def report_date(self, obj) -> str | None:
+        if obj.report_datetime:
+            return obj.report_datetime.date()
+        return None

meta_pharmacy/admin_site.py

@@ -0,0 +1,9 @@
+from edc_model_admin.admin_site import EdcAdminSite
+
+from .apps import AppConfig
+
+meta_pharmacy_admin = EdcAdminSite(
+    name="meta_pharmacy_admin",
+    app_label=AppConfig.name,
+    keep_delete_action=True,
+)

meta_pharmacy/apps.py

@@ -1,6 +1,7 @@
 from django.apps import AppConfig as DjangoAppConfig
 from django.db.models.signals import post_migrate
 from django_extensions.management.color import color_style
+from edc_list_data import site_list_data
 
 from .prepare_meta_pharmacy import prepare_meta_pharmacy
 
@@ -9,12 +10,16 @@ style = color_style()
 
 def post_migrate_populate_pharmacy_models(sender=None, **kwargs):  # noqa
     """Create or update pharmacy static models."""
+    site_list_data.load_data()
     prepare_meta_pharmacy()
 
 
 class AppConfig(DjangoAppConfig):
     name = "meta_pharmacy"
     verbose_name = "META Pharmacy"
+    include_in_administration_section = True
+    has_exportable_data = True
+    default_auto_field = "django.db.models.BigAutoField"
 
     def ready(self):
         post_migrate.connect(post_migrate_populate_pharmacy_models, sender=self)

meta_pharmacy/constants.py

@@ -1 +1,11 @@
+from edc_constants.constants import OK
+
 METFORMIN = "metformin"
+REVIEW = "REVIEW"
+MISSING_SUBJECT_IDENTIFIER = "MISSING_SUBJECT_IDENTIFIER"
+
+SUBSTITUTION_STATUS = (
+    (OK, "ok"),
+    (MISSING_SUBJECT_IDENTIFIER, "Missing Subject ID"),
+    (REVIEW, "review"),
+)

meta_pharmacy/forms/__init__.py

@@ -0,0 +1,2 @@
+from .rx_form import RxForm
+from .substitutions_form import SubstitutionsForm

meta_pharmacy/forms/rx_form.py

@@ -0,0 +1,16 @@
+from django import forms
+
+from ..models import Rx
+
+
+class RxForm(forms.ModelForm):
+
+    subject_identifier = forms.CharField(
+        label="Subject Identifier",
+        required=False,
+        widget=forms.TextInput(attrs={"readonly": "readonly"}),
+    )
+
+    class Meta:
+        model = Rx
+        fields = "__all__"

meta_pharmacy/forms/substitutions_form.py

@@ -0,0 +1,54 @@
+from django import forms
+from django.core.exceptions import ObjectDoesNotExist
+from edc_form_validators.form_validator import FormValidator
+from edc_form_validators.form_validator_mixins import FormValidatorMixin
+from edc_model_form.mixins import BaseModelFormMixin
+from edc_offstudy.modelform_mixins import OffstudyNonCrfModelFormMixin
+from edc_prn.modelform_mixins import PrnFormValidatorMixin
+from edc_sites.forms import SiteModelFormMixin
+
+from meta_rando.models import RandomizationList
+
+from ..models import Rx, Substitutions
+
+
+class SubstitutionsFormValidator(PrnFormValidatorMixin, FormValidator):
+    pass
+
+
+class SubstitutionsForm(
+    SiteModelFormMixin,
+    OffstudyNonCrfModelFormMixin,
+    BaseModelFormMixin,
+    FormValidatorMixin,
+    forms.ModelForm,
+):
+    form_validator_cls = SubstitutionsFormValidator
+
+    def clean(self):
+        if self.cleaned_data.get("sid"):
+            try:
+                obj = Rx.objects.get(rando_sid=self.cleaned_data.get("sid"))
+            except ObjectDoesNotExist:
+                raise forms.ValidationError({"sid": "Unknown SID for this trial"})
+            else:
+                if obj.site.id != self.site.id:
+                    raise forms.ValidationError(
+                        {
+                            "sid": (
+                                "Unknown SID for this trial site. "
+                                f"Expected SITE {obj.site.id}."
+                            )
+                        }
+                    )
+        if self.cleaned_data.get("dispensed_sid"):
+            try:
+                RandomizationList.objects.get(
+                    sid=self.cleaned_data.get("dispensed_sid"),
+                )
+            except ObjectDoesNotExist:
+                raise forms.ValidationError({"dispensed_sid": "Invalid SID for this trial"})
+
+    class Meta:
+        model = Substitutions
+        fields = "__all__"

