class OnSchedulePreFlourish(OnScheduleModelMixin, BaseUuidModel):
"""A model used by the system. Auto-completed by enrollment model.
"""
subject_identifier = models.CharField(
verbose_name="Subject Identifier",
max_length=50)
schedule_name = models.CharField(max_length=25, blank=True, null=True)
on_site = CurrentSiteManager()
objects = SubjectIdentifierManager()
history = HistoricalRecords()
def put_on_schedule(self):
pass
def save(self, *args, **kwargs):
self.consent_version = '1'
super().save(*args, **kwargs)
class Meta:
unique_together = ('subject_identifier', 'schedule_name')
class SubjectVisit(VisitModelMixin, ReferenceModelMixin, CreatesMetadataModelMixin,
SiteModelMixin, RequiresConsentFieldsModelMixin, BaseUuidModel):
"""A model completed by the user that captures the covering
information for the data collected for this timepoint/appointment,
e.g.report_datetime.
"""
appointment = models.OneToOneField(Appointment, on_delete=models.PROTECT)
reason = models.CharField(
verbose_name='What is the reason for this visit report?',
max_length=25,
choices=VISIT_REASON)
reason_unscheduled = models.CharField(
verbose_name=(
'If \'Unscheduled\' above, provide reason for '
'the unscheduled visit'),
max_length=25,
choices=VISIT_UNSCHEDULED_REASON,
default=NOT_APPLICABLE)
info_source = models.CharField(
verbose_name='What is the main source of this information?',
max_length=25,
choices=INFO_SOURCE)
on_site = CurrentSiteManager()
objects = VisitModelManager()
history = HistoricalRecords()
class Meta(VisitModelMixin.Meta):
pass
class Appointment(AppointmentModelMixin, SiteModelMixin, BaseUuidModel):
appt_datetime = models.DateTimeField(
verbose_name=('Appointment date and time'),
validators=[datetime_not_before_study_start],
db_index=True)
site = models.ForeignKey(Site,
on_delete=models.PROTECT,
null=True,
editable=False,
related_name='appoimtment_site')
on_site = CurrentSiteManager()
objects = AppointmentManager()
history = HistoricalRecords()
def natural_key(self):
return (self.subject_identifier, self.visit_schedule_name,
self.schedule_name, self.visit_code, self.visit_code_sequence)
natural_key.dependencies = ['sites.Site']
class Meta(AppointmentModelMixin.Meta):
pass
class OutgoingTransaction(TransactionModelMixin, SiteModelMixin,
BaseUuidModel):
""" Transactions produced locally to be consumed/sent to a queue or
consumer.
"""
site = models.ForeignKey(Site,
on_delete=models.CASCADE,
null=True,
editable=False)
is_consumed_middleman = models.BooleanField(default=False)
is_consumed_server = models.BooleanField(default=False)
using = models.CharField(max_length=25, null=True)
on_site = CurrentSiteManager()
objects = models.Manager()
def save(self, *args, **kwargs):
if not self.using:
raise ValueError('Value for \'{}.using\' cannot be None.'.format(
self._meta.model_name))
if self.is_consumed_server and not self.consumed_datetime:
self.consumed_datetime = get_utcnow()
super().save(*args, **kwargs)
class Meta:
ordering = ['timestamp']
class InfantOffSchedule(ConsentVersionModelModelMixin, OffScheduleModelMixin,
BaseUuidModel):
schedule_name = models.CharField(max_length=25, blank=True, null=True)
on_site = CurrentSiteManager()
objects = SubjectIdentifierManager()
history = HistoricalRecords()
def take_off_schedule(self):
pass
def get_consent_version(self):
subject_consent_cls = django_apps.get_model(
'td_infant.infantdummysubjectconsent')
subject_consent_objs = subject_consent_cls.objects.filter(
subject_identifier=self.subject_identifier).order_by(
'-consent_datetime')
if subject_consent_objs:
return subject_consent_objs.first().version
else:
raise ValidationError(
'Missing Infant Dummy Consent form. Cannot proceed.')
class Meta:
unique_together = ('subject_identifier', 'schedule_name')
class CaregiverOffSchedule(OffScheduleModelMixin, BaseUuidModel):
schedule_name = models.CharField(max_length=25, blank=True, null=True)
objects = SubjectIdentifierManager()
on_site = CurrentSiteManager()
history = HistoricalRecords()
def take_off_schedule(self):
pass
@property
def latest_consent_obj_version(self):
caregiver_consent_cls = django_apps.get_model(
'flourish_caregiver.subjectconsent')
subject_consents = caregiver_consent_cls.objects.filter(
subject_identifier=self.subject_identifier, )
if subject_consents:
latest_consent = subject_consents.latest('consent_datetime')
return latest_consent.version
else:
raise forms.ValidationError(
'Missing Subject Consent form, cannot proceed.')
def save(self, *args, **kwargs):
self.consent_version = self.latest_consent_obj_version
super().save(*args, **kwargs)
class Meta:
unique_together = ('subject_identifier', 'schedule_name')
class OnSchedule(OnScheduleModelMixin, BaseUuidModel):
"""A model used by the system. Auto-completed by subject_consent.
