clinicedc 2.0.1__py3-none-any.whl → 2.0.2__py3-none-any.whl

edc_identifier/migrations/0007_auto_20161204_2227.py

@@ -4,10 +4,11 @@ from __future__ import unicode_literals
 
 import django_audit_fields.fields.uuid_auto_field
 import django_revision.revision_field
+from django.db import migrations, models
+
 import edc_model_fields.fields.hostname_modification_field
 import edc_model_fields.fields.userfield
 import edc_utils
-from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
@@ -19,15 +20,11 @@ class Migration(migrations.Migration):
             fields=[
                 (
                     "created",
-                    models.DateTimeField(
-                        default=edc_utils.date.get_utcnow, editable=False
-                    ),
+                    models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
                 ),
                 (
                     "modified",
-                    models.DateTimeField(
-                        default=edc_utils.date.get_utcnow, editable=False
-                    ),
+                    models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
                 ),
                 (
                     "user_created",

edc_identifier/migrations/0009_auto_20161221_2323.py

@@ -3,6 +3,7 @@
 from __future__ import unicode_literals
 
 from django.db import migrations, models
+
 from edc_utils import get_utcnow
 
 

edc_identifier/migrations/0010_auto_20170112_0602.py

@@ -2,10 +2,11 @@
 # Generated by Django 1.10.4 on 2017-01-12 04:02
 from __future__ import unicode_literals
 
+from django.db import migrations, models
+
 import edc_model_fields.fields.hostname_modification_field
 import edc_model_fields.fields.userfield
 import edc_utils
-from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

edc_identifier/migrations/0012_auto_20171116_1606.py

@@ -1,9 +1,10 @@
 # Generated by Django 2.0b1 on 2017-11-16 14:06
 
 import _socket
-import edc_model_fields.fields.userfield
 from django.db import migrations, models
 
+import edc_model_fields.fields.userfield
+
 
 class Migration(migrations.Migration):
     dependencies = [("edc_identifier", "0011_auto_20170511_1323")]

edc_identifier/migrations/0013_auto_20171230_1316.py

@@ -13,15 +13,9 @@ class Migration(migrations.Migration):
     ]
 
     operations = [
-        migrations.RemoveField(
-            model_name="historicalidentifierhistory", name="history_user"
-        ),
-        migrations.RemoveField(
-            model_name="historicalidentifiertracker", name="history_user"
-        ),
-        migrations.RemoveField(
-            model_name="historicalsubjectidentifier", name="history_user"
-        ),
+        migrations.RemoveField(model_name="historicalidentifierhistory", name="history_user"),
+        migrations.RemoveField(model_name="historicalidentifiertracker", name="history_user"),
+        migrations.RemoveField(model_name="historicalsubjectidentifier", name="history_user"),
         migrations.DeleteModel(name="IdentifierHistory"),
         migrations.DeleteModel(name="IdentifierTracker"),
         migrations.DeleteModel(name="Sequence"),

edc_identifier/research_identifier.py

@@ -49,9 +49,7 @@ class ResearchIdentifier:
         self.template = template or self.template
         app_config = django_apps.get_app_config("edc_device")
         self.device_id = device_id or app_config.device_id
-        self.protocol_number = (
-            protocol_number or ResearchProtocolConfig().protocol_number
-        )
+        self.protocol_number = protocol_number or ResearchProtocolConfig().protocol_number
         self.site = site or django_apps.get_model("sites.site").objects.get_current()
         if identifier:
             # load an existing identifier
@@ -120,14 +118,8 @@ class ResearchIdentifier:
         """
         template_opts: dict = {}
         formatter = Formatter()
-        keys = [
-            opt[1]
-            for opt in formatter.parse(self.template)
-            if opt[1] not in ["sequence"]
-        ]
-        template_opts.update(
-            sequence=str(self.sequence_number).rjust(self.padding, "0")
-        )
+        keys = [opt[1] for opt in formatter.parse(self.template) if opt[1] not in ["sequence"]]
+        template_opts.update(sequence=str(self.sequence_number).rjust(self.padding, "0"))
         for key in keys:
             try:
                 value = getattr(self, key)

