class CrfModelMixin(CrfNoManagerModelMixin):
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords(inherit=True)
class Meta(CrfNoManagerModelMixin.Meta):
abstract = True
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 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 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 Week16(CrfModelMixin):
patient_alive = models.CharField(verbose_name="Is the patient alive?",
max_length=15,
choices=YES_NO_UNKNOWN)
death_datetime = models.DateTimeField(
verbose_name="If deceased, date and time of death",
validators=[datetime_not_future],
null=True,
blank=True,
help_text="Leave blank if date is unknown.",
)
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,
default=NOT_APPLICABLE,
)
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 = "Week 16"
verbose_name_plural = "Week 16"
class CrfWithActionModelMixin(
CrfNoManagerModelMixin,
ActionNoManagersModelMixin,
TrackingModelMixin,
):
action_name = None
tracking_identifier_prefix = ""
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords(inherit=True)
class Meta(CrfNoManagerModelMixin.Meta):
abstract = True
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 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 BloodResultsModelMixin(
CrfNoManagerModelMixin, ActionModelMixin, TrackingModelMixin
):
action_name = None
results_abnormal = models.CharField(
verbose_name="Are any of the above results abnormal?",
choices=YES_NO,
max_length=25,
)
results_reportable = models.CharField(
verbose_name="If any results are abnormal, are results within grade III "
"or above?",
max_length=25,
choices=YES_NO_NA,
help_text=(
"If YES, this value will open Adverse Event Form.<br/><br/>"
"Note: On Day 1 only abnormal bloods should not be reported as adverse"
"events."
),
)
summary = models.TextField(null=True, blank=True)
on_site = CurrentSiteManager()
objects = CrfModelManager()
def save(self, *args, **kwargs):
# self.subject_identifier = self.subject_visit.subject_identifier
self.summary = "\n".join(self.get_summary())
super().save(*args, **kwargs)
def get_summary(self):
registered_subject = RegisteredSubject.objects.get(
subject_identifier=self.subject_visit.subject_identifier
)
opts = dict(
gender=registered_subject.gender,
dob=registered_subject.dob,
report_datetime=self.subject_visit.report_datetime,
)
summary = []
for field in [f.name for f in self._meta.fields]:
grp = site_reportables.get("meta").get(field)
value = getattr(self, field)
if value and grp:
units = getattr(self, f"{field}_units")
opts.update(units=units)
grade = grp.get_grade(value, **opts)
if grade and grade.grade:
summary.append(f"{field}: {grade.description}.")
elif not grade:
normal = grp.get_normal(value, **opts)
if not normal:
summary.append(f"{field}: {value} {units} is abnormal")
return summary
def get_action_item_reason(self):
return self.summary
@property
def abnormal(self):
return self.results_abnormal
@property
def reportable(self):
return self.results_reportable
class Meta(CrfNoManagerModelMixin.Meta):
abstract = True
class LumbarPunctureCsf(CrfModelMixin, BiosynexSemiQuantitativeCragMixin):
lp_datetime = models.DateTimeField(verbose_name="LP Date and Time",
validators=[datetime_not_future])
qc_requisition = models.ForeignKey(
SubjectRequisition,
on_delete=PROTECT,
related_name="qcrequisition",
verbose_name="QC Requisition",
null=True,
blank=True,
help_text=
"Start typing the requisition identifier or select one from this visit",
)
qc_assay_datetime = models.DateTimeField(
verbose_name="QC Result Report Date and Time",
validators=[datetime_not_future],
blank=True,
null=True,
)
csf_requisition = models.ForeignKey(
SubjectRequisition,
on_delete=PROTECT,
related_name="csfrequisition",
verbose_name="CSF Requisition",
null=True,
blank=True,
help_text=
"Start typing the requisition identifier or select one from this visit",
)
csf_assay_datetime = models.DateTimeField(
verbose_name="CSF Result Report Date and Time",
validators=[datetime_not_future],
null=True,
blank=True,
)
reason_for_lp = models.CharField(verbose_name="Reason for LP",
max_length=50,
choices=LP_REASON)
opening_pressure = models.IntegerField(
validators=[MinValueValidator(1),
MaxValueValidator(99)],
help_text=mark_safe("Units cm of H<sub>2</sub>O"),
)
closing_pressure = models.IntegerField(
blank=True,
null=True,
validators=[MinValueValidator(0),
MaxValueValidator(99)],
help_text=mark_safe("Units cm of H<sub>2</sub>O"),
)
csf_amount_removed = models.IntegerField(
blank=True,
null=True,
verbose_name="CSF amount removed ",
validators=[MinValueValidator(1)],
help_text="Units ml",
)
quantitative_culture = models.IntegerField(
blank=True,
null=True,
validators=[MinValueValidator(0),
MaxValueValidator(100_000_000)],
help_text="Units CFU/ml",
)
csf_culture = models.CharField(
verbose_name="Other organism (non-Cryptococcus)",
max_length=18,
choices=YES_NO_NOT_DONE_WAIT_RESULTS,
default=AWAITING_RESULTS,
help_text="Complete after getting the results.",
)
other_csf_culture = models.CharField(
verbose_name="If YES, specify organism:",
max_length=75,
blank=True,
null=True)
csf_wbc_cell_count = models.IntegerField(
verbose_name="Total CSF WBC cell count:",
help_text=mark_safe(f"acceptable units are {MM3_DISPLAY}"),
validators=[MinValueValidator(0)],
null=True,
blank=True,
)
differential_lymphocyte_count = models.IntegerField(
verbose_name="Differential lymphocyte cell count:",
validators=[MinValueValidator(0)],
blank=True,
null=True,
help_text=mark_safe(f"acceptable units are {MM3_DISPLAY} or %"),
)
differential_lymphocyte_unit = models.CharField(choices=MM3_PERC_UNITS,
max_length=6,
null=True,
blank=True)
differential_neutrophil_count = models.IntegerField(
verbose_name="Differential neutrophil cell count:",
validators=[MinValueValidator(0)],
blank=True,
null=True,
help_text=mark_safe(f"acceptable units are {MM3_DISPLAY} or %"),
)
differential_neutrophil_unit = models.CharField(choices=MM3_PERC_UNITS,
max_length=6,
null=True,
blank=True)
india_ink = models.CharField(max_length=15,
choices=POS_NEG,
null=True,
blank=True)
csf_glucose = models.DecimalField(
verbose_name="CSF glucose:",
decimal_places=1,
max_digits=3,
blank=True,
null=True,
help_text=
f"Units in {MILLIMOLES_PER_LITER} or {MILLIGRAMS_PER_DECILITER}",
)
csf_glucose_units = models.CharField(
