class IAssayRequest(BaseModel):
"""Object that will be attached to sample. It will be the instance object
that has a workflow that can be tracked in the LIMS.
"""
assay_name = schema.Choice(
title=_(u"Assay Name"),
description=_(u"Assay Name"),
source=IChipAssayListVocabulary,
required=True,
)
date_ordered = schema.Date(
title=_(u"Date Ordered"),
description=_(u"Date Ordered"),
defaultFactory=currentDate,
required=True,
)
date_resulted = schema.Date(
title=_(u"Assay Result Date"),
description=_(u"Assay Result Date"),
required=False,
)
aliquot_evaluated = schema.TextLine(
title=_(u"Aliquot ID Used For Assay Request"),
description=_(u"Aliquot ID Used For Assay Request"),
required=False,
)
comment = schema.Text(
title=_(u"Any Notes or Comments About the Assay Request"),
description=_(u"Any Notes or Comments About the Assay Request"),
required=False,
)
def NonZeroConstraint(value):
"""Check that the Int field has a value >0
"""
try:
int(value)
except:
raise Invalid(_(u"Value must be an integer, not '%s'" % value))
if value < 1:
raise Invalid(_(u"Value must be >0, not '%s'" % value))
return True
class IRack(BaseModel):
"""Letters of the alphabet single letter to double letter to triple
letter, have two types of racks and that determines the number of boxes
it will hold. (5x4=20 boxes, or 4x4=16 boxes)
"""
rack_name = schema.TextLine(
title=_(u"Rack ID"),
description=_(u"Rack ID"),
required=True,
)
size = schema.Int(
title=_(u'Rack Size'),
description=_(u'Number of boxes rack can hold'),
)
freezer = schema.TextLine(
title=_(u"Freezer"),
description=_(u"Freezer where rack is stored"),
required=True,
)
remaining_volume = schema.Int(
title=_(u"Remaining Rack Spaces"),
description=_(u"Remaining Rack Spaces"),
required=True,
)
class IAliquot(BaseModel):
"""Common schema fields for all types of Aliquots
"""
initial_volume = schema.Int(
title=_(u"Initial Volume"),
description=_(u"Volume of aliquot in micro liters (uL)"),
required=True,
)
remaining_volume = schema.Int(
title=_(u"Remaining Volume"),
description=_(u"Remaining aliquot volume in micro liters (uL)"),
required=True,
)
class ISample(BaseModel):
"""Common schema fields for all types of Samples
"""
initial_volume = schema.Int(
title=_(u"Initial Volume"),
description=_(u"Volume of sample in micro liters (uL)"),
required=True,
)
remaining_volume = schema.Int(
title=_(u"Remaining Volume"),
description=_(u"Remaining sample volume in micro liters (uL)"),
required=True,
readonly=True,
)
class BaseModel(model.Schema):
"""This is a base for all schema interfaces presented here. It contains
fields that we know will be present on all objects.
"""
title = schema.TextLine(
title=_(u"Title"),
required=False,
readonly=True,
)
class ITestRequisition(BaseModel):
"""
"""
sample_id = schema.TextLine(
title=_(u"Sample ID"),
required=True,
)
patient = schema.Choice(
title=_(u"Patient"),
description=_(u""),
vocabulary=u"immunarray.lims.interfaces.patient.PatientVocabulary",
required=True,
)
repeat_order = schema.Bool(
title=_(u"Repeat Order"),
default=False,
required=False,
)
doctor = schema.Choice(
title=_(u"Doctor"),
description=_(u""),
vocabulary=u"immunarray.lims.interfaces.doctor.DoctorVocabulary",
required=True,
)
class IMedicalHistoryPatient(BaseModel):
""" Interface for clinical information input given by patient"""
form.widget(symptoms_choice=CheckBoxFieldWidget)
clinical_impression = schema.List(
title=_(u"Clinical Impression"),
description=_(u"Clinical Impression of the Referring Physicain/"
u", Select All That Apply"),
required=False,
value_type=schema.Choice(values=[
_(u"Systemic Lupus Erythematosus (SLE)"),
_(u"Antiphospholipid Syndrome"),
_(u"Asthma"),
_(u"Autoimmune Hepatitis"),
_(u"Seizures or psychosis"),
_(u"Hair loss")
]),
)
class IAliquotPlate(ISample):
"""Aliquot Plate!