edc_identifier/short_identifier.py

@@ -63,9 +63,9 @@ class ShortIdentifier:
             )
 
         if self.prefix_pattern:
-            if not self.prefix_pattern.startswith(
-                "^"
-            ) or not self.prefix_pattern.endswith("$"):
+            if not self.prefix_pattern.startswith("^") or not self.prefix_pattern.endswith(
+                "$"
+            ):
                 raise ShortIdentifierPrefixPatternError(
                     f"Invalid prefix pattern. Got {self.prefix_pattern}."
                 )
@@ -93,9 +93,7 @@ class ShortIdentifier:
     def get_identifier(self):
         """Returns a new unique identifier."""
         identifier = None
-        allowed_chars = self.random_string_pattern.match(
-            "ABCDEFGHKMNPRTUVWXYZ2346789"
-        ).group()
+        allowed_chars = self.random_string_pattern.match("ABCDEFGHKMNPRTUVWXYZ2346789").group()
         max_tries = len(allowed_chars) ** (self.random_string_length + 1)
         tries = 0
         while not identifier:
@@ -106,9 +104,7 @@ class ShortIdentifier:
                     for _ in range(self.random_string_length)
                 ]
             )
-            identifier = self.template.format(
-                random_string=random_string, prefix=self.prefix
-            )
+            identifier = self.template.format(random_string=random_string, prefix=self.prefix)
             try:
                 self.identifier_model_cls.objects.get(
                     identifier=identifier, identifier_type=self.name

edc_identifier/utils.py

@@ -6,9 +6,7 @@ from edc_protocol.research_protocol_config import ResearchProtocolConfig
 from .exceptions import SubjectIdentifierError
 
 
-def is_subject_identifier_or_raise(
-    subject_identifier, reference_obj=None, raise_on_none=None
-):
+def is_subject_identifier_or_raise(subject_identifier, reference_obj=None, raise_on_none=None):
     """Returns the given subject identifier.
 
     * If the format of the `subject_identifier` is invalid,

edc_lab/admin/modeladmin_mixins.py

@@ -49,9 +49,7 @@ class RequisitionAdminMixin:
             )
         return format_html(
             "{html}",
-            html=mark_safe(
-                '<span style="color:red;">not drawn</span>'
-            ),  # nosec B703, B308
+            html=mark_safe('<span style="color:red;">not drawn</span>'),  # nosec B703, B308
         )
 
     def formfield_for_foreignkey(self, db_field, request, **kwargs):
@@ -85,11 +83,7 @@ class RequisitionAdminMixin:
     def get_readonly_fields(self, request, obj=None) -> Tuple[str, ...]:
         readonly_fields = super().get_readonly_fields(request, obj=obj)
         return tuple(
-            set(
-                readonly_fields
-                + requisition_identifier_fields
-                + requisition_verify_fields
-            )
+            set(readonly_fields + requisition_identifier_fields + requisition_verify_fields)
         )
 
     def get_changeform_initial_data(self, request) -> dict:

edc_lab/aliquot_types.py

@@ -19,9 +19,7 @@ csf_supernatant = AliquotType(
     name="CSF Supernatant", alpha_code="SUPERNATANT", numeric_code="68"
 )
 csf = AliquotType(name="Cerebro Spinal Fluid", alpha_code="CSF", numeric_code="56")
-tissue_biopsy = AliquotType(
-    name="Tissue biopsy", alpha_code="TISSUE", numeric_code="44"
-)
+tissue_biopsy = AliquotType(name="Tissue biopsy", alpha_code="TISSUE", numeric_code="44")
 