verbose_name="CSF glucose units:",
max_length=6,
choices=MG_MMOL_UNITS,
blank=True,
null=True,
)
csf_protein = models.DecimalField(
verbose_name="CSF protein:",
decimal_places=2,
max_digits=4,
blank=True,
null=True,
help_text=f"Units in {GRAMS_PER_LITER}",
)
csf_cr_ag = models.CharField(verbose_name="CSF CrAg:",
max_length=15,
choices=POS_NEG,
blank=True,
null=True)
csf_cr_ag_lfa = models.CharField(
verbose_name="CSF CrAg done by IMMY CrAg LFA:",
max_length=5,
choices=YES_NO_NA,
default=NOT_APPLICABLE,
)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = "Lumbar Puncture/Cerebrospinal Fluid"
verbose_name_plural = "Lumbar Puncture/Cerebrospinal Fluid"
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,
)
days_hospitalized = models.DecimalField(
verbose_name=("Over the ten weeks spent in the study how "
"many days did the patient spend in hospital?"),
decimal_places=3,
max_digits=5,
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_transfusions = models.CharField(
verbose_name=
"Has the patient had any blood transfusions since week two? ",
max_length=5,
choices=YES_NO,
null=True,
)
blood_transfusions_units = models.DecimalField(
verbose_name="If YES, no. of units? ",
decimal_places=3,
max_digits=5,
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 PatientHistory(CrfModelMixin):
symptom = models.ManyToManyField(
Symptom,
blank=True,
related_name="symptoms",
verbose_name="What are your current symptoms?",
)
headache_duration = models.IntegerField(
verbose_name="If headache, how many days did it last?",
validators=[MinValueValidator(1)],
null=True,
blank=True,
)
visual_loss_duration = models.IntegerField(
verbose_name="If visual loss, how many days did it last?",
validators=[MinValueValidator(1)],
null=True,
blank=True,
)
tb_history = models.CharField(
verbose_name="Previous medical history of Tuberculosis?",
max_length=5,
choices=YES_NO,
)
tb_site = models.CharField(
verbose_name="If YES, site of TB?",
max_length=15,
choices=TB_SITE,
default=NOT_APPLICABLE,
)
tb_treatment = models.CharField(
verbose_name="Are you currently taking TB treatment?",
max_length=5,
choices=YES_NO,
)
taking_rifampicin = models.CharField(
verbose_name="If YES, are you currently also taking Rifampicin?",
max_length=5,
choices=YES_NO_NA,
default=NOT_APPLICABLE,
)
rifampicin_started_date = models.DateField(
verbose_name="If YES, when did you first start taking Rifampicin?",
validators=[date_not_future],
null=True,
blank=True,
)
new_hiv_diagnosis = models.CharField(
verbose_name="Is this a new HIV diagnosis?", max_length=5, choices=YES_NO
)
taking_arv = models.CharField(
verbose_name="If NO, has the patient ever been on ART?",
max_length=5,
choices=YES_NO_NA,
default=NOT_APPLICABLE,
)
# retired
first_arv_regimen = models.CharField(
verbose_name="If YES, which drugs were prescribed for their first ART regimen?",
max_length=50,
choices=FIRST_ARV_REGIMEN_RETIRED,
default=QUESTION_RETIRED,
editable=False,
)
# retired
first_arv_regimen_other = OtherCharField(editable=False)
# retired
first_line_choice = models.CharField(
verbose_name="If first line:",
max_length=25,
choices=FIRST_LINE_REGIMEN_RETIRED,
default=QUESTION_RETIRED,
editable=False,
)
initial_arv_date = models.DateField(
verbose_name=mark_safe(
"If YES, when did the patient <u>start</u> ART for the first time."
),
validators=[date_not_future],
null=True,
blank=True,
)
initial_arv_date_estimated = IsDateEstimatedFieldNa(
verbose_name="If YES, is this ART date estimated?", default=NOT_APPLICABLE
)
initial_arv_regimen = models.ManyToManyField(
ArvRegimens,
verbose_name=mark_safe(
"If YES, which drugs were prescribed for their first ART regimen?"
),
related_name="initial_arv",
)
initial_arv_regimen_other = OtherCharField()
has_switched_regimen = models.CharField(
verbose_name="Has the patient ever switched ART regimen?",
max_length=5,
choices=YES_NO_NA,
default=NOT_APPLICABLE,
)
current_arv_date = models.DateField(
verbose_name=mark_safe(
"If YES, when was their <u>current or most recent</u> "
"ART regimen started?"
),
validators=[date_not_future],
null=True,
blank=True,
)
current_arv_date_estimated = IsDateEstimatedFieldNa(
verbose_name="If YES, is this ART date estimated?", default=NOT_APPLICABLE
)
current_arv_regimen = models.ManyToManyField(
ArvRegimens,
verbose_name=mark_safe(
"If YES, what is their current or most recent ART regimen?"
),
related_name="current_arv",
)
current_arv_regimen_other = OtherCharField()
current_arv_is_defaulted = models.CharField(
verbose_name=mark_safe(
"Has the patient <u>now</u> defaulted from their ART regimen?"
),
max_length=5,
choices=YES_NO_NA,
default=NOT_APPLICABLE,
help_text="'DEFAULTED' means no ART for at least one month.",
)
current_arv_defaulted_date = models.DateField(
verbose_name=mark_safe(
"If the patient has DEFAULTED, on what date did they default "
"from their <u>most recent</u> ART regimen?"
),
validators=[date_not_future],
null=True,
blank=True,
)
current_arv_defaulted_date_estimated = IsDateEstimatedFieldNa(
verbose_name="If DEFAULTED, is this date estimated?", default=NOT_APPLICABLE
)
current_arv_is_adherent = models.CharField(
verbose_name=mark_safe(
"If the patient is currently on ART, are they ADHERENT to "
"their <u>current</u> ART regimen?"
),
max_length=5,
choices=YES_NO_NA,
default=NOT_APPLICABLE,
)
current_arv_tablets_missed = models.IntegerField(
verbose_name=("If not ADHERENT, how many doses missed in the last month?"),
validators=[MinValueValidator(0), MaxValueValidator(31)],
null=True,
blank=True,
)
current_arv_decision = models.CharField(
verbose_name=mark_safe(
"What decision was made at admission regarding their "
"<u>current</u> ART regimen?"
),
max_length=25,
choices=ARV_DECISION,
default=NOT_APPLICABLE,
)
# retired
second_arv_regimen = models.CharField(
verbose_name="Second line ARV regimen",
max_length=50,
choices=SECOND_ARV_REGIMEN_RETIRED,
default=QUESTION_RETIRED,
editable=False,
)
# retired
second_arv_regimen_other = OtherCharField(editable=False)
# retired
patient_adherence = models.CharField(
verbose_name="Is the patient reportedly adherent?",
max_length=25,
choices=YES_NO_NA_RETIRED,
default=QUESTION_RETIRED,
editable=False,
)
# retired
last_dose = models.IntegerField(
verbose_name=(
"If no tablets taken this month, how many months "
"since the last dose taken?"