meta_pharmacy/label_configs.py

@@ -0,0 +1,30 @@
+from edc_pharmacy.labels import (
+    draw_bulk_stock_label_code128,
+    draw_vertical_barcode_only_code128,
+)
+from edc_pylabels.site_label_configs import site_label_configs
+
+from .labels import draw_label_for_subject_with_code128, draw_label_with_test_data
+
+# create a label class to pass instead of a model
+
+site_label_configs.register(
+    "stock_vertical_barcode",
+    draw_vertical_barcode_only_code128,
+    "edc_pharmacy.stock",
+    test_data_func=draw_label_with_test_data,
+)
+
+site_label_configs.register(
+    "stock_bulk_barcode",
+    draw_bulk_stock_label_code128,
+    "edc_pharmacy.stock",
+    test_data_func=draw_label_with_test_data,
+)
+
+site_label_configs.register(
+    "patient_barcode",
+    draw_label_for_subject_with_code128,
+    "edc_pharmacy.stock",
+    test_data_func=draw_label_with_test_data,
+)

meta_pharmacy/labels/__init__.py

@@ -0,0 +1,5 @@
+from .draw_label_for_subject_with_code128 import draw_label_for_subject_with_code128
+from .draw_label_with_test_data import draw_label_with_test_data
+
+# from .label_data import LabelData
+# from .print_sheets import print_sheets

meta_pharmacy/labels/draw_label_for_subject_with_barcode.py

@@ -0,0 +1,62 @@
+from edc_pharmacy.labels import draw_label_watermark
+from edc_pharmacy.models import Stock
+from edc_pharmacy.utils import format_qty
+from edc_sites.site import sites as site_sites
+from reportlab.graphics.shapes import Drawing, Group, String
+from reportlab.pdfbase.pdfmetrics import stringWidth
+
+
+def draw_label_for_subject_with_barcode(
+    barcode_cls,
+    barcode_opts: dict,
+    label: Drawing,
+    width: int | float,
+    height: int | float,
+    obj: Stock,
+) -> Drawing:
+    """Callable to draw a single study medication label given a model
+    instance `obj`
+    """
+    try:
+        single_site = site_sites.get(
+            obj.allocation.stock_request_item.stock_request.location.site.id
+        )
+    except AttributeError:
+        label.add(String(15, height - 20, "Error: Unable to generate label", fontSize=10))
+        label.add(String(15, height - 40, str(obj.code), fontSize=10))
+        label.add(String(15, height - 60, str(obj.location), fontSize=10))
+    else:
+
+        draw_label_watermark(label, width, height, fontSize=18)
+
+        br = barcode_cls(**barcode_opts)
+        br.value = obj.code
+        br.x = width - 110
+        br.y = 40
+        label.add(br)
+
+        label.add(String(15, height - 35, single_site.title, fontSize=10))
+
+        label.add(String(15, height - 20, "META III Study", fontSize=12))
+        label.add(String(15, height - 55, "Dawa kwa ajili ya utafiti", fontSize=10))
+        label.add(String(15, height - 67, "wa META III.", fontSize=10))
+        label.add(String(15, height - 79, "Meza vidonge vinne usiku tu.", fontSize=10))
+
+        text_group = Group()
+        subject_identifier = (
+            obj.allocation.registered_subject.subject_identifier or "999-99-99999-9"
+        )
+        text_width = stringWidth(subject_identifier, "Helvetica", 12)
+        text_string = String(
+            width - text_width - 10, height - 20, subject_identifier, fontSize=12
+        )
+        text_group.add(text_string)
+
+        qty_text = f"{format_qty(obj.container.qty, obj.container)} tabs"
+        text_width = stringWidth(qty_text, "Helvetica", 10)
+        text_string = String(width - text_width - 10, height - 95, qty_text, fontSize=10)
+        text_group.add(text_string)
+
+        label.add(text_group)
+
+    return label

meta_pharmacy/labels/draw_label_for_subject_with_code128.py

@@ -0,0 +1,14 @@
+from reportlab.graphics.barcode.widgets import BarcodeCode128
+from reportlab.graphics.shapes import Drawing
+
+from .draw_label_for_subject_with_barcode import draw_label_for_subject_with_barcode
+
+
+def draw_label_for_subject_with_code128(*args) -> Drawing:
+    barcode_opts = dict(
+        humanReadable=True,
+        barHeight=30,
+        barWidth=0.7,
+        gap=1.7,
+    )
+    return draw_label_for_subject_with_barcode(BarcodeCode128, barcode_opts, *args)

meta_pharmacy/labels/draw_label_with_test_data.py

@@ -0,0 +1,26 @@
+from django.apps import apps as django_apps
+from edc_utils import get_utcnow
+
+
+def draw_label_with_test_data() -> dict:
+    receive_model_cls = django_apps.get_model("edc_pharmacy.receive")
+    receive_item_model_cls = django_apps.get_model("edc_pharmacy.receiveitem")
+    location_model_cls = django_apps.get_model("edc_pharmacy.location")
+    lot_model_cls = django_apps.get_model("edc_pharmacy.lot")
+    container_type_model_cls = django_apps.get_model("edc_pharmacy.containertype")
+    container_model_cls = django_apps.get_model("edc_pharmacy.container")
+    container_type = container_type_model_cls(name="bottle")
+    container = container_model_cls(
+        name="bottle of 128", container_type=container_type, qty=128
+    )
+    return dict(
+        subject_identifier="999-99999-9",
+        code="A9B8C7",
+        location=location_model_cls.objects.filter(site__isnull=False).first(),
+        container=container,
+        lot=lot_model_cls(lot_no="999999999", expiration_date=get_utcnow().date()),
+        receive_item=receive_item_model_cls(
+            receive=receive_model_cls(receive_identifier="99999999"),
+            receive_item_identifier="99999999",
+        ),
+    )