"""
on_site = CurrentSiteManager()
objects = SubjectIdentifierManager()
history = HistoricalRecords()
class FollowUp(ClinicalAssessmentModelMixin, CrfModelMixin):
fluconazole_dose = models.CharField(
verbose_name='Fluconazole dose (day prior to visit)',
max_length=25,
choices=FLUCONAZOLE_DOSE)
fluconazole_dose_other = OtherCharField(
verbose_name='If other, specify dose:', max_length=25)
rifampicin_started = models.CharField(
verbose_name='Rifampicin started since last visit?',
max_length=25,
choices=YES_NO_ALREADY_ND)
rifampicin_start_date = models.DateField(
verbose_name='Date Rifampicin started',
validators=[date_not_future],
null=True,
blank=True,
)
patient_help = models.CharField(
verbose_name=('Does the patient require help from'
' anybody for everyday activities? '),
max_length=10,
choices=YES_NO_ND,
help_text=('For example eating, drinking, washing,'
' brushing teeth, going to the toilet'))
patient_problems = models.CharField(
verbose_name=
'Has the illness left the patient with any other problems?',
max_length=10,
choices=YES_NO_ND)
rankin_score = models.CharField(verbose_name='Modified Rankin score',
choices=RANKIN_SCORE,
max_length=10,
null=True)
other_significant_dx = models.CharField(
verbose_name='Other significant diagnosis since last visit?',
max_length=5,
choices=YES_NO_NA)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = 'Follow-up'
verbose_name_plural = 'Follow-up'
class EducationHoh(EducationModelMixin, CrfModelMixin):
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = 'Health Economics: Education (Person who earns the highest income)'
verbose_name_plural = 'Health Economics: Education (Person who earns the highest income)'
class MedicalExpensesTwo(CrfModelMixin):
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = 'Health Economics: Medical Expenses Part 2'
verbose_name_plural = 'Health Economics: Medical Expenses Part 2'
class ChildOffSchedule(OffScheduleModelMixin, BaseUuidModel):
schedule_name = models.CharField(max_length=25, blank=True, null=True)
objects = SubjectIdentifierManager()
on_site = CurrentSiteManager()
history = HistoricalRecords()
def take_off_schedule(self):
pass
def get_consent_version(self):
preg_subject_screening_cls = django_apps.get_model(
'flourish_caregiver.screeningpregwomen')
prior_subject_screening_cls = django_apps.get_model(
'flourish_caregiver.screeningpriorbhpparticipants')
consent_version_cls = django_apps.get_model(
'flourish_caregiver.flourishconsentversion')
subject_screening_obj = None
try:
subject_screening_obj = preg_subject_screening_cls.objects.get(
subject_identifier=self.subject_identifier[:-3])
except preg_subject_screening_cls.DoesNotExist:
try:
subject_screening_obj = prior_subject_screening_cls.objects.get(
subject_identifier=self.subject_identifier[:-3])
except prior_subject_screening_cls.DoesNotExist:
raise ValidationError(
'Missing Subject Screening form. Please complete '
'it before proceeding.')
if subject_screening_obj:
try:
consent_version_obj = consent_version_cls.objects.get(
screening_identifier=subject_screening_obj.
screening_identifier)
except consent_version_cls.DoesNotExist:
raise ValidationError(
'Missing Consent Version form. Please complete '
'it before proceeding.')
return consent_version_obj.version
def save(self, *args, **kwargs):
self.consent_version = self.get_consent_version()
super().save(*args, **kwargs)
class Meta:
unique_together = ('subject_identifier', 'schedule_name')
class OnScheduleModelMixin(BaseOnScheduleModelMixin, BaseUuidModel):
"""A model used by the system. Auto-completed by enrollment model.
"""
subject_identifier = models.CharField(
verbose_name="Subject Identifier",
max_length=50)
schedule_name = models.CharField(max_length=25,
blank=True,
null=True)
on_site = CurrentSiteManager()
objects = SubjectIdentifierManager()
history = HistoricalRecords()
def put_on_schedule(self):
pass
def save(self, *args, **kwargs):
self.consent_version = self.latest_consent_obj_version
super().save(*args, **kwargs)
@property
def consent_version_cls(self):
return django_apps.get_model('flourish_caregiver.flourishconsentversion')
@property
def subject_consent_cls(self):
return django_apps.get_model('flourish_caregiver.subjectconsent')
@property
def latest_consent_obj_version(self):
child_consent_cls = django_apps.get_model(
'flourish_child.childdummysubjectconsent')
subject_consents = child_consent_cls.objects.filter(
subject_identifier=self.subject_identifier,)
if subject_consents:
latest_consent = subject_consents.latest('consent_datetime')
return latest_consent.version
else:
raise forms.ValidationError('Missing dummy consent obj, cannot proceed.')
class Meta:
unique_together = ('subject_identifier', 'schedule_name')
abstract = True
class CaregiverOffSchedule(OffScheduleModelMixin, BaseUuidModel):
schedule_name = models.CharField(max_length=25, blank=True, null=True)
objects = SubjectIdentifierManager()
on_site = CurrentSiteManager()
history = HistoricalRecords()
def take_off_schedule(self):
pass
class Meta:
unique_together = ('subject_identifier', 'schedule_name')
class SubjectRequisition(
NonUniqueSubjectIdentifierFieldMixin, RequisitionModelMixin,
RequisitionStatusMixin, RequisitionIdentifierMixin,
VisitTrackingCrfModelMixin, SubjectScheduleCrfModelMixin,
RequiresConsentFieldsModelMixin, PreviousVisitModelMixin,
RequisitionReferenceModelMixin, UpdatesRequisitionMetadataModelMixin,
SearchSlugModelMixin, BaseUuidModel):
lab_profile_name = 'ambition_subject'
subject_visit = models.ForeignKey(SubjectVisit, on_delete=PROTECT)
reason_not_drawn = models.CharField(
verbose_name='If not drawn, please explain',
max_length=25,
default=NOT_APPLICABLE,
choices=REASON_NOT_DRAWN)
on_site = CurrentSiteManager()
objects = Manager()
history = HistoricalRecords()
def __str__(self):
return (f'{self.requisition_identifier} '
f'{self.panel_object.verbose_name}')
def save(self, *args, **kwargs):
if not self.id:
edc_protocol_app_config = django_apps.get_app_config(
'edc_protocol')
self.protocol_number = edc_protocol_app_config.protocol_number
self.subject_identifier = self.subject_visit.subject_identifier
super().save(*args, **kwargs)
def get_search_slug_fields(self):
fields = super().get_search_slug_fields()
fields.extend([
'requisition_identifier', 'human_readable_identifier',
'identifier_prefix'
])
return fields
class Meta:
unique_together = ('panel', 'subject_visit')
class Week16(CrfModelMixin):
patient_alive = models.CharField(verbose_name='Is the patient alive?',
max_length=5,
choices=YES_NO)
death_datetime = models.DateTimeField(
verbose_name='If dead, date and time of death',
validators=[date_not_future],
null=True,
blank=True)
activities_help = models.CharField(
verbose_name=
('Does the patient require help from anybody for everyday activities?'