),
validators=[MinValueValidator(0)],
null=True,
blank=True,
editable=False,
)
last_viral_load = models.DecimalField(
verbose_name="Last Viral Load, if known?",
decimal_places=3,
max_digits=10,
null=True,
blank=True,
help_text="copies/mL",
)
viral_load_date = models.DateField(
verbose_name="Viral Load date",
validators=[date_not_future],
null=True,
blank=True,
)
vl_date_estimated = IsDateEstimatedFieldNa(
verbose_name=("Is the subject's Viral Load date estimated?"),
default=NOT_APPLICABLE,
)
last_cd4 = models.IntegerField(
verbose_name="Last CD4, if known?",
validators=[MinValueValidator(1), MaxValueValidator(2500)],
null=True,
blank=True,
help_text=mark_safe("acceptable units are mm<sup>3</sup>"),
)
cd4_date = models.DateField(
verbose_name="CD4 date", validators=[date_not_future], null=True, blank=True
)
cd4_date_estimated = IsDateEstimatedFieldNa(
verbose_name=("Is the subject's CD4 date estimated?"), default=NOT_APPLICABLE
)
temp = models.DecimalField(
verbose_name="Temperature:",
validators=[MinValueValidator(30), MaxValueValidator(45)],
decimal_places=1,
max_digits=3,
help_text="in degrees Celcius",
)
heart_rate = models.IntegerField(
verbose_name="Heart rate:",
validators=[MinValueValidator(30), MaxValueValidator(200)],
help_text="bpm",
)
sys_blood_pressure = models.IntegerField(
verbose_name="Blood pressure: systolic",
validators=[MinValueValidator(50), MaxValueValidator(220)],
help_text="in mm. format SYS, e.g. 120",
)
dia_blood_pressure = models.IntegerField(
verbose_name="Blood pressure: diastolic",
validators=[MinValueValidator(20), MaxValueValidator(150)],
help_text="in Hg. format DIA, e.g. 80",
)
respiratory_rate = models.IntegerField(
verbose_name="Respiratory rate:",
validators=[MinValueValidator(6), MaxValueValidator(50)],
help_text="breaths/min",
)
weight = models.DecimalField(
verbose_name="Weight:",
validators=[MinValueValidator(20), MaxValueValidator(150)],
decimal_places=1,
max_digits=4,
help_text="kg",
)
weight_determination = models.CharField(
verbose_name="Is weight estimated or measured?",
max_length=15,
choices=WEIGHT_DETERMINATION,
)
glasgow_coma_score = models.IntegerField(
verbose_name="Glasgow Coma Score:",
validators=[MinValueValidator(3), MaxValueValidator(15)],
help_text="/15",
)
neurological = models.ManyToManyField(Neurological, blank=True)
neurological_other = OtherCharField(
verbose_name='If "Other CN palsy", specify',
max_length=250,
blank=True,
null=True,
)
focal_neurologic_deficit = models.TextField(
verbose_name='If "Focal neurologic deficit" chosen, please specify details:',
null=True,
blank=True,
)
visual_acuity_day = models.DateField(
verbose_name="Study day visual acuity recorded?",
validators=[date_not_future],
null=True,
blank=True,
)
left_acuity = models.DecimalField(
verbose_name="Visual acuity left eye:",
decimal_places=3,
max_digits=4,
null=True,
blank=True,
)
right_acuity = models.DecimalField(
verbose_name="Visual acuity right eye",
decimal_places=3,
max_digits=4,
null=True,
blank=True,
)
ecog_score = models.CharField(
verbose_name="ECOG Disability Score", max_length=15, choices=ECOG_SCORE
)
ecog_score_value = models.CharField(
verbose_name="ECOG Score", max_length=15, choices=ECOG_SCORE
)
lung_exam = models.CharField(
verbose_name="Abnormal lung exam:", max_length=5, choices=YES_NO
)
cryptococcal_lesions = models.CharField(
verbose_name="Cryptococcal related skin lesions:", max_length=5, choices=YES_NO
)
specify_medications = models.ManyToManyField(Medication, blank=True)
specify_medications_other = models.TextField(max_length=150, blank=True, null=True)
previous_oi = models.CharField(
verbose_name="Previous opportunistic infection other than TB?",
max_length=5,
choices=YES_NO,
)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = "Patient's History"
verbose_name_plural = "Patient's History"
class Radiology(CrfModelMixin):
cxr_done = models.CharField(verbose_name="Is CXR done",
choices=YES_NO,
max_length=5)
cxr_date = models.DateField(
verbose_name="If yes, when was CXR done",
validators=[date_not_future],
blank=True,
null=True,
)
cxr_type = models.ManyToManyField(CXRType,
verbose_name="If YES, result",
blank=True)
infiltrate_location = models.ManyToManyField(
InfiltrateLocation,
verbose_name="If infiltrates, specify location",
blank=True)
cxr_description = models.TextField(verbose_name="Description/Comments",
blank=True,
null=True)
ct_performed = models.CharField(
verbose_name="CT/MRI brain scan performed?",
choices=YES_NO,
max_length=5)
ct_performed_date = models.DateTimeField(
verbose_name="Date CT performed",
validators=[datetime_not_future],
editable=True,
blank=True,
null=True,
)
scanned_with_contrast = models.CharField(
verbose_name="CT/MRI brain scan performed with contrast?",
blank=False,
choices=YES_NO_NA,
default=NOT_APPLICABLE,
max_length=5,
null=False,
)
brain_imaging_reason = models.CharField(
verbose_name="Reason for brain imaging",
blank=False,
choices=BRAIN_IMAGINING_REASON,
default=NOT_APPLICABLE,
max_length=25,
null=True,
)
brain_imaging_reason_other = models.CharField(
verbose_name="If other, please specify",
blank=True,
max_length=50,
null=True)
are_results_abnormal = models.CharField(blank=False,
choices=YES_NO_NA,
default=NOT_APPLICABLE,
null=False,
max_length=5)
abnormal_results_reason = models.ManyToManyField(
AbnormalResultsReason,
verbose_name="If results are abnormal, what is the reason?",
blank=True,
)
abnormal_results_reason_other = models.CharField(
verbose_name="If other, please specify reason",
blank=True,
max_length=50,
null=True,
)
infarcts_location = models.CharField(
verbose_name=
"If results are abnormal because of Infarcts, what is the location?",
blank=True,
max_length=50,
null=True,
)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = "Radiology"
verbose_name_plural = "Radiology"
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 MedicalExpenses(CrfModelMixin):
info_source = models.CharField(
verbose_name="What is the main source of this information?",
max_length=25,
choices=PATIENT_REL,
)
currency = models.CharField(verbose_name="Which currency do you use?",
max_length=20,
choices=CURRENCY)
food_spend = models.DecimalField(
verbose_name="How much do you/your family spend on food in a week?",
decimal_places=2,
max_digits=15,
null=True,
validators=[MinValueValidator(0)],
)
utilities_spend = models.DecimalField(
verbose_name=
"How much do you/your family spent on rent and utilities a month?",
decimal_places=2,
max_digits=15,
null=True,
validators=[MinValueValidator(0)],
)
item_spend = models.DecimalField(
verbose_name=
("How much have you spent on large items (e.g. furniture, electrical "
"items, cars) in the last year?"),
decimal_places=2,
max_digits=15,
null=True,
validators=[MinValueValidator(0)],
)
subject_spent_last_4wks = models.DecimalField(
verbose_name=("Over the last 4/10 weeks, how much have you "
"spent on activities relating to your health?"),
decimal_places=2,
max_digits=15,
null=True,
validators=[MinValueValidator(0)],
help_text=(
"On D1 record data for the four weeks prior to recruitment. "
"On W10 record data for the ten weeks since recruitment."),
)
someone_spent_last_4wks = models.DecimalField(
verbose_name=("Over the last 4/10 weeks, how much has someone else "
"spent on activities relating to your health?"),
decimal_places=2,
max_digits=15,
null=True,
validators=[MinValueValidator(0)],
help_text=(
"On D1 record data for the four weeks prior to recruitment. "
"On W10 record data for the ten weeks since recruitment."),
)
total_spent_last_4wks = models.DecimalField(
verbose_name=
("How much in total has been spent on your healthcare in the last 4/10 weeks?"