 
 # dummy

edc_lab/form_validators/requisition_form_validator_mixin.py

@@ -23,9 +23,7 @@ class RequisitionFormValidatorMixin:
     def clean(self) -> None:
         if self.instance:
             if self.cleaned_data.get("packed") != self.instance.packed:
-                raise forms.ValidationError(
-                    {"packed": "Value may not be changed here."}
-                )
+                raise forms.ValidationError({"packed": "Value may not be changed here."})
             elif self.cleaned_data.get("processed") != self.instance.processed:
                 if self.aliqout_model_cls.objects.filter(
                     requisition_identifier=self.instance.requisition_identifier

edc_lab/forms/box_type_form.py

@@ -7,12 +7,10 @@ class BoxTypeForm(forms.ModelForm):
     def clean(self) -> dict:
         cleaned_data = super().clean()
         if cleaned_data.get("across") and cleaned_data.get("down"):
-            if cleaned_data.get("across") * cleaned_data.get(
-                "down"
-            ) != cleaned_data.get("total"):
-                raise forms.ValidationError(
-                    {"total": "Invalid total for given dimensions"}
-                )
+            if cleaned_data.get("across") * cleaned_data.get("down") != cleaned_data.get(
+                "total"
+            ):
+                raise forms.ValidationError({"total": "Invalid total for given dimensions"})
         return cleaned_data
 
     class Meta:

edc_lab/lab/aliquot_type.py

@@ -17,9 +17,7 @@ class AliquotType:
     aliquot type, e.g. WB->Plasma, WB->Buffy Coat.
     """
 
-    def __init__(
-        self, name: str = None, alpha_code: str = None, numeric_code: str = None
-    ):
+    def __init__(self, name: str = None, alpha_code: str = None, numeric_code: str = None):
         self.derivatives = []
         self.name = name
         if not alpha_code or not re.match(r"^[A-Z]+$", alpha_code, re.ASCII):
@@ -27,9 +25,7 @@ class AliquotType:
         else:
             self.alpha_code = alpha_code
         if not numeric_code or not re.match(r"^\d+$", numeric_code, re.ASCII):
-            raise AliquotTypeNumericCodeError(
-                f"Invalid numeric code. Got {numeric_code}."
-            )
+            raise AliquotTypeNumericCodeError(f"Invalid numeric code. Got {numeric_code}.")
         else:
             self.numeric_code = numeric_code
 

edc_lab/lab/manifest.py

@@ -67,9 +67,7 @@ class Manifest:
                             "manifest_identifier": manifest_item.manifest.manifest_identifier
                         },
                     )
-                    manifest_identifier = (
-                        manifest_item.manifest.human_readable_identifier
-                    )
+                    manifest_identifier = manifest_item.manifest.human_readable_identifier
                     message = format_html(
                         "Item is already in a manifest. See "
                         '<a href="{}" class="alert-link">'
@@ -98,9 +96,7 @@ class Manifest:
     def validate_box_verified(self, box=None):
         """Returns True if box status is verified."""
         if box.status != VERIFIED:
-            message = "Box is not verified. Got {}.".format(
-                box.human_readable_identifier
-            )
+            message = "Box is not verified. Got {}.".format(box.human_readable_identifier)
             messages.error(self.request, message)
             return False
         return True

edc_lab/lab/primary_aliquot.py

@@ -39,7 +39,5 @@ class PrimaryAliquot:
                 requisition_identifier=self.requisition_identifier,
                 subject_identifier=self.subject_identifier,
             )
-            self._object = aliquot_creator.create_primary(
-                aliquot_type=self.aliquot_type
-            )
+            self._object = aliquot_creator.create_primary(aliquot_type=self.aliquot_type)
         return self._object

edc_lab/lab/requisition_panel.py

@@ -27,9 +27,7 @@ class PanelAttrs:
         title = " ".join(name.split("_")).title()
         alpha_code = alpha_code or ""
         self.abbreviation = f"{name[0:2]}{name[-1:]}".upper()
-        self.verbose_name = f"{title} {alpha_code} {self.abbreviation}".replace(
-            "  ", " "
-        )
+        self.verbose_name = f"{title} {alpha_code} {self.abbreviation}".replace("  ", " ")
 