),
max_length=5,
choices=YES_NO_NA,
help_text=('For example eating, drinking, washing, brushing teeth, '
'going to the toilet.'))
illness_problems = models.CharField(
verbose_name=
'Has the illness left the patient with any other problems?',
max_length=5,
choices=YES_NO_NA)
rankin_score = models.CharField(verbose_name='Modified Rankin score',
max_length=10,
choices=RANKIN_SCORE)
week16_narrative = models.TextField(verbose_name='Narrative',
max_length=1000,
null=True,
blank=True)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name_plural = 'Week16'
class Education(EducationModelMixin, CrfModelMixin):
household_head = models.CharField(
verbose_name='Are you the person who earns the highest income?',
max_length=5,
choices=YES_NO,
help_text=('If NO, please complete the form "Health Economics: '
'Education (Person who earns the highest income)" on behalf of the '
'Person who earns the highest income.'))
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = 'Health Economics: Education'
verbose_name_plural = 'Health Economics: Education'
class StudyTerminationConclusionW10(OffScheduleModelMixin,
ActionItemModelMixin,
TrackingIdentifierModelMixin,
BaseUuidModel):
action_cls = StudyTerminationConclusionW10Action
tracking_identifier_prefix = 'ST'
last_study_fu_date = models.DateField(
verbose_name='Date of last research follow up (if different):',
validators=[date_not_future],
blank=True,
null=True)
termination_reason = models.CharField(
verbose_name='Reason for study termination',
max_length=75,
choices=REASON_STUDY_TERMINATED_W10,
help_text=(
'If included in error, be sure to fill in protocol deviation form.'
))
death_date = models.DateField(verbose_name='Date of Death',
validators=[date_not_future],
blank=True,
null=True)
consent_withdrawal_reason = models.CharField(
verbose_name='Reason for withdrawing consent',
max_length=75,
blank=True,
null=True)
on_site = CurrentSiteManager()
objects = SubjectIdentifierManager()
history = HistoricalRecords()
class Meta:
verbose_name = 'W10 Study Termination/Conclusion'
verbose_name_plural = 'W10 Study Terminations/Conclusions'
class IncomingTransaction(TransactionModelMixin, SiteModelMixin,
BaseUuidModel):
""" Transactions received from a remote host.
"""
site = models.ForeignKey(Site,
on_delete=models.CASCADE,
null=True,
editable=False)
is_consumed = models.BooleanField(default=False)
is_self = models.BooleanField(default=False)
on_site = CurrentSiteManager()
objects = models.Manager()
class Meta:
ordering = ['timestamp']
class OnScheduleMaternalLabourDel(ConsentVersionModelModelMixin,
OnScheduleModelMixin, BaseUuidModel):
"""A model used by the system. Auto-completed by subject_consent.
"""
subject_identifier = models.CharField(verbose_name="Subject Identifier",
max_length=50)
schedule_name = models.CharField(max_length=25, blank=True, null=True)
on_site = CurrentSiteManager()
objects = SubjectIdentifierManager()
history = HistoricalRecords()
def put_on_schedule(self):
pass
class Meta:
unique_together = ('subject_identifier', 'schedule_name')
class Week4(ClinicalAssessmentModelMixin, CrfModelMixin):
fluconazole_dose = models.CharField(
verbose_name='Fluconazole dose (day prior to visit)',
max_length=25,
choices=FLUCONAZOLE_DOSE)
fluconazole_dose_other = OtherCharField(max_length=25)
rifampicin_started = models.CharField(
verbose_name='Rifampicin started since last visit?',
max_length=25,
choices=YES_NO_ALREADY_ND)
rifampicin_start_date = models.DateField(
verbose_name='Date Rifampicin started',
validators=[date_not_future],
null=True,
blank=True)
lp_done = models.CharField(verbose_name='LP done?',
max_length=5,
choices=YES_NO,
help_text='If yes, ensure LP CRF completed.')
other_significant_dx = models.CharField(
verbose_name='Other significant diagnosis since last visit?',
max_length=5,
choices=YES_NO_NA)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = 'Week 4'
verbose_name_plural = 'Week 4'
class Appointment(AppointmentModelMixin, SiteModelMixin, BaseUuidModel):
site = models.ForeignKey(Site,
on_delete=models.PROTECT,
null=True,
editable=False,
related_name='appoimtment_site')
on_site = CurrentSiteManager()
objects = AppointmentManager()
history = HistoricalRecords()
def natural_key(self):
return (self.subject_identifier, self.visit_schedule_name,
self.schedule_name, self.visit_code, self.visit_code_sequence)
natural_key.dependencies = ['sites.Site']
class Meta(AppointmentModelMixin.Meta):
pass
class SubjectLocator(LocatorModelMixin, RequiresConsentFieldsModelMixin,
ActionItemModelMixin, SiteModelMixin,
TrackingIdentifierModelMixin, BaseUuidModel):
"""A model completed by the user to that captures participant
locator information and permission to contact.
"""
action_cls = SubjectLocatorAction
tracking_identifier_prefix = 'SL'
on_site = CurrentSiteManager()
objects = LocatorManager()
history = HistoricalRecords()
def natural_key(self):
return (self.subject_identifier, )
natural_key.dependencies = ['sites.Site']
class Meta:
verbose_name = 'Subject Locator'
class OnScheduleInfantBirth(OnScheduleModelMixin, BaseUuidModel):
"""A model used by the system. Auto-completed by infant birth.