),
decimal_places=2,
max_digits=16,
null=True,
validators=[MinValueValidator(0)],
help_text=(
"On D1 record data for the four weeks prior to recruitment. "
"On W10 record data for the ten weeks since recruitment."),
)
care_before_hospital = models.CharField(
verbose_name=(
"Have you received any treatment or care "
"for your present condition, before coming to the hospital?"),
max_length=5,
choices=YES_NO,
help_text="If YES, please complete medical expenses part 2",
)
duration_present_condition = models.IntegerField(
verbose_name="How long have you been sick with your current condition?",
validators=[MinValueValidator(0)],
null=True,
help_text="in days",
)
activities_missed = models.CharField(
verbose_name=("What would you have been doing if you were not sick "
"with your present condition"),
max_length=25,
null=True,
choices=ACTIVITIES_MISSED,
)
activities_missed_other = OtherCharField(max_length=25,
blank=True,
null=True)
time_off_work = models.DecimalField(
verbose_name="How much time did you take off work?",
max_digits=4,
decimal_places=1,
validators=[MinValueValidator(0)],
blank=True,
null=True,
help_text="in days",
)
carer_time_off = models.IntegerField(
verbose_name=("How much time did a caring family member "
"take to accompany you to the hospital?"),
validators=[MinValueValidator(0)],
blank=True,
null=True,
help_text="in days",
)
loss_of_earnings = models.CharField(
verbose_name="Did you lose earnings as a result?",
max_length=5,
choices=YES_NO_NA,
)
earnings_lost_amount = models.DecimalField(
verbose_name="How much did you lose?",
decimal_places=2,
max_digits=15,
validators=[MinValueValidator(0)],
null=True,
blank=True,
)
form_of_transport = models.CharField(
verbose_name="Which form of transport did you take to get here today?",
max_length=25,
default=NOT_APPLICABLE,
choices=TRANSPORT,
)
transport_fare = models.DecimalField(
verbose_name="How much did you spend on the transport (in total)?",
decimal_places=2,
max_digits=15,
validators=[MinValueValidator(0)],
blank=True,
null=True,
)
travel_time = models.CharField(
verbose_name="How long did it take you to reach there?",
validators=[hm_validator],
max_length=8,
help_text="Specify as hours:minutes (format HH:MM)",
null=True,
blank=True,
)
loans = models.CharField(
verbose_name="Did you take out any loans to pay for your healthcare?",
max_length=5,
choices=YES_NO,
)
sold_anything = models.CharField(
verbose_name="Did you sell anything to pay for your healthcare?",
max_length=5,
choices=YES_NO,
)
private_healthcare = models.CharField(
verbose_name="Do you have private healthcare insurance?",
max_length=5,
choices=YES_NO,
)
healthcare_insurance = models.CharField(
verbose_name="Did you use it to help pay for your healthcare?",
max_length=5,
choices=YES_NO_NA,
)
welfare = models.CharField(
verbose_name="Do you receive any welfare or social service support?",
max_length=5,
choices=YES_NO,
)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = "Health Economics: Medical Expenses"
verbose_name_plural = "Health Economics: Medical Expenses"
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'
class LumbarPunctureCsf(CrfModelMixin, BiosynexSemiQuantitativeCragMixin):
lp_datetime = models.DateTimeField(verbose_name='LP Date and Time',
validators=[datetime_not_future])
qc_requisition = models.ForeignKey(
SubjectRequisition,
on_delete=PROTECT,
related_name='qcrequisition',
verbose_name='QC Requisition',
null=True,
blank=True,
help_text=
'Start typing the requisition identifier or select one from this visit'
)
qc_assay_datetime = models.DateTimeField(
verbose_name='QC Result Report Date and Time',
validators=[datetime_not_future],
blank=True,
null=True)
csf_requisition = models.ForeignKey(
SubjectRequisition,
on_delete=PROTECT,
related_name='csfrequisition',
verbose_name='CSF Requisition',
null=True,
blank=True,
help_text=
'Start typing the requisition identifier or select one from this visit'
)
csf_assay_datetime = models.DateTimeField(
verbose_name='CSF Result Report Date and Time',
validators=[datetime_not_future],
null=True,
blank=True)
reason_for_lp = models.CharField(verbose_name='Reason for LP',
max_length=50,
choices=LP_REASON)
opening_pressure = models.IntegerField(
validators=[MinValueValidator(1),
MaxValueValidator(99)],
help_text=mark_safe('Units cm of H<sub>2</sub>O'))
closing_pressure = models.IntegerField(
validators=[MinValueValidator(0),
MaxValueValidator(99)],
help_text=mark_safe('Units cm of H<sub>2</sub>O'))
csf_amount_removed = models.IntegerField(
blank=True,
null=True,
verbose_name='CSF amount removed ',
validators=[MinValueValidator(1)],
help_text='Units ml')
quantitative_culture = models.IntegerField(
blank=True,
null=True,
validators=[MinValueValidator(0),
MaxValueValidator(9999999)],
help_text='Units CFU/ml')
csf_culture = models.CharField(
verbose_name='Other organism (non-Cryptococcus)',
max_length=18,
choices=YES_NO_NOT_DONE_WAIT_RESULTS,
default=AWAITING_RESULTS,
help_text='Complete after getting the results.')
other_csf_culture = models.CharField(
verbose_name='If YES, specify organism:',
max_length=75,
blank=True,
null=True)
csf_wbc_cell_count = models.IntegerField(
verbose_name='Total CSF WBC cell count:',
help_text=mark_safe('acceptable units are mm<sup>3</sup>'),
validators=[MinValueValidator(0),
MaxValueValidator(999)],
null=True,
blank=True)
differential_lymphocyte_count = models.IntegerField(
verbose_name='Differential lymphocyte cell count:',
validators=[MinValueValidator(0),
MaxValueValidator(999)],
blank=True,
null=True,
help_text=mark_safe('acceptable units are mm<sup>3</sup> or %'))
differential_lymphocyte_unit = models.CharField(choices=MM3_PERC_UNITS,
max_length=6,
null=True,
blank=True)
differential_neutrophil_count = models.IntegerField(
verbose_name='Differential neutrophil cell count:',
validators=[MinValueValidator(0),
MaxValueValidator(999)],
blank=True,
null=True,
help_text=mark_safe('acceptable units are mm<sup>3</sup> or %'))
differential_neutrophil_unit = models.CharField(choices=MM3_PERC_UNITS,
max_length=6,
null=True,
blank=True)
india_ink = models.CharField(
max_length=15,
choices=POS_NEG,
null=True,
)
csf_glucose = models.DecimalField(verbose_name='CSF glucose:',
decimal_places=1,
max_digits=3,
blank=True,
null=True,
help_text='Units in mmol/L or mg/dL')
csf_glucose_units = models.CharField(
verbose_name='CSF glucose units:',
max_length=6,
choices=MG_MMOL_UNITS,
blank=True,
null=True,
)
csf_protein = models.DecimalField(verbose_name='CSF protein:',
decimal_places=2,
max_digits=4,
blank=True,
null=True,
help_text='Units in g/dL')
csf_cr_ag = models.CharField(verbose_name='CSF CrAg:',
max_length=15,
choices=POS_NEG,
null=True)
csf_cr_ag_lfa = models.CharField(
verbose_name='CSF CrAg done by CSF CrAg LFA:',
max_length=5,
choices=YES_NO_NA,
default=NOT_APPLICABLE)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = 'Lumbar Puncture/Cerebrospinal Fluid'
verbose_name_plural = 'Lumbar Puncture/Cerebrospinal Fluid'
class BloodResult(CrfModelMixin, ActionItemModelMixin,
TrackingIdentifierModelMixin,
BiosynexSemiQuantitativeCragMixin):
action_cls = BloodResultAction
tracking_identifier_prefix = 'BR'
ft_fields = [
'creatinine', 'urea', 'sodium', 'potassium', 'magnesium', 'alt'
]
cbc_fields = ['haemoglobin', 'wbc', 'neutrophil', 'platelets']
ft_requisition = models.ForeignKey(
SubjectRequisition,
on_delete=PROTECT,
related_name='ft',
verbose_name='Requisition',
null=True,
blank=True,
help_text=
'Start typing the requisition identifier or select one from this visit'
)