 
 class RequisitionPanel:

edc_lab/lab/requisition_panel_group.py

@@ -26,8 +26,7 @@ class RequisitionPanelGroup(RequisitionPanel):
             utest_ids.extend(panel.utest_ids)
             if (
                 panel.reference_range_collection_name
-                and reference_range_collection_name
-                != panel.reference_range_collection_name
+                and reference_range_collection_name != panel.reference_range_collection_name
             ):
                 raise RequisitionPanelGroupError(
                     "Panels in a panel group must use the same reference range "
@@ -36,10 +35,7 @@ class RequisitionPanelGroup(RequisitionPanel):
                     f"{panel.reference_range_collection_name}. "
                     f"See {self}."
                 )
-            if (
-                panel.aliquot_type
-                and panel.aliquot_type != processing_profile.aliquot_type
-            ):
+            if panel.aliquot_type and panel.aliquot_type != processing_profile.aliquot_type:
                 raise RequisitionPanelGroupError(
                     "Panels in a panel group must use the same aliquot_type "
                     f"Got {panel.aliquot_type} != "

edc_lab/lab/specimen.py

@@ -69,9 +69,7 @@ class Specimen:
     @property
     def aliquots(self):
         aliquot_model_cls = django_apps.get_model(self.aliquot_model)
-        return aliquot_model_cls.objects.filter(
-            identifier_prefix=self.identifier_prefix
-        )
+        return aliquot_model_cls.objects.filter(identifier_prefix=self.identifier_prefix)
 
     @property
     def identifier_prefix(self):

edc_lab/labels/aliquot_label.py

@@ -47,9 +47,9 @@ class AliquotLabel(BaseLabel):
 
     @property
     def label_context(self):
-        registered_subject = django_apps.get_model(
-            self.registered_subject_model
-        ).objects.get(subject_identifier=self.requisition.subject_identifier)
+        registered_subject = django_apps.get_model(self.registered_subject_model).objects.get(
+            subject_identifier=self.requisition.subject_identifier
+        )
         return {
             "aliquot_identifier": self.model_obj.human_readable_identifier,
             "aliquot_count": 1 if self.model_obj.is_primary else self.model_obj.count,
@@ -61,9 +61,7 @@ class AliquotLabel(BaseLabel):
             "site_name": str(self.requisition.site.name),
             "site_title": str(self.requisition.site.siteprofile.title),
             "clinician_initials": self.requisition.user_created[0:2].upper(),
-            "drawn_datetime": self.requisition.drawn_datetime.strftime(
-                "%Y-%m-%d %H:%M"
-            ),
+            "drawn_datetime": self.requisition.drawn_datetime.strftime("%Y-%m-%d %H:%M"),
             "subject_identifier": registered_subject.subject_identifier,
             "gender": registered_subject.gender,
             "dob": registered_subject.dob.strftime("%Y-%m-%d"),

edc_lab/labels/manifest_label.py

@@ -14,9 +14,7 @@ class ManifestLabel(BaseLabel):
             "manifest_identifier": self.model_obj.human_readable_identifier,
             "protocol": ResearchProtocolConfig().protocol,
             "site": str(self.model_obj.site.id),
-            "manifest_datetime": self.model_obj.manifest_datetime.strftime(
-                "%Y-%m-%d %H:%M"
-            ),
+            "manifest_datetime": self.model_obj.manifest_datetime.strftime("%Y-%m-%d %H:%M"),
             "shipper": self.model_obj.shipper,
             "category": self.model_obj.get_category_display().upper(),
             "site_name": str(self.model_obj.site.siteprofile.title),