"""
subject_identifier = models.CharField(verbose_name="Subject Identifier",
max_length=50)
schedule_name = models.CharField(max_length=25, blank=True, null=True)
on_site = CurrentSiteManager()
objects = SubjectIdentifierManager()
history = HistoricalRecords()
def put_on_schedule(self):
pass
def save(self, *args, **kwargs):
self.consent_version = self.get_consent_version()
super(OnScheduleInfantBirth, self).save(*args, **kwargs)
def get_consent_version(self):
subject_consent_cls = django_apps.get_model(
'td_infant.infantdummysubjectconsent')
subject_consent_objs = subject_consent_cls.objects.filter(
subject_identifier=self.subject_identifier).order_by(
'-consent_datetime')
if subject_consent_objs:
return subject_consent_objs.first().version
else:
raise ValidationError(
'Missing Infant Dummy Consent form. Cannot proceed.')
class Meta:
unique_together = ('subject_identifier', 'schedule_name')
class RandomizationList(BaseUuidModel):
subject_identifier = models.CharField(
verbose_name="Subject Identifier",
max_length=50,
null=True,
unique=True)
sid = models.IntegerField(unique=True)
drug_assignment = EncryptedTextField(
choices=(
(SINGLE_DOSE, SINGLE_DOSE_NAME),
(CONTROL, CONTROL_NAME)))
site_name = models.CharField(max_length=100)
allocation = EncryptedTextField(
verbose_name='Original integer allocation',
null=True)
allocated = models.BooleanField(default=False)
allocated_datetime = models.DateTimeField(null=True)
allocated_user = models.CharField(max_length=50, null=True)
allocated_site = models.ForeignKey(
Site, null=True, on_delete=models.CASCADE)
verified = models.BooleanField(default=False)
verified_datetime = models.DateTimeField(null=True)
verified_user = models.CharField(max_length=50, null=True)
objects = RandomizationListManager()
history = HistoricalRecords()
on_site = CurrentSiteManager('allocated_site')
def __str__(self):
return f'{self.site_name}.{self.sid} subject={self.subject_identifier}'
def save(self, *args, **kwargs):
try:
self.treatment_description
except RandomizationError as e:
raise RandomizationListModelError(e)
try:
Site.objects.get(name=self.site_name)
except ObjectDoesNotExist:
site_names = [obj.name for obj in Site.objects.all()]
raise RandomizationListModelError(
f'Invalid site name. Got {self.site_name}. '
f'Expected one of {site_names}.')
super().save(*args, **kwargs)
@property
def short_label(self):
return (f'{self.drug_assignment} SID:{self.site_name}.{self.sid}')
@property
def treatment_description(self):
if self.drug_assignment == CONTROL:
return CONTROL_NAME
elif self.drug_assignment == SINGLE_DOSE:
return SINGLE_DOSE_NAME
raise RandomizationError(
f'Invalid drug assignment. Got {self.drug_assignment}')
def natural_key(self):
return (self.sid, )
class Meta:
ordering = ('site_name', 'sid', )
unique_together = ('site_name', 'sid')
class RecurrenceSymptom(NonUniqueSubjectIdentifierFieldMixin,
ActionItemModelMixin, TrackingIdentifierModelMixin,
SiteModelMixin, BaseUuidModel):
tracking_identifier_prefix = 'RS'
action_cls = RecurrenceOfSymptomsAction
report_datetime = models.DateTimeField(
verbose_name="Report Date and Time",
default=get_utcnow)
meningitis_symptom = models.ManyToManyField(
MeningitisSymptom,
verbose_name='What are your current symptoms?')
meningitis_symptom_other = models.CharField(
verbose_name='If other symptom, please specify',
max_length=50,
null=True,
blank=True)
patient_readmitted = models.CharField(
verbose_name=(
'Has the patient been re-admitted due to these recurrent symptoms?'),
max_length=5,
choices=YES_NO)
glasgow_coma_score = models.IntegerField(
verbose_name='Score:',
validators=[MinValueValidator(3), MaxValueValidator(15)],
help_text='/15')
recent_seizure = models.CharField(
verbose_name=(
'Recent seizure (<72 hrs):'),
max_length=5,
choices=YES_NO)
behaviour_change = models.CharField(
max_length=5,
choices=YES_NO)
confusion = models.CharField(
max_length=5,
choices=YES_NO)
neurological = models.ManyToManyField(
Neurological,
verbose_name='neurologic:')
focal_neurologic_deficit = models.CharField(
verbose_name='If "Focal neurologic deficit" chosen, please specify',
max_length=15,
null=True,
blank=True)
cn_palsy_chosen_other = models.CharField(
verbose_name='If other CN Palsy',
max_length=15,
null=True,
blank=True)
lp_completed = models.CharField(
verbose_name='LP completed',
max_length=5,
choices=YES_NO,
help_text='If YES, complete LP form')
amb_administered = models.CharField(
max_length=5,
choices=YES_NO)
amb_duration = models.IntegerField(
verbose_name='If YES, specify length of course',
validators=[MinValueValidator(1)],
null=True,
blank=True)
tb_treatment = models.CharField(
verbose_name='TB treatment:',
max_length=5,
choices=YES_NO)
steroids_administered = models.CharField(
max_length=5,
choices=YES_NO)
steroids_duration = models.IntegerField(
verbose_name='If YES, specify the length of course in days:',
validators=[MinValueValidator(1)],
null=True,
blank=True)
steroids_choices = models.CharField(
verbose_name='If YES',
max_length=25,
default=NOT_APPLICABLE,
choices=STEROIDS_CHOICES)
steroids_choices_other = models.CharField(
blank=True,
max_length=50,
verbose_name='If other steroids, please specify')
CD4_count = models.IntegerField(
verbose_name='CD4 count (if available)',
validators=[MinValueValidator(1)],
null=True,
blank=True)
antibiotic_treatment = models.ManyToManyField(
AntibioticTreatment,
verbose_name='Antibiotics treatment')
antibiotic_treatment_other = models.CharField(
verbose_name='If other antibiotic treatment, please specify',