ft_assay_datetime = models.DateTimeField(
verbose_name='Result Report Date and Time',
validators=[datetime_not_future],
null=True,
blank=True)
cbc_requisition = models.ForeignKey(
SubjectRequisition,
on_delete=PROTECT,
related_name='cbc',
verbose_name='Requisition',
null=True,
blank=True,
help_text=
'Start typing the requisition identifier or select one from this visit'
)
cbc_assay_datetime = models.DateTimeField(
verbose_name='Result Report Date and Time',
validators=[datetime_not_future],
null=True,
blank=True)
cd4_requisition = models.ForeignKey(
SubjectRequisition,
on_delete=PROTECT,
related_name='cd4',
verbose_name='Requisition',
null=True,
blank=True,
help_text=
'Start typing the requisition identifier or select one from this visit'
)
cd4_assay_datetime = models.DateTimeField(
verbose_name='Result Report Date and Time',
validators=[datetime_not_future],
null=True,
blank=True)
vl_requisition = models.ForeignKey(
SubjectRequisition,
on_delete=PROTECT,
related_name='vl',
verbose_name='Requisition',
null=True,
blank=True,
help_text=
'Start typing the requisition identifier or select one from this visit'
)
vl_assay_datetime = models.DateTimeField(
verbose_name='Result Report Date and Time',
validators=[datetime_not_future],
null=True,
blank=True)
wbc = models.DecimalField(verbose_name='WBC',
decimal_places=1,
max_digits=6,
null=True,
blank=True)
wbc_units = models.CharField(verbose_name='units',
max_length=10,
choices=((TEN_X_9_PER_LITER,
TEN_X_9_PER_LITER), ),
null=True,
blank=True)
wbc_abnormal = models.CharField(verbose_name='abnormal',
choices=YES_NO,
max_length=25,
null=True,
blank=True)
wbc_reportable = models.CharField(verbose_name='reportable',
choices=REPORTABLE,
max_length=25,
null=True,
blank=True)
platelets = models.IntegerField(
validators=[MinValueValidator(1),
MaxValueValidator(9999)],
null=True,
blank=True)
platelets_units = models.CharField(verbose_name='units',
max_length=10,
choices=((TEN_X_9_PER_LITER,
TEN_X_9_PER_LITER), ),
null=True,
blank=True)
platelets_abnormal = models.CharField(verbose_name='abnormal',
choices=YES_NO,
max_length=25,
null=True,
blank=True)
platelets_reportable = models.CharField(verbose_name='reportable',
choices=REPORTABLE,
max_length=25,
null=True,
blank=True)
haemoglobin = models.DecimalField(decimal_places=1,
max_digits=6,
null=True,
blank=True)
haemoglobin_units = models.CharField(verbose_name='units',
max_length=10,
choices=((GRAMS_PER_DECILITER,
GRAMS_PER_DECILITER), ),
null=True,
blank=True)
haemoglobin_abnormal = models.CharField(verbose_name='abnormal',
choices=YES_NO,
max_length=25,
null=True,
blank=True)
haemoglobin_reportable = models.CharField(verbose_name='reportable',
choices=REPORTABLE,
max_length=25,
null=True,
blank=True)
neutrophil = models.DecimalField(decimal_places=2,
max_digits=6,
null=True,
blank=True)
neutrophil_units = models.CharField(verbose_name='units',
max_length=10,
choices=((TEN_X_9_PER_LITER,
TEN_X_9_PER_LITER), ),
null=True,
blank=True)
neutrophil_abnormal = models.CharField(verbose_name='abnormal',
choices=YES_NO,
max_length=25,
null=True,
blank=True)
neutrophil_reportable = models.CharField(verbose_name='reportable',
choices=REPORTABLE,
max_length=25,
null=True,
blank=True)
creatinine = models.DecimalField(decimal_places=2,
max_digits=6,
null=True,
blank=True)
creatinine_units = models.CharField(verbose_name='units',
choices=MG_UMOL_UNITS,
max_length=25,
null=True,
blank=True)
creatinine_abnormal = models.CharField(verbose_name='abnormal',
choices=YES_NO,
max_length=25,
null=True,
blank=True)
creatinine_reportable = models.CharField(verbose_name='reportable',
choices=REPORTABLE,
max_length=25,
null=True,
blank=True)
sodium = models.IntegerField(
validators=[MinValueValidator(1),
MaxValueValidator(999)],
null=True,
blank=True)
sodium_units = models.CharField(verbose_name='units',
max_length=10,
choices=((MILLIMOLES_PER_LITER,
MILLIMOLES_PER_LITER), ),
null=True,
blank=True)
sodium_abnormal = models.CharField(verbose_name='abnormal',
choices=YES_NO,
max_length=25,
null=True,
blank=True)
sodium_reportable = models.CharField(verbose_name='reportable',
choices=REPORTABLE,
max_length=25,
null=True,
blank=True)
potassium = models.DecimalField(decimal_places=1,
max_digits=2,
null=True,
blank=True)
potassium_units = models.CharField(verbose_name='units',
max_length=10,
choices=((MILLIMOLES_PER_LITER,
MILLIMOLES_PER_LITER), ),
null=True,
blank=True)
potassium_abnormal = models.CharField(
verbose_name='abnormal',
choices=YES_NO,
# default=NO,
max_length=25,
null=True,
blank=True)
potassium_reportable = models.CharField(
verbose_name='reportable',
choices=REPORTABLE,
# default=NOT_APPLICABLE,
max_length=25,
null=True,
blank=True)
magnesium = models.DecimalField(decimal_places=2,
max_digits=6,
null=True,
blank=True)
magnesium_units = models.CharField(verbose_name='units',
choices=MG_MMOL_UNITS,
null=True,
blank=True,
max_length=25)
magnesium_abnormal = models.CharField(verbose_name='abnormal',
choices=YES_NO,
null=True,
blank=True,
max_length=25)
magnesium_reportable = models.CharField(verbose_name='reportable',
choices=REPORTABLE,
null=True,
blank=True,
max_length=25)
alt = models.IntegerField(
validators=[MinValueValidator(1),
MaxValueValidator(2999)],
verbose_name='ALT',
null=True,
blank=True)
alt_units = models.CharField(verbose_name='units',
max_length=10,
choices=((IU_LITER, IU_LITER), ),
null=True,
blank=True)
alt_abnormal = models.CharField(verbose_name='abnormal',
choices=YES_NO,
max_length=25,
null=True,
blank=True)
alt_reportable = models.CharField(verbose_name='reportable',
choices=REPORTABLE,
max_length=25,
null=True,
blank=True)
urea = models.DecimalField(decimal_places=2,
max_digits=6,
null=True,
blank=True)
urea_units = models.CharField(verbose_name='units',
choices=MG_MMOL_UNITS,
max_length=25,
null=True,
blank=True)
urea_abnormal = models.CharField(
verbose_name='abnormal',
choices=YES_NO,
# default=NO,
max_length=25,
null=True,
blank=True)
urea_reportable = models.CharField(verbose_name='reportable',
choices=REPORTABLE,
max_length=25,
null=True,
blank=True)
cd4 = models.IntegerField(
verbose_name='abs CD4',
validators=[MinValueValidator(1),
MaxValueValidator(999)],
blank=True,
null=True)
cd4_units = models.CharField(verbose_name='units',
max_length=10,
choices=((CELLS_PER_MILLIMETER_CUBED,
CELLS_PER_MILLIMETER_CUBED), ),
null=True,
blank=True)
cd4_abnormal = models.CharField(verbose_name='abnormal',
choices=YES_NO,
max_length=25,
null=True,
blank=True)
cd4_reportable = models.CharField(verbose_name='reportable',
choices=REPORTABLE,
max_length=25,
null=True,
blank=True)
vl = models.FloatField(verbose_name='Viral Load',
validators=[MinValueValidator(0.0)],
blank=True,
null=True)
vl_units = models.CharField(verbose_name='units',
max_length=10,
choices=((COPIES_PER_MILLILITER,
COPIES_PER_MILLILITER), ),
null=True,
blank=True)
vl_abnormal = models.CharField(verbose_name='abnormal',
choices=YES_NO,
max_length=25,
null=True,
blank=True)
vl_reportable = models.CharField(verbose_name='reportable',
choices=REPORTABLE,
max_length=25,
null=True,
blank=True)
results_abnormal = models.CharField(
verbose_name='Are any of the above results abnormal?',
choices=YES_NO,
max_length=25)
results_reportable = models.CharField(
verbose_name='If any results are abnormal, are results within grade III '
'or above?',
max_length=25,
choices=YES_NO_NA,
help_text=
('If YES, this value will open Adverse Event Form.<br/><br/>'
'Note: On Day 1 only abnormal bloods should not be reported as adverse'
'events.'))