meta_pharmacy/labels/label_data.py

@@ -0,0 +1,14 @@
+import random
+import string
+
+
+class LabelData:
+
+    def __init__(self):
+        self.subject_identifier = "999-99-9999-9"  # nosec B311
+        self.reference = "".join(
+            random.choices(string.ascii_letters.upper() + "23456789", k=6)  # nosec B311
+        )
+        self.sid = "12345"
+        self.site_name = "AMANA"
+        self.pills_per_bottle = 128

meta_pharmacy/labels/print_sheets.py

@@ -0,0 +1,97 @@
+import os.path
+from pathlib import Path
+
+from edc_sites.site import sites
+from pylabels import Sheet, Specification
+from reportlab.graphics.barcode.widgets import BarcodeStandard39
+from reportlab.graphics.charts.textlabels import Label as RlLabel
+from reportlab.graphics.shapes import String
+
+from ..models import LabelData
+
+
+class Label:
+    """
+    this should be based on a generated dataset using the stock transfer
+    request data.
+
+    maybe include a printout for the site to review the IN-STOCK vs ORDER
+    status for each subject in a stock transfer request
+
+    subject1 IN-STOCK
+    subject2 ORDER
+    subject3 ORDER
+    """
+
+    def __init__(self, obj: LabelData):
+        self.label = obj
+        self.gender = obj.gender
+        self.site_id = obj.site_id
+        self.subject_identifier = obj.subject_identifier
+        self.reference = obj.reference
+        self.sid = obj.sid
+        self.site_name = sites.get(self.site_id).title
+
+
+def draw_label(label, width, height, data: LabelData):
+    data = Label(data)
+    br = BarcodeStandard39(
+        humanReadable=True, checksum=False, barHeight=30, barWidth=0.7, gap=1.7
+    )
+    br.value = data.reference
+    br.x = width - 140
+    br.y = 25
+    label.add(br)
+    label.add(String(15, height - 20, f"META III Study - {data.site_name}", fontSize=10))
+    label.add(
+        String(
+            width - 120, height - 40, f"{data.subject_identifier}{data.gender}", fontSize=12
+        )
+    )
+    label.add(String(15, height - 40, "Dawa kwa ajili ya utafiti", fontSize=10))
+    label.add(String(15, height - 50, "wa META III.", fontSize=10))
+    label.add(String(15, height - 70, "Meza vidonge vinne usiku tu.", fontSize=10))
+    label.add(String(15, 20, "128 tabs", fontSize=10))
+    lab = RlLabel(x=width - 20, y=40, fontSize=10, angle=90)
+    # lab.boxAnchor = "ne"
+    # lab.dx = 0
+    # lab.dy = -20
+    lab.setText(data.sid)
+    label.add(lab)
+    return label
+
+
+def print_sheets(labels: list[Label], path: Path | None = None, verbose: bool | None = None):
+    specs = Specification(
+        210,
+        297,
+        2,
+        6,
+        96,
+        42,
+        corner_radius=0,
+        top_margin=21,
+        left_margin=8,
+        right_margin=8,
+        bottom_margin=22,
+        left_padding=2,
+        right_padding=2,
+        top_padding=2,
+        bottom_padding=2,
+    )
+
+    if not path:
+        path = Path(os.path.dirname(__file__))
+    path = str(path / "meta_labels.pdf")
+    sheet = Sheet(specs, draw_label, border=True)
+
+    sheet.add_labels(labels)
+
+    # Save the file and we are done.
+    sheet.save(path)
+    msg = "{0:d} label(s) output on {1:d} page(s) to {2}.".format(
+        sheet.label_count, sheet.page_count, path
+    )
+    if verbose:
+        print(msg)
+    return msg

meta_pharmacy/list_data.py

@@ -0,0 +1,8 @@
+from edc_sites.site import sites as site_sites
+
+list_data = {
+    "edc_pharmacy.location": [
+        ("central", "Central"),
+        *[(ss.name, ss.description) for ss in site_sites.all(aslist=True)],
+    ],
+}

meta_pharmacy/management/commands/update_initial_pharmacy_data.py

@@ -0,0 +1,10 @@
+from django.core.management import BaseCommand
+
+from meta_pharmacy.utils import update_initial_pharmacy_data
+
+
+class Command(BaseCommand):
+
+    def handle(self, *args, **options):
+        update_initial_pharmacy_data()
+        print("Done")