max_length=50,
blank=True,
null=True)
on_arvs = models.CharField(
verbose_name='On ARVs:',
max_length=26,
choices=YES_NO_ALREADY_ARV)
arv_date = models.DateField(
verbose_name='Study date ARVs started.',
validators=[date_not_future],
null=True,
blank=True)
arvs_stopped = models.CharField(
verbose_name='ARVs stopped this clinical episode?',
max_length=5,
choices=YES_NO_NA)
narrative_summary = models.TextField(
verbose_name='Narrative summary of recurrence of symptoms:',
help_text=(
'Please ensure the following forms have been completed: '
'LP, Bloods, Microbiology, Radiology'))
dr_opinion = models.CharField(
verbose_name='Study doctor\'s opinion:',
max_length=10,
choices=DR_OPINION)
dr_opinion_other = models.CharField(
verbose_name='If other doctor\'s opinion, please specify',
blank=True,
max_length=50,
null=True)
on_site = CurrentSiteManager()
objects = TrackingIdentifierManager()
history = HistoricalRecords()
def natural_key(self):
return (self.tracking_identifier, )
class Meta:
verbose_name = 'Recurrence of Symptoms'
verbose_name_plural = 'Recurrence of Symptoms'
class ProtocolDeviationViolation(NonUniqueSubjectIdentifierFieldMixin,
SiteModelMixin, ActionItemModelMixin,
TrackingIdentifierModelMixin, BaseUuidModel):
tracking_identifier_prefix = 'PD'
action_cls = ProtocolDeviationViolationAction
report_datetime = models.DateTimeField(verbose_name="Report Date and Time",
default=get_utcnow)
short_description = models.CharField(
verbose_name='Provide a short description of this occurrence',
max_length=35,
null=True,
blank=False,
help_text=(
'Max 35 characters. Note: If this occurrence is a "violation" '
'there is additional space below for a more detailed '
'description'))
report_type = models.CharField(verbose_name='Type of occurrence',
max_length=25,
choices=DEVIATION_VIOLATION)
safety_impact = models.CharField(
verbose_name='Could this occurrence have an impact on safety of the '
'participant?',
max_length=25,
choices=YES_NO)
safety_impact_details = models.TextField(
verbose_name='If "Yes", provide details', null=True, blank=True)
study_outcomes_impact = models.CharField(
verbose_name='Could this occurrence have an impact on study outcomes?',
max_length=25,
choices=YES_NO)
study_outcomes_impact_details = models.TextField(
verbose_name='If "Yes", provide details', null=True, blank=True)
violation_datetime = models.DateTimeField(
verbose_name='Date violation occurred',
validators=[datetime_not_future],
null=True,
blank=True)
violation_type = models.CharField(verbose_name='Type of violation',
max_length=75,
choices=PROTOCOL_VIOLATION,
default=NOT_APPLICABLE)
violation_type_other = models.CharField(
null=True,
blank=True,
verbose_name='If other, please specify',
max_length=75)
violation_description = models.TextField(
verbose_name='Describe the violation',
null=True,
blank=True,
help_text=('Describe in full. Explain how the violation '
'happened, what occurred, etc.'))
violation_reason = models.TextField(
verbose_name='Explain the reason why the violation occurred',
null=True,
blank=True)
corrective_action_datetime = models.DateTimeField(
verbose_name='Corrective action date and time',
validators=[datetime_not_future],
null=True,
blank=True)
corrective_action = models.TextField(
verbose_name='Corrective action taken', null=True, blank=True)
preventative_action_datetime = models.DateTimeField(
verbose_name='Preventative action date and time',
validators=[datetime_not_future],
null=True,
blank=True)
preventative_action = models.TextField(
verbose_name='Preventative action taken', null=True, blank=True)
action_required = models.CharField(max_length=45, choices=ACTION_REQUIRED)
report_status = models.CharField(
verbose_name='What is the status of this report?',
max_length=25,
choices=REPORT_STATUS)
report_closed_datetime = models.DateTimeField(
blank=True,
null=True,
validators=[datetime_not_future],
verbose_name=('Date and time report closed.'))
on_site = CurrentSiteManager()
objects = TrackingIdentifierManager()
history = HistoricalRecords()
def natural_key(self):
return (self.tracking_identifier, )
natural_key.dependencies = ['sites.Site']
class Meta:
verbose_name = 'Protocol Deviation/Violation'
verbose_name_plural = 'Protocol Deviations/Violations'
class ActionItem(NonUniqueSubjectIdentifierFieldMixin, SiteModelMixin,
BaseUuidModel):
subject_identifier_model = 'edc_registration.registeredsubject'
action_identifier = models.CharField(max_length=25, unique=True)
report_datetime = models.DateTimeField(default=get_utcnow)
action_type = models.ForeignKey(ActionType,
on_delete=PROTECT,
related_name='action_type',
verbose_name='Action')
reference_model = models.CharField(max_length=50, null=True)
reference_identifier = models.CharField(
max_length=50,
null=True,
help_text='e.g. tracking identifier updated from the reference model')
related_reference_model = models.CharField(max_length=100,
null=True,
editable=False)
related_reference_identifier = models.CharField(
max_length=50,
null=True,
blank=True,
help_text=('May be left blank. e.g. tracking identifier from '
'source model that opened the item.'))
parent_reference_model = models.CharField(max_length=100,
null=True,
editable=False)
parent_reference_identifier = models.CharField(
max_length=50,
null=True,
blank=True,
help_text=('May be left blank. e.g. tracking identifier from '
'source model that opened the item.'))
priority = models.CharField(
max_length=25,
choices=PRIORITY,
null=True,
blank=True,
help_text='Leave blank to use default for this action type.')