summary = models.TextField(null=True, blank=True)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
def save(self, *args, **kwargs):
self.summary = '\n'.join(self.get_summary())
super().save(*args, **kwargs)
def get_summary(self):
registered_subject = RegisteredSubject.objects.get(
subject_identifier=self.subject_visit.subject_identifier)
opts = dict(gender=registered_subject.gender,
dob=registered_subject.dob,
report_datetime=self.subject_visit.report_datetime)
summary = []
for field in [f.name for f in self._meta.fields]:
value = getattr(self, field)
grp = site_reportables.get('ambition').get(field)
if value and grp:
units = getattr(self, f'{field}_units')
opts.update(units=units)
grade = grp.get_grade(value, **opts)
if grade and grade.grade:
summary.append(f'{field}: {grade.description}.')
elif not grade:
normal = grp.get_normal(value, **opts)
if not normal:
summary.append(f'{field}: {value} {units} is abnormal')
return summary
@property
def action_item_reason(self):
return self.summary
@property
def abnormal(self):
return self.results_abnormal
@property
def reportable(self):
return self.results_reportable
class Meta(CrfModelMixin.Meta):
verbose_name = 'Blood Result'
verbose_name_plural = 'Blood Results'
class PatientHistory(CrfModelMixin):
symptom = models.ManyToManyField(
Symptom,
blank=True,
related_name='symptoms',
verbose_name='What are your current symptoms?')
headache_duration = models.IntegerField(
verbose_name='If headache, how many days did it last?',
validators=[MinValueValidator(1)],
null=True,
blank=True)
visual_loss_duration = models.IntegerField(
verbose_name='If visual loss, how many days did it last?',
validators=[MinValueValidator(1)],
null=True,
blank=True)
tb_history = models.CharField(
verbose_name='Previous medical history of Tuberculosis?',
max_length=5,
choices=YES_NO)
tb_site = models.CharField(verbose_name='If YES, site of TB?',
max_length=15,
choices=TB_SITE,
default=NOT_APPLICABLE)
tb_treatment = models.CharField(
verbose_name='Are you currently taking TB treatment?',
max_length=5,
choices=YES_NO)
taking_rifampicin = models.CharField(
verbose_name='If YES, are you currently also taking Rifampicin?',
max_length=5,
choices=YES_NO_NA,
default=NOT_APPLICABLE)
rifampicin_started_date = models.DateField(
verbose_name='If YES, when did you first start taking Rifampicin?',
validators=[date_not_future],
null=True,
blank=True)
new_hiv_diagnosis = models.CharField(
verbose_name='Is this a new HIV diagnosis?',
max_length=5,
choices=YES_NO)
taking_arv = models.CharField(verbose_name='If NO, already taking ARVs?',
max_length=5,
choices=YES_NO_NA,
default=NOT_APPLICABLE)
arv_date = models.DateField(verbose_name='If YES, date ARVs were started.',
validators=[date_not_future],
null=True,
blank=True)
arv_date_estimated = IsDateEstimatedFieldNa(
verbose_name=("Is the subject's ARV date estimated?"),
default=NOT_APPLICABLE)
first_arv_regimen = models.CharField(
verbose_name='Drug used in first line ARV regimen',
max_length=50,
choices=FIRST_ARV_REGIMEN,
default=NOT_APPLICABLE)
first_arv_regimen_other = OtherCharField()
second_arv_regimen = models.CharField(
verbose_name='Second line ARV regimen',
max_length=50,
choices=SECOND_ARV_REGIMEN,
default=NOT_APPLICABLE)
second_arv_regimen_other = OtherCharField()
first_line_choice = models.CharField(verbose_name='If first line:',
max_length=5,
choices=FIRST_LINE_REGIMEN,
default=NOT_APPLICABLE)
patient_adherence = models.CharField(
verbose_name='Is the patient reportedly adherent?',
max_length=5,
choices=YES_NO_NA,
default=NOT_APPLICABLE)
tablets_missed = models.IntegerField(
verbose_name=('If not adherent, how many tablets missed in '
'the last month?'),
validators=[MinValueValidator(0),
MaxValueValidator(31)],
null=True,
blank=True)
last_dose = models.IntegerField(
verbose_name=('If no tablets taken this month, how many months '
'since the last dose taken?'),
validators=[MinValueValidator(0)],
null=True,
blank=True)
last_viral_load = models.DecimalField(
verbose_name='Last Viral Load, if known?',
decimal_places=3,
max_digits=10,
null=True,
blank=True,
help_text='copies/mL')
viral_load_date = models.DateField(verbose_name='Viral Load date',
validators=[date_not_future],
null=True,
blank=True)
vl_date_estimated = IsDateEstimatedFieldNa(
verbose_name=("Is the subject's Viral Load date estimated?"),
default=NOT_APPLICABLE)
last_cd4 = models.IntegerField(
verbose_name='Last CD4, if known?',
validators=[MinValueValidator(1),
MaxValueValidator(2500)],
null=True,
blank=True,
help_text=mark_safe('acceptable units are mm<sup>3</sup>'))
cd4_date = models.DateField(verbose_name='CD4 date',
validators=[date_not_future],
null=True,
blank=True)
cd4_date_estimated = IsDateEstimatedFieldNa(
verbose_name=("Is the subject's CD4 date estimated?"),
default=NOT_APPLICABLE)
temp = models.DecimalField(
verbose_name='Temperature:',
validators=[MinValueValidator(30),
MaxValueValidator(45)],
decimal_places=1,
max_digits=3,
help_text='in degrees Celcius')
heart_rate = models.IntegerField(
verbose_name='Heart rate:',
validators=[MinValueValidator(30),
MaxValueValidator(200)],
help_text='bpm')
sys_blood_pressure = models.IntegerField(
verbose_name='Blood pressure: systolic',
validators=[MinValueValidator(50),
MaxValueValidator(220)],
help_text='in mm. format SYS, e.g. 120')
dia_blood_pressure = models.IntegerField(
verbose_name='Blood pressure: diastolic',
validators=[MinValueValidator(20),
MaxValueValidator(150)],
help_text='in Hg. format DIA, e.g. 80')
respiratory_rate = models.IntegerField(
verbose_name='Respiratory rate:',
validators=[MinValueValidator(6),
MaxValueValidator(50)],
help_text='breaths/min')
weight = models.DecimalField(
verbose_name='Weight:',
validators=[MinValueValidator(20),
MaxValueValidator(150)],
decimal_places=1,
max_digits=4,
help_text='kg')
weight_determination = models.CharField(
verbose_name='Is weight estimated or measured?',
max_length=15,
choices=WEIGHT_DETERMINATION)
glasgow_coma_score = models.IntegerField(
verbose_name='Glasgow Coma Score:',
validators=[MinValueValidator(3),
MaxValueValidator(15)],
help_text='/15')
neurological = models.ManyToManyField(Neurological, blank=True)
neurological_other = OtherCharField(
verbose_name='If "Other CN palsy", specify',
max_length=250,
blank=True,
null=True)
focal_neurologic_deficit = models.TextField(
verbose_name=
'If "Focal neurologic deficit" chosen, please specify details:',
null=True,
blank=True)
visual_acuity_day = models.DateField(
verbose_name='Study day visual acuity recorded?',
validators=[date_not_future],
null=True,
blank=True)
left_acuity = models.DecimalField(verbose_name='Visual acuity left eye:',
decimal_places=3,
max_digits=4,
null=True,
blank=True)
right_acuity = models.DecimalField(verbose_name='Visual acuity right eye',
decimal_places=3,
max_digits=4,
null=True,
blank=True)
ecog_score = models.CharField(verbose_name='ECOG Disability Score',
max_length=15,
choices=ECOG_SCORE)
ecog_score_value = models.CharField(verbose_name='ECOG Score',