"""
id = schema.TextLine(
title=_(u"Aliquot Plate ID"),
description=_(u"Aliquot Plate ID"),
defaultFactory=assignPlateID(),
required=True,
)
#date info
date_added = schema.Date(
title=_(u"Date Aliquot Plate was added to LIMS"),
description=_(u"Date Aliquot Platee was added to LIMS"),
defaultFactory=currentDate,
required=True,
)
added_by = schema.Choice(
title=_(u"Operator that Added Aliquot Plate to LIMS"),
description=_(u"Operator that Added Aliquot Plate to LIMS"),
vocabulary=u"plone.principalsource.Users",
required=False,
)
assay_uid = Attribute("""Assay UID
Link directly back to the iChipAssay so that the edit form has a copy
when required. Also used to link QC aliquots back to the HQC and LQC
of the selected Assay.
""")
assay_name = Attribute("""Assay Name
For convenience, I'll store the assay_name too, but it should not be used
for lookup.
""")
plates_96_well = Attribute("""Plates
A map of aliquots to wells on a plate and is stored here as a list
of dictionaries. The format matches what is excpected by the form,
which is the same as the data returned when creating a new test run.
A-H, and 12 wells
The format of each 96 well plate looks like this:
{'A01': UID,
'A02': UID,
'A03': UID,
'A04': UID,
'A05': UID,
'A06': UID,
'A07': UID,
'A08': UID,
'A09': UID,
'A10': UID,
'A11': UID,
'A12': UID,
'B01': UID,
'B02': UID,
'B03': UID,
'B04': UID,
'B05': UID,
'B06': UID,
'B07': UID,
'B08': UID,
'B09': UID,
'B10': UID,
'B11': UID,
'B12': UID,
'C01': UID,
'C02': UID,
'C03': UID,
'C04': UID,
'C05': UID,
'C06': UID,
'C07': UID,
'C08': UID,
'C09': UID,
'C10': UID,
'C11': UID,
'C12': UID,
'D01': UID,
'D02': UID,
'D03': UID,
'D04': UID,
'D05': UID,
'D06': UID,
'D07': UID,
'D08': UID,
'D09': UID,
'D10': UID,
'D11': UID,
'D12': UID,
'E01': UID,
'E02': UID,
'E03': UID,
'E04': UID,
'E05': UID,
'E06': UID,
'E07': UID,
'E08': UID,
'E09': UID,
'E10': UID,
'E11': UID,
'E12': UID,
'F01': UID,
'F02': UID,
'F03': UID,
'F04': UID,
'F05': UID,
'F06': UID,
'F07': UID,
'F08': UID,
'F09': UID,
'F10': UID,
'F11': UID,
'F12': UID,
'G01': UID,
'G02': UID,
'G03': UID,
'G04': UID,
'G05': UID,
'G06': UID,
'G07': UID,
'G08': UID,
'G09': UID,
'G10': UID,
'G11': UID,
'G12': UID,
'H01': UID,
'H02': UID,
'H03': UID,
'H04': UID,
'H05': UID,
'H06': UID,
'H07': UID,
'H08': UID,
'H09': UID,
'H10': UID,
'H11': UID,
'H12': UID,
}
""")
# source_id_one = schema.TextLine(
# title=_(u"Primary QC Source Sample ID"),
# description=_(u"Primary QC Source Sample ID"),
# required=True,
# )
#
# source_id_two = schema.TextLine(
# title=_(u"Secondary QC Source Sample ID"),
# description=_(u"Secondary QC Source Sample ID"),
# required=False,
# )
#
# source_id_three = schema.TextLine(
# title=_(u"Tertiary QC Source Sample ID"),
# description=_(u"Tertiary QC Source Sample ID"),
# required=False,
# )
description = schema.TextLine(
title=_(u"Description of Aliquot Plate"),
description=_(u"Description of Aliquot Plate"),
required=False,
)
comment = schema.Text(
title=_(u"Any Notes or Comments About the QC Sample"),
description=_(u"Any Notes or Comments About the QC Sample"),
required=False,
)
class IQCAliquot(IAliquot):
"""QC Sample!