parent_action_item = models.ForeignKey('self',
on_delete=PROTECT,
null=True,
blank=True)
status = models.CharField(max_length=25,
default=NEW,
choices=ACTION_STATUS)
instructions = models.TextField(null=True,
blank=True,
help_text='populated by action class')
auto_created = models.BooleanField(default=False)
auto_created_comment = models.CharField(max_length=25,
null=True,
blank=True)
on_site = CurrentSiteManager()
objects = ActionItemManager()
history = HistoricalRecords()
def __str__(self):
return (f'{self.action_identifier[-9:]} {self.action_type.name} '
f'({self.get_status_display()})')
def save(self, *args, **kwargs):
"""See also signals."""
if not self.id:
# a new action item always has a unique action identifier
self.action_identifier = ActionIdentifier().identifier
self.check_registered_subject()
self.priority = self.priority or self.action_type.priority
self.reference_model = self.action_type.reference_model
self.related_reference_model = self.action_type.related_reference_model
self.instructions = self.action_type.instructions
super().save(*args, **kwargs)
def check_registered_subject(self):
# subject_identifier
if self.subject_identifier:
subject_identifier_model_cls = django_apps.get_model(
self.subject_identifier_model)
try:
subject_identifier_model_cls.objects.get(
subject_identifier=self.subject_identifier)
except ObjectDoesNotExist:
raise SubjectDoesNotExist(
f'Invalid subject identifier. Subject does not exist '
f'in \'{self.subject_identifier_model}\'. '
f'Got \'{self.subject_identifier}\'.')
def natural_key(self):
return (self.action_identifier, )
natural_key.dependencies = ['sites.Site']
@property
def last_updated(self):
return None if self.status == NEW else self.modified
@property
def user_last_updated(self):
return None if self.status == NEW else self.user_modified or self.user_created
@property
def action_cls(self):
"""Returns the action_cls.
"""
return site_action_items.get(self.action_type.name)
@property
def parent_reference_model_obj(self):
"""Returns the parent reference model instance or None.
"""
try:
reference_model = self.parent_action_item.reference_model
except AttributeError:
pass
else:
return django_apps.get_model(reference_model).objects.get(
tracking_identifier=self.parent_action_item.
reference_identifier)
return None
@property
def related_reference_model_obj(self):
"""Returns the related reference model instance or None.
"""
try:
reference_model = self.related_reference_model
except AttributeError:
pass
else:
return django_apps.get_model(reference_model).objects.get(
tracking_identifier=self.related_reference_identifier)
return None
@property
def identifier(self):
"""Returns a shortened action identifier.
"""
return self.action_identifier[-9:]
@property
def parent(self):
"""Returns a url to the parent action item
for display in admin.
"""
if self.parent_action_item:
url_name = '_'.join(self._meta.label_lower.split('.'))
namespace = edc_action_item_admin.name
url = reverse(f'{namespace}:{url_name}_changelist')
return mark_safe(
f'<a data-toggle="tooltip" title="go to parent action item" '
f'href="{url}?q={self.parent_action_item.action_identifier}">'
f'{self.parent_action_item.identifier}</a>')
return None
@property
def reference(self):
"""Returns a shortened reference_identifier which in
most cases is the reference model's tracking identifier.
"""
if self.reference_identifier:
return self.reference_identifier[-9:]
return None
@property
def parent_reference(self):
"""Returns a shortened reference_identifier of the
parent model reference which in most cases is the
parent reference model's tracking identifier.
"""
try:
reference_identifier = self.parent_action_item.reference_identifier
except AttributeError:
reference_identifier = None
if reference_identifier:
return reference_identifier[-9:]
return None
@property
def related_reference(self):
"""Returns a shortened reference_identifier of the
parent model reference which in most cases is the
parent reference model's tracking identifier.
"""
try:
reference_identifier = self._related_reference_identifier
except AttributeError:
reference_identifier = None
if reference_identifier:
return reference_identifier[-9:]
return None
class Meta:
verbose_name = 'Action Item'
verbose_name_plural = 'Action Items'
unique_together = ('subject_identifier', 'action_type',
'reference_identifier')
class Microbiology(CrfModelMixin):
urine_culture_performed = models.CharField(
max_length=5,
choices=YES_NO,
help_text='only for patients with >50 white cells in urine')
urine_taken_date = models.DateField(
validators=[date_not_before_study_start, date_not_future],
null=True,
blank=True)
urine_culture_results = models.CharField(
verbose_name='Urine culture results, if completed',
max_length=10,
choices=CULTURE_RESULTS,
default=NOT_APPLICABLE)
urine_culture_organism = models.CharField(
verbose_name='If positive, organism',
max_length=25,
choices=URINE_CULTURE_RESULTS_ORGANISM,
default=NOT_APPLICABLE)
urine_culture_organism_other = OtherCharField(
max_length=50,
null=True,
blank=True)
blood_culture_performed = models.CharField(
max_length=5,
choices=YES_NO)
blood_culture_results = models.CharField(
verbose_name='Blood culture results, if completed',
max_length=10,
choices=CULTURE_RESULTS,
default=NOT_APPLICABLE)
blood_taken_date = models.DateField(
validators=[date_not_before_study_start, date_not_future],
null=True,
blank=True)
day_blood_taken = models.IntegerField(
verbose_name='If positive, study day positive culture sample taken',
validators=[MinValueValidator(1)],
null=True,
blank=True)
blood_culture_organism = models.CharField(
verbose_name='If growth positive, organism',
max_length=50,
choices=BLOOD_CULTURE_RESULTS_ORGANISM,
default=NOT_APPLICABLE)
blood_culture_organism_other = OtherCharField(
max_length=50,
null=True,
blank=True)
bacteria_identified = models.CharField(
verbose_name='If bacteria, type',
max_length=50,
choices=BACTERIA_TYPE,
default=NOT_APPLICABLE)
bacteria_identified_other = OtherCharField(
max_length=100,
null=True,
blank=True)
sputum_afb_performed = models.CharField(
verbose_name='AFB microscopy performed?',
max_length=5,
choices=YES_NO,
help_text='Was sputum AFB done?')