max_length=15,
choices=ECOG_SCORE)
lung_exam = models.CharField(verbose_name='Abnormal lung exam:',
max_length=5,
choices=YES_NO)
cryptococcal_lesions = models.CharField(
verbose_name='Cryptococcal related skin lesions:',
max_length=5,
choices=YES_NO)
specify_medications = models.ManyToManyField(Medication, blank=True)
specify_medications_other = models.TextField(max_length=150,
blank=True,
null=True)
previous_oi = models.CharField(
verbose_name='Previous opportunistic infection other than TB?',
max_length=5,
choices=YES_NO)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = 'Patient\'s History'
verbose_name_plural = 'Patient\'s History'
class Week2(
ClinicalAssessmentModelMixin,
StudyMedicationModelMixin,
MedAndDrugInterventionModelMixin,
BloodTransfusionModelMixin,
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
)
research_discharge_date = models.DateField(
verbose_name="On which date did the research team feel the patient was well "
"enough to go home",
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
)
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",
)
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"
class BloodResult(
CrfModelMixin,
ActionModelMixin,
TrackingModelMixin,
BiosynexSemiQuantitativeCragMixin,
):
action_name = BLOOD_RESULTS_ACTION
tracking_identifier_prefix = "BR"
ft_fields = [
"creatinine", "urea", "sodium", "potassium", "magnesium", "alt"
]
cbc_fields = ["haemoglobin", "wbc", "neutrophil", "platelets"]
ft_requisition = models.ForeignKey(
SubjectRequisition,
on_delete=PROTECT,
related_name="ft",
verbose_name="Requisition",
null=True,
blank=True,
help_text=
"Start typing the requisition identifier or select one from this visit",
)
ft_assay_datetime = models.DateTimeField(
verbose_name="Result Report Date and Time",
validators=[datetime_not_future],
null=True,
blank=True,
)
cbc_requisition = models.ForeignKey(
SubjectRequisition,
on_delete=PROTECT,
related_name="cbc",
verbose_name="Requisition",
null=True,
blank=True,
help_text=
"Start typing the requisition identifier or select one from this visit",
)
cbc_assay_datetime = models.DateTimeField(
verbose_name="Result Report Date and Time",
validators=[datetime_not_future],
null=True,
blank=True,
)
cd4_requisition = models.ForeignKey(
SubjectRequisition,
on_delete=PROTECT,
related_name="cd4",
verbose_name="Requisition",
null=True,
blank=True,
help_text=
"Start typing the requisition identifier or select one from this visit",
)
cd4_assay_datetime = models.DateTimeField(
verbose_name="Result Report Date and Time",
validators=[datetime_not_future],
null=True,
blank=True,
)
vl_requisition = models.ForeignKey(
SubjectRequisition,
on_delete=PROTECT,
related_name="vl",
verbose_name="Requisition",
null=True,
blank=True,
help_text=
"Start typing the requisition identifier or select one from this visit",
)
vl_assay_datetime = models.DateTimeField(
verbose_name="Result Report Date and Time",
validators=[datetime_not_future],
null=True,
blank=True,
)
wbc = models.DecimalField(verbose_name="WBC",
decimal_places=2,
max_digits=6,
null=True,
blank=True)
wbc_units = models.CharField(
verbose_name="units",
max_length=10,
choices=((TEN_X_9_PER_LITER, TEN_X_9_PER_LITER), ),
null=True,
blank=True,
)
wbc_abnormal = models.CharField(verbose_name="abnormal",
choices=YES_NO,
max_length=25,
null=True,
blank=True)
wbc_reportable = models.CharField(
verbose_name="reportable",
choices=REPORTABLE,
max_length=25,
null=True,
blank=True,
)
platelets = models.IntegerField(
validators=[MinValueValidator(1),
MaxValueValidator(9999)],
null=True,
blank=True,
)
platelets_units = models.CharField(
verbose_name="units",
max_length=10,
choices=((TEN_X_9_PER_LITER, TEN_X_9_PER_LITER), ),
null=True,
blank=True,
)
platelets_abnormal = models.CharField(verbose_name="abnormal",
choices=YES_NO,
max_length=25,
null=True,
blank=True)
platelets_reportable = models.CharField(
verbose_name="reportable",
choices=REPORTABLE,
max_length=25,
null=True,
blank=True,
)
haemoglobin = models.DecimalField(decimal_places=1,
max_digits=6,
null=True,
blank=True)
haemoglobin_units = models.CharField(
verbose_name="units",
max_length=10,
choices=((GRAMS_PER_DECILITER, GRAMS_PER_DECILITER), ),
null=True,
blank=True,
)
haemoglobin_abnormal = models.CharField(verbose_name="abnormal",
choices=YES_NO,
max_length=25,
null=True,
blank=True)
haemoglobin_reportable = models.CharField(
verbose_name="reportable",
choices=REPORTABLE,
max_length=25,
null=True,
blank=True,
)
neutrophil = models.DecimalField(decimal_places=2,
max_digits=6,
null=True,
blank=True)
neutrophil_units = models.CharField(
verbose_name="units",
max_length=10,
choices=((TEN_X_9_PER_LITER, TEN_X_9_PER_LITER), ),
null=True,
blank=True,
)
neutrophil_abnormal = models.CharField(verbose_name="abnormal",
choices=YES_NO,
max_length=25,
null=True,
blank=True)
neutrophil_reportable = models.CharField(
verbose_name="reportable",
choices=REPORTABLE,
max_length=25,
null=True,
blank=True,
)
creatinine = models.DecimalField(decimal_places=2,
max_digits=6,
null=True,
blank=True)
creatinine_units = models.CharField(
verbose_name="units",
choices=MG_UMOL_UNITS,
max_length=25,
null=True,
blank=True,
)
creatinine_abnormal = models.CharField(verbose_name="abnormal",
choices=YES_NO,
max_length=25,
null=True,
blank=True)
creatinine_reportable = models.CharField(
verbose_name="reportable",
choices=REPORTABLE,
max_length=25,
null=True,
blank=True,
)
sodium = models.IntegerField(
validators=[MinValueValidator(1),
MaxValueValidator(999)],
null=True,
blank=True)
sodium_units = models.CharField(
verbose_name="units",
max_length=10,
choices=((MILLIMOLES_PER_LITER, MILLIMOLES_PER_LITER), ),
null=True,
blank=True,
)
sodium_abnormal = models.CharField(verbose_name="abnormal",
choices=YES_NO,
max_length=25,
null=True,
blank=True)
sodium_reportable = models.CharField(
verbose_name="reportable",
choices=REPORTABLE,
max_length=25,
null=True,
blank=True,
)
potassium = models.DecimalField(decimal_places=1,
max_digits=2,
null=True,
blank=True)
potassium_units = models.CharField(
verbose_name="units",
max_length=10,
choices=((MILLIMOLES_PER_LITER, MILLIMOLES_PER_LITER), ),
null=True,
blank=True,
)
potassium_abnormal = models.CharField(
verbose_name="abnormal",
choices=YES_NO,
# default=NO,
max_length=25,
null=True,
blank=True,
)
potassium_reportable = models.CharField(
verbose_name="reportable",
choices=REPORTABLE,
# default=NOT_APPLICABLE,
max_length=25,
null=True,
blank=True,
)
magnesium = models.DecimalField(decimal_places=2,
max_digits=6,
null=True,
blank=True)
magnesium_units = models.CharField(
verbose_name="units",
choices=MG_MMOL_UNITS,
null=True,
blank=True,
max_length=25,
)
magnesium_abnormal = models.CharField(verbose_name="abnormal",
choices=YES_NO,
null=True,
blank=True,
max_length=25)
magnesium_reportable = models.CharField(
verbose_name="reportable",
choices=REPORTABLE,
null=True,
blank=True,
max_length=25,
)
alt = models.IntegerField(