"""
source_id_one = schema.TextLine(
title=_(u"Primary QC Source Sample ID"),
description=_(u"Primary QC Source Sample ID"),
required=False,
)
source_id_two = schema.TextLine(
title=_(u"Secondary QC Source Sample ID"),
description=_(u"Secondary QC Source Sample ID"),
required=False,
)
source_id_three = schema.TextLine(
title=_(u"Tertiary QC Source Sample ID"),
description=_(u"Tertiary QC Source Sample ID"),
required=False,
)
date_added = schema.Date(
title=_(u"Date QC Sample was added to LIMS"),
description=_(u"Date QC Sample was added to LIMS"),
defaultFactory=currentDate,
required=True,
)
added_by = schema.Choice(
title=_(u"Operator that Added QC Sample to LIMS"),
description=_(u"Operator that Added QC Sample to LIMS"),
vocabulary=u"plone.principalsource.Users",
required=False,
)
consume_date = schema.Date(
title=_(u"Aliquot Consume Date"),
description=_(u"Aliquot Consume Date"),
required=False,
)
source = schema.TextLine(
title=_(u"Source of QC Sample"),
description=_(u"Source of QC Sample"),
required=False,
)
description = schema.TextLine(
title=_(u"Description of QC Sample"),
description=_(u"Description of QC Sample"),
required=False,
)
aliquot_type = schema.Choice(
title=_(u"Aliquot Type"),
description=_(u"Aliquot Type"),
required=True,
values=[_(u'Bulk'), _(u'Working')],
)
fluid_type = schema.Choice(
title=_(u"QC Fluid Type"),
description=_(u"QC Fluid Type"),
values=[_(u"Serum"),
_(u"Plasma"),
_(u"CSF"), _(u"Tissue")],
required=True,
)
date_received = schema.Date(
title=_(u"Date QC Sample was Received"),
description=_(u"Date QC Sample was Received"),
required=True,
)
comment = schema.Text(
title=_(u"Any Notes or Comments About the QC Sample"),
description=_(u"Any Notes or Comments About the QC Sample"),
required=False,
)
class IRandDSample(ISample):
"""R and D sample!
"""
department = schema.Choice(
title=_(u"Department"),
description=_(u"Department that controls material"),
values=[_(u"TBI"), _(u"Commercial"), _(u"BrainBox"), _(u"Other")],
required=False,
)
source_id_one = schema.TextLine(
title=_(u"Primary R&D Source Sample ID"),
description=_(u"Primary R&D Source Sample ID"),
required=False,
)
source_id_two = schema.TextLine(
title=_(u"Secondary R&D Source Sample ID"),
description=_(u"Secondary R&D Source Sample ID"),
required=False,
)
source_id_three = schema.TextLine(
title=_(u"Tertiary R&D Source Sample ID"),
description=_(u"Tertiary R&D Source Sample ID"),
required=False,
)