edc_lab/migrations/0001_initial.py

@@ -7,11 +7,12 @@ import django.db.models.deletion
 import django.utils.timezone
 import django_audit_fields.fields.uuid_auto_field
 import django_revision.revision_field
+from django.conf import settings
+from django.db import migrations, models
+
 import edc_model_fields.fields.hostname_modification_field
 import edc_model_fields.fields.userfield
 import edc_utils
-from django.conf import settings
-from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
@@ -146,15 +147,11 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "original_measure",
-                    models.DecimalField(
-                        decimal_places=2, default="5.00", max_digits=10
-                    ),
+                    models.DecimalField(decimal_places=2, default="5.00", max_digits=10),
                 ),
                 (
                     "current_measure",
-                    models.DecimalField(
-                        decimal_places=2, default="5.00", max_digits=10
-                    ),
+                    models.DecimalField(decimal_places=2, default="5.00", max_digits=10),
                 ),
                 (
                     "measure_units",
@@ -205,9 +202,7 @@ class Migration(migrations.Migration):
                     "alpha_code",
                     models.CharField(
                         max_length=25,
-                        validators=[
-                            django.core.validators.RegexValidator("^[A-Z]{2}$")
-                        ],
+                        validators=[django.core.validators.RegexValidator("^[A-Z]{2}$")],
                         verbose_name="Aliquot Type Alpha Code",
                     ),
                 ),
@@ -215,9 +210,7 @@ class Migration(migrations.Migration):
                     "numeric_code",
                     models.CharField(
                         max_length=25,
-                        validators=[
-                            django.core.validators.RegexValidator("^[0-9]{2}$")
-                        ],
+                        validators=[django.core.validators.RegexValidator("^[0-9]{2}$")],
                         verbose_name="Aliquot Type Numeric Code",
                     ),
                 ),
@@ -520,9 +513,7 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "total",
-                    models.IntegerField(
-                        help_text="total number of cells in this box type"
-                    ),
+                    models.IntegerField(help_text="total number of cells in this box type"),
                 ),
                 (
                     "fill_order",
@@ -738,15 +729,11 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "original_measure",
-                    models.DecimalField(
-                        decimal_places=2, default="5.00", max_digits=10
-                    ),
+                    models.DecimalField(decimal_places=2, default="5.00", max_digits=10),
                 ),
                 (
                     "current_measure",
-                    models.DecimalField(
-                        decimal_places=2, default="5.00", max_digits=10
-                    ),
+                    models.DecimalField(decimal_places=2, default="5.00", max_digits=10),
                 ),
                 (
                     "measure_units",
@@ -797,9 +784,7 @@ class Migration(migrations.Migration):
                     "alpha_code",
                     models.CharField(
                         max_length=25,
-                        validators=[
-                            django.core.validators.RegexValidator("^[A-Z]{2}$")
-                        ],
+                        validators=[django.core.validators.RegexValidator("^[A-Z]{2}$")],
                         verbose_name="Aliquot Type Alpha Code",
                     ),
                 ),
@@ -807,9 +792,7 @@ class Migration(migrations.Migration):
                     "numeric_code",
                     models.CharField(
                         max_length=25,
-                        validators=[
-                            django.core.validators.RegexValidator("^[0-9]{2}$")
-                        ],
+                        validators=[django.core.validators.RegexValidator("^[0-9]{2}$")],
                         verbose_name="Aliquot Type Numeric Code",
                     ),
                 ),

edc_lab/migrations/0002_auto_20170305_1939.py

@@ -40,9 +40,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="consignee",
             name="address",
-            field=models.CharField(
-                default="address", max_length=50, verbose_name="Address"
-            ),
+            field=models.CharField(default="address", max_length=50, verbose_name="Address"),
             preserve_default=False,
         ),
         migrations.AlterField(
@@ -65,9 +63,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalconsignee",
             name="address",
-            field=models.CharField(
-                default="address", max_length=50, verbose_name="Address"
-            ),
+            field=models.CharField(default="address", max_length=50, verbose_name="Address"),
             preserve_default=False,
         ),
         migrations.AlterField(
@@ -90,9 +86,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalshipper",
             name="address",
-            field=models.CharField(
-                default="address", max_length=50, verbose_name="Address"
-            ),
+            field=models.CharField(default="address", max_length=50, verbose_name="Address"),
             preserve_default=False,
         ),
         migrations.AlterField(
@@ -115,9 +109,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="shipper",
             name="address",
-            field=models.CharField(
-                default="address", max_length=50, verbose_name="Address"
-            ),
+            field=models.CharField(default="address", max_length=50, verbose_name="Address"),
             preserve_default=False,
         ),
         migrations.AlterField(