validators=[MinValueValidator(1),
MaxValueValidator(2999)],
verbose_name="ALT",
null=True,
blank=True,
)
alt_units = models.CharField(
verbose_name="units",
max_length=10,
choices=((IU_LITER, IU_LITER), ),
null=True,
blank=True,
)
alt_abnormal = models.CharField(verbose_name="abnormal",
choices=YES_NO,
max_length=25,
null=True,
blank=True)
alt_reportable = models.CharField(
verbose_name="reportable",
choices=REPORTABLE,
max_length=25,
null=True,
blank=True,
)
urea = models.DecimalField(decimal_places=2,
max_digits=6,
null=True,
blank=True)
urea_units = models.CharField(
verbose_name="units",
choices=MG_MMOL_UNITS,
max_length=25,
null=True,
blank=True,
)
urea_abnormal = models.CharField(
verbose_name="abnormal",
choices=YES_NO,
# default=NO,
max_length=25,
null=True,
blank=True,
)
urea_reportable = models.CharField(
verbose_name="reportable",
choices=REPORTABLE,
max_length=25,
null=True,
blank=True,
)
cd4 = models.IntegerField(
verbose_name="abs CD4",
validators=[MinValueValidator(0),
MaxValueValidator(999)],
blank=True,
null=True,
)
cd4_units = models.CharField(
verbose_name="units",
max_length=10,
choices=((CELLS_PER_MILLIMETER_CUBED, CELLS_PER_MILLIMETER_CUBED), ),
null=True,
blank=True,
)
cd4_abnormal = models.CharField(verbose_name="abnormal",
choices=YES_NO,
max_length=25,
null=True,
blank=True)
cd4_reportable = models.CharField(
verbose_name="reportable",
choices=REPORTABLE,
max_length=25,
null=True,
blank=True,
)
vl = models.FloatField(
verbose_name="Viral Load",
validators=[MinValueValidator(0.0)],
blank=True,
null=True,
)
vl_units = models.CharField(
verbose_name="units",
max_length=10,
choices=((COPIES_PER_MILLILITER, COPIES_PER_MILLILITER), ),
null=True,
blank=True,
)
vl_abnormal = models.CharField(verbose_name="abnormal",
choices=YES_NO,
max_length=25,
null=True,
blank=True)
vl_reportable = models.CharField(
verbose_name="reportable",
choices=REPORTABLE,
max_length=25,
null=True,
blank=True,
)
results_abnormal = models.CharField(
verbose_name="Are any of the above results abnormal?",
choices=YES_NO,
max_length=25,
)
results_reportable = models.CharField(
verbose_name="If any results are abnormal, are results within grade III "
"or above?",
max_length=25,
choices=YES_NO_NA,
help_text=
("If YES, this value will open Adverse Event Form.<br/><br/>"
"Note: On Day 1 only abnormal bloods should not be reported as adverse"
"events."),
)
summary = models.TextField(null=True, blank=True)
on_site = CurrentSiteManager()
objects = CrfModelManager()
def save(self, *args, **kwargs):
self.summary = "\n".join(self.get_summary())
super().save(*args, **kwargs)
def get_summary(self):
registered_subject = RegisteredSubject.objects.get(
subject_identifier=self.subject_visit.subject_identifier)
opts = dict(
gender=registered_subject.gender,
dob=registered_subject.dob,
report_datetime=self.subject_visit.report_datetime,
)
summary = []
for field in [f.name for f in self._meta.fields]:
value = getattr(self, field)
grp = site_reportables.get("ambition").get(field)
if value and grp:
units = getattr(self, f"{field}_units")
opts.update(units=units)
grade = grp.get_grade(value, **opts)
if grade and grade.grade:
summary.append(f"{field}: {grade.description}.")
elif not grade:
normal = grp.get_normal(value, **opts)
if not normal:
summary.append(f"{field}: {value} {units} is abnormal")
return summary
def get_action_item_reason(self):
return self.summary
@property
def abnormal(self):
return self.results_abnormal
@property
def reportable(self):
return self.results_reportable
class Meta(CrfModelMixin.Meta):
verbose_name = "Blood Result"
verbose_name_plural = "Blood Results"
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="Sputum 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)
csf_genexpert_performed = models.CharField(
verbose_name="CSF Gene-Xpert performed?",
max_length=15,
choices=YES_NO_NA,
default=NOT_APPLICABLE,
)
csf_genexpert_date = models.DateField(
verbose_name="Date CSF Gene-Xpert taken",
validators=[date_not_before_study_start, date_not_future],
null=True,
blank=True,
)
csf_result_genexpert = models.CharField(
verbose_name="CSF Gene-Xpert results",
max_length=45,
choices=SPUTUM_GENEXPERT,
default=NOT_APPLICABLE,
)
on_site = CurrentSiteManager()
objects = CrfModelManager()
history = HistoricalRecords()
class Meta(CrfModelMixin.Meta):
verbose_name = "Microbiology"
verbose_name_plural = "Microbiology"
class PkPdCrf(CrfModelMixin):
# removed v 0.1.61
albumin = models.IntegerField(verbose_name="Albumin",
null=True,
blank=True,
help_text="Units in g/L")
amphotericin_given = models.CharField(
verbose_name=("Did the patient receive any amphotericin "
"formulation in the last 24 hours?"),
choices=YES_NO,
max_length=5,
null=True,
)
amphotericin_formulation = models.CharField(
verbose_name=("If Yes, Which formulation of amphotericin?"),
choices=AMPHOTERICIN_FORMULATION,
max_length=25,
blank=True,
null=True,
)
amphotericin_dose = models.IntegerField(verbose_name="Dose given",
null=True,
blank=True,
help_text="Units in mg")
amphotericin_started_datetime = models.DateTimeField(
verbose_name="Date and time started", null=True, blank=True)
amphotericin_ended_datetime = models.DateTimeField(
verbose_name="Date and time stopped", null=True, blank=True)
amphotericin_full_dose_given = models.CharField(
verbose_name="Was the entire 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="Total of all doses given. Units in mg",
)
flucytosine_dose_one_given = models.CharField(
verbose_name="Flucytosine <b><u>DOSE 1</u></b> 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_one = models.IntegerField(
verbose_name="Flucytosine <u>DOSE 1</u>",
validators=[MinValueValidator(0),
MaxValueValidator(9999)],
null=True,
blank=True,
help_text="Units in mg",
)
flucytosine_dose_two_given = models.CharField(
verbose_name="Flucytosine <b><u>DOSE 2</u></b> given? ",
choices=YES_NO_NA,
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_two = models.IntegerField(
verbose_name="Flucytosine <u>DOSE 2</u>",
validators=[MinValueValidator(0),
MaxValueValidator(9999)],
null=True,
blank=True,
help_text="Units in mg",
)
flucytosine_dose_three_given = models.CharField(
verbose_name="Flucytosine <b><u>DOSE 3</u></b> given? ",
choices=YES_NO_NA,
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_three = models.IntegerField(
verbose_name="Flucytosine <u>DOSE 3</u>",
validators=[MinValueValidator(0),
MaxValueValidator(9999)],
null=True,
blank=True,
help_text="Units in mg",
)
flucytosine_dose_four_given = models.CharField(
verbose_name="Flucytosine <b><u>DOSE 4</u></b> given? ",
choices=YES_NO_NA,
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_four = models.IntegerField(
verbose_name="Flucytosine <u>DOSE 4</u>",
validators=[MinValueValidator(0),
MaxValueValidator(9999)],
null=True,
blank=True,
help_text="Units in mg",
)
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_NA,
default=NOT_APPLICABLE,
max_length=11,
null=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"