# Unlike Clinical Samples which store this value in "usn" field,
# RandD/QC samples have a dedicated veracis_id field.
veracis_id = schema.TextLine(
title=_(u"R&D Veracis Sample ID"),
description=_(u"R&D Veracis Sample ID"),
defaultFactory=assignVeracisId(),
required=True,
)
date_added = schema.Date(
title=_(u"Date R&D Sample was added to LIMS"),
description=_(u"Date R&D Sample was added to LIMS"),
defaultFactory=currentDate,
required=True,
)
added_by = schema.Choice(
title=_(u"Operator that Added R&D Sample to LIMS"),
description=_(u"Operator that Added R&D Sample to LIMS"),
vocabulary=u"plone.principalsource.Users",
required=False,
)
source = schema.TextLine(
title=_(u"Source of R&D Sample"),
description=_(u"Source of R&D Sample"),
required=False,
)
pi = schema.TextLine(
title=_(u"Primary Investigator (PI) of R&D Sample"),
description=_(u"Primary Investigator (PI) of R&D Sample"),
required=False,
)
description = schema.TextLine(
title=_(u"Description of R&D Sample"),
description=_(u"Description of R&D Sample"),
required=False,
)
fluid_type = schema.Choice(
title=_(u"R&D Fluid Type"),
description=_(u"R&D Fluid Type"),
values=[_(u"Serum"), _(u"Plasma"), _(u"CSF"), _(u"Tissue")],
required=True,
)
date_received = schema.Date(
title=_(u"Date R&D Sample was Received"),
description=_(u"Date R&D Sample was Received"),
required=True,
)
comment = schema.Text(
title=_(u"Any Notes or Comments About the R&D Sample"),
description=_(u"Any Notes or Comments About the R&D Sample"),
required=False,
)
class IProvider(IPerson):
"""Care provider
"""
site_ID = schema.Int(
title=_(u"Site ID"),
description=_(u"Site ID"),
required=False,
)
npi = schema.TextLine(
title=_(u"NPI"),
description=_(u"NPI (unique to each provider)"),
required=True,
)
credentials = schema.Choice(
title=_(u"Provider Credentials"),
description=_(u"Provider credentials (M.D. D.O.)"),
values=[_(u'MD'), _(u'DO'), _(u'PA-C'), _(u'MD/PhD'), _(u'PhD'),
_(u'NP'), ],
required=False,
)
tax_id = schema.TextLine(
title=_(u"Tax ID"),
description=_(u"Tax ID"),
required=False,
)
pin = schema.TextLine(
title=_(u"PIN"),
description=_(u"PIN"),
required=False,
)
upin = schema.TextLine(
title=_(u"UPIN"),
description=_(u"UPIN"),
required=False,
)
publishing_preference = schema.Choice(
title=_(u"Publishing Preference"),
description=_(u"Providers desired publincation of resutls"),
values=[_(u'Fax'), _(u'Mail'), _(u'EMR')],
required=True,
)
form.widget(test_report_preference=CheckBoxFieldWidget)
test_report_preference = schema.List(
title=_(u"Laboratory Report Preference"),
description=_(u"Laboratory Report Preference"),
required=False,
value_type=schema.Choice(source=TestRunReportsVocabulary),
)
class INCE(BaseModel):
"""General NCE Item to be used to track non conformance events in the lab
"""
nce_tracking_number = schema.TextLine(
title=_(u"Tracking Number"),
description=_(u"Tracking Number"),
required=False,
)
date_of_NCE = schema.Date(
title=_(u"Date of NCE"),
description=_(u"Date of NCE"),
required=True,
)
date_of_nce_discovery = schema.Date(
title=_(u"Date of NCE Discovery"),
description=_(u"Date of NCE Discovery"),
required=True,
)
reporter = schema.Choice(
title=_(u"Operator that is Reporting NCE"),
description=_(u"Operator that is Reporting NCE"),
vocabulary=u"plone.principalsource.Users",
required=False,
)
position = schema.TextLine(
title=_(u"Position of Reporter"),
description=_(u"Position of Reporter"),
required=False,
)
area_of_operation = schema.Choice(
title=_(u"Area of Operation"),
description=_(u"Area of Operation"),
values=[
_(u'Scanning'),
_(u'Accessioning'),
_(u'Test Preparation'),
_(u'Blocking'),
_(u'Testing'),
_(u'Data Analysis')
],
required=False,
)
accession_number = schema.TextLine(
title=_(u"Accession Number or Batch Number"),
description=_(u"Accession Number or Batch Number"),
required=False,
)
assay = schema.TextLine(
title=_(u"Assay"),
description=_(u"Assay"),
required=False,
)
facility = schema.TextLine(
title=_(u"Facility where NCE Happened"),
description=_(u"Facility where NCE