edc_lab/migrations/0007_auto_20170321_1119.py

@@ -12,15 +12,11 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="consignee",
             name="name",
-            field=models.CharField(
-                help_text="Company name", max_length=50, unique=True
-            ),
+            field=models.CharField(help_text="Company name", max_length=50, unique=True),
         ),
         migrations.AlterField(
             model_name="historicalconsignee",
             name="name",
-            field=models.CharField(
-                db_index=True, help_text="Company name", max_length=50
-            ),
+            field=models.CharField(db_index=True, help_text="Company name", max_length=50),
         ),
     ]

edc_lab/migrations/0008_auto_20170921_0719.py

@@ -5,10 +5,11 @@ from __future__ import unicode_literals
 import _socket
 import django_audit_fields.fields.uuid_auto_field
 import django_revision.revision_field
+from django.db import migrations, models
+
 import edc_model_fields.fields.hostname_modification_field
 import edc_model_fields.fields.userfield
 import edc_utils
-from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

edc_lab/migrations/0010_auto_20171127_1541.py

@@ -5,12 +5,13 @@ import django.db.models.deletion
 import django.utils.timezone
 import django_audit_fields.fields.uuid_auto_field
 import django_revision.revision_field
+from django.conf import settings
+from django.db import migrations, models
+
 import edc_model.models
 import edc_model_fields.fields.hostname_modification_field
 import edc_model_fields.fields.userfield
 import edc_utils
-from django.conf import settings
-from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

edc_lab/migrations/0012_auto_20180114_1438.py

@@ -4,10 +4,11 @@ import _socket
 import django.db.models.deletion
 import django_audit_fields.fields.uuid_auto_field
 import django_revision.revision_field
+from django.db import migrations, models
+
 import edc_model_fields.fields.hostname_modification_field
 import edc_model_fields.fields.userfield
 import edc_utils
-from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

edc_lab/migrations/0013_auto_20180117_1438.py

@@ -1,9 +1,10 @@
 # Generated by Django 2.0.1 on 2018-01-17 12:38
 
 import django.db.models.deletion
-import edc_sites.models
 from django.db import migrations, models
 
+import edc_sites.models
+
 
 class Migration(migrations.Migration):
     dependencies = [

edc_lab/migrations/0022_auto_20211210_1839.py

@@ -1,6 +1,7 @@
 # Generated by Django 3.2.9 on 2021-12-10 15:39
 
 from django.db import migrations
+
 import edc_lab.models.aliquot
 import edc_lab.models.box
 import edc_lab.models.box_item

edc_lab/migrations/0024_alter_manifestitem_managers.py

@@ -1,7 +1,8 @@
 # Generated by Django 3.2.13 on 2022-09-29 14:42
 
-from django.db import migrations
 import django.db.models.manager
+from django.db import migrations
+
 import edc_sites.models
 
 

edc_lab/migrations/0027_alter_aliquot_managers_alter_box_managers_and_more.py

@@ -1,6 +1,5 @@
 # Generated by Django 4.2.1 on 2023-07-07 19:32
 
-import edc_sites.models
 from django.db import migrations
 
 import edc_lab.models.aliquot
@@ -9,6 +8,7 @@ import edc_lab.models.manifest.manifest
 import edc_lab.models.order
 import edc_lab.models.result
 import edc_lab.models.result_item
+import edc_sites.models
 
 
 class Migration(migrations.Migration):