sputum_afb_date = models.DateField(
validators=[date_not_before_study_start, date_not_future],
null=True,
blank=True)
sputum_results_afb = models.CharField(
verbose_name='AFB results',
max_length=10,
choices=POS_NEG_NA,
default=NOT_APPLICABLE)
sputum_performed = models.CharField(
verbose_name='Culture performed?',
max_length=15,
choices=YES_NO_NA,
default=NOT_APPLICABLE)
sputum_taken_date = models.DateField(
validators=[date_not_before_study_start, date_not_future],
null=True,
blank=True)
sputum_results_culture = models.CharField(
verbose_name='Culture results',
max_length=10,
choices=POS_NEG_NA,
default=NOT_APPLICABLE)
sputum_results_positive = models.CharField(
verbose_name='If culture is positive, please specify:',
max_length=50,
null=True,
blank=True)
sputum_genexpert_performed = models.CharField(
verbose_name='Sputum Gene-Xpert performed?',
max_length=15,
choices=YES_NO_NA,
default=NOT_APPLICABLE)
sputum_genexpert_date = models.DateField(
verbose_name='Date sputum Gene-Xpert taken',
validators=[date_not_before_study_start, date_not_future],
null=True,
blank=True)
sputum_result_genexpert = models.CharField(
verbose_name='Gene-Xpert results',
max_length=45,
choices=SPUTUM_GENEXPERT,
default=NOT_APPLICABLE)
tissue_biopsy_taken = models.CharField(
max_length=5,
choices=YES_NO)
tissue_biopsy_results = models.CharField(
verbose_name='If YES, results',
max_length=10,
choices=CULTURE_RESULTS,
default=NOT_APPLICABLE)
biopsy_date = models.DateField(
validators=[date_not_before_study_start, date_not_future],
null=True,
blank=True)
day_biopsy_taken = models.IntegerField(
verbose_name='If positive, Study day positive culture sample taken',
validators=[MinValueValidator(1)],
null=True,
blank=True)
tissue_biopsy_organism = models.CharField(
verbose_name='If growth positive, organism',
max_length=50,
choices=BIOPSY_RESULTS_ORGANISM,
default=NOT_APPLICABLE)
tissue_biopsy_organism_other = OtherCharField(
max_length=50,
null=True,
blank=True)
histopathology_report = models.TextField(
null=True,
blank=True)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = 'Microbiology'
verbose_name_plural = 'Microbiology'
class PkPdCrf(CrfModelMixin):
albumin = models.IntegerField(verbose_name='Albumin',
null=True,
blank=True,
help_text='Units in g/L')
ambisome_dose = models.IntegerField(verbose_name='Ambisome dose given',
null=True,
blank=True,
help_text='Units in mg')
ambisome_started_datetime = models.DateTimeField(
verbose_name='Date and time Ambisome infusion started?',
null=True,
blank=True)
ambisome_ended_datetime = models.DateTimeField(
verbose_name='Date and time Ambisome infusion stopped',
null=True,
blank=True)
full_ambisome_dose_given = models.CharField(
verbose_name='Was the entire Ambisome dose given?',
choices=YES_NO,
max_length=5,
null=True,
blank=True)
flucytosine_dose = models.IntegerField(verbose_name='Flucytosine dose?',
null=True,
blank=True,
help_text='Units in mg')
flucytosine_dose_one_given = models.CharField(
verbose_name='Flucytosine <u>DOSE 1</u> given? ',
choices=YES_NO,
max_length=5,
null=True,
blank=True)
flucytosine_dose_one_datetime = models.DateTimeField(
verbose_name=mark_safe(
'Date and time Flucytosine <u>DOSE 1</u> was swallowed?'),
null=True,
blank=True)
flucytosine_dose_two_given = models.CharField(
verbose_name='Flucytosine <u>DOSE 2</u> given? ',
choices=YES_NO,
max_length=5,
null=True,
blank=True)
flucytosine_dose_two_datetime = models.DateTimeField(
verbose_name=mark_safe(
'Date and time Flucytosine <u>DOSE 2</u> was swallowed?'),
null=True,
blank=True)
flucytosine_dose_three_given = models.CharField(
verbose_name='Flucytosine <u>DOSE 3</u> given? ',
choices=YES_NO,
max_length=5,
null=True,
blank=True)
flucytosine_dose_three_datetime = models.DateTimeField(
verbose_name=mark_safe(
'Date and time Flucytosine <u>DOSE 3</u> was swallowed?'),
null=True,
blank=True)
flucytosine_dose_four_given = models.CharField(
verbose_name='Flucytosine <u>DOSE 4</u> given? ',
choices=YES_NO,
max_length=5,
null=True,
blank=True)
flucytosine_dose_four_datetime = models.DateTimeField(
verbose_name=mark_safe(
'Date and time Flucytosine <u>DOSE 4</u> was swallowed?'),
null=True,
blank=True)
flucytosine_dose_reason_missed = models.TextField(
verbose_name='If any Flucytosine doses not given, provide reason',
max_length=75,
null=True,
blank=True)
fluconazole_dose = models.IntegerField(verbose_name='Fluconazole dose?',
null=True,
blank=True,
help_text='Units in mg')
fluconazole_dose_given = models.CharField(
verbose_name='Was the Fluconazole dose given?',
choices=YES_NO,
max_length=5,
null=True,
blank=True)
fluconazole_dose_datetime = models.DateTimeField(
verbose_name='Date and time Fluconazole was swallowed?',
null=True,
blank=True)
fluconazole_dose_reason_missed = models.TextField(
verbose_name='If Fluconazole dose not given, provide reason',
max_length=75,
null=True,
blank=True)
blood_sample_one_datetime = models.DateTimeField(verbose_name=mark_safe(
'Date and time blood <u>SAMPLE 1</u> taken?'),
null=True,
blank=True)
blood_sample_two_datetime = models.DateTimeField(verbose_name=mark_safe(
'Date and time blood <u>SAMPLE 2</u> taken?'),
null=True,
blank=True)
blood_sample_three_datetime = models.DateTimeField(verbose_name=mark_safe(
'Date and time blood <u>SAMPLE 3</u> taken?'),
null=True,
blank=True)
blood_sample_four_datetime = models.DateTimeField(verbose_name=mark_safe(
'Date and time blood <u>SAMPLE 4</u> taken?'),
null=True,
blank=True)
blood_sample_five_datetime = models.DateTimeField(verbose_name=mark_safe(
'Date and time blood <u>SAMPLE 5</u> taken?'),
null=True,
blank=True)
blood_sample_six_datetime = models.DateTimeField(verbose_name=mark_safe(
'Date and time blood <u>SAMPLE 6</u> taken?'),
null=True,
blank=True)
blood_sample_missed = models.CharField(
verbose_name='Were any blood samples missed?',
choices=YES_NO,
max_length=5,
null=True,
blank=True)
blood_sample_reason_missed = models.TextField(
verbose_name='If any blood samples missed, provide reason',
max_length=75,
null=True,
blank=True)
pre_dose_lp = models.CharField(verbose_name='Is this a pre-dose LP?',
choices=YES_NO,
max_length=5,
null=True,
blank=True)
post_dose_lp = models.CharField(verbose_name='Is this a post-dose LP?',
choices=YES_NO,
max_length=5,
null=True,
blank=True)
time_csf_sample_taken = models.DateTimeField(
verbose_name='What date and time was the CSF sample taken?',
null=True,
blank=True)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = 'PK/PD'
verbose_name_plural = 'PK/PD'
class Week2(ClinicalAssessmentModelMixin, CrfModelMixin):
discharged = models.CharField(verbose_name='Discharged?',
max_length=25,
choices=YES_NO)
discharge_date = models.DateField(validators=[date_not_future],
null=True,
blank=True)
died = models.CharField(verbose_name='Died?',
max_length=25,
choices=YES_NO)
death_date_time = models.DateTimeField(validators=[datetime_not_future],
null=True,
blank=True)
ampho_start_date = models.DateField(
verbose_name='Amphotericin B start date: ',
validators=[date_not_future],
null=True,
blank=True)
ampho_end_date = models.DateField(verbose_name='Amphotericin B end date: ',
validators=[date_not_future],
null=True,
blank=True)
ampho_duration = models.IntegerField(
verbose_name='Amphotericin B treatment duration',
null=True,
blank=True)
flucon_start_date = models.DateField(
verbose_name='Fluconazole start date:',
validators=[date_not_future],
null=True,
blank=True)
flucon_stop_date = models.DateField(verbose_name='Fluconazole end date:',
validators=[date_not_future],
null=True,
blank=True)
flucon_duration = models.IntegerField(
verbose_name='Fluconazole treatment duration:', null=True, blank=True)
flucy_start_date = models.DateField(verbose_name='Flucytosine start date:',
validators=[date_not_future],
null=True,
blank=True)
flucy_stop_date = models.DateField(verbose_name='Flucytosine end date:',
validators=[date_not_future],
null=True,
blank=True)
flucy_duration = models.IntegerField(
verbose_name='Flucytosine treatment duration:', null=True, blank=True)
ambi_start_date = models.DateField(verbose_name='Ambisome start date:',
validators=[date_not_future],
null=True,
blank=True)
ambi_stop_date = models.DateField(verbose_name='Ambisome end date:',
validators=[date_not_future],
null=True,
blank=True)
ambi_duration = models.IntegerField(
verbose_name='Ambisome treatment duration:', null=True, blank=True)
drug_intervention = models.ManyToManyField(
OtherDrug,
verbose_name="Other drugs/interventions given during first 14 days",
)
drug_intervention_other = models.CharField(
verbose_name='If other, please specify:',
blank=True,
max_length=50,
null=True)
antibiotic = models.ManyToManyField(
Antibiotic,
blank=True,
verbose_name="Were any of the following antibiotics given?",
)
antibiotic_other = models.CharField(
verbose_name='If other antibiotics, please specify:',
max_length=50,
null=True,
blank=True)
blood_received = models.CharField(
verbose_name='Blood transfusion received?',
max_length=25,
choices=YES_NO)
units = models.IntegerField(verbose_name='If YES, no. of units',
validators=[MinValueValidator(1)],
null=True,
blank=True)
temperature = models.FloatField(verbose_name='Temperature',
null=True,
blank=True,
default=None)
weight = models.DecimalField(
verbose_name='Weight:',
validators=[MinValueValidator(20),
MaxValueValidator(150)],
decimal_places=1,
max_digits=4,
help_text='kg')
medicines = models.ManyToManyField(Day14Medication,
verbose_name='Medicine day 14:')
medicine_other = models.CharField(verbose_name='If other, please specify:',
max_length=50,
null=True,
blank=True)
significant_dx = models.CharField(
verbose_name='Other significant diagnoses since enrolment?',
max_length=25,
choices=YES_NO)
significant_dx_datetime = models.DateTimeField(
validators=[date_not_future], null=True, blank=True)
flucon_missed_doses = models.CharField(
verbose_name='Were any Fluconazole drug doses missed?',
max_length=25,
choices=YES_NO)
amphotericin_missed_doses = models.CharField(
verbose_name='Were any Amphotericin B drug doses missed?',
max_length=25,
choices=YES_NO)
other_significant_dx = models.CharField(
verbose_name='Other significant diagnosis since enrollment?',
max_length=5,
choices=YES_NO)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = 'Week 2'
verbose_name_plural = 'Week 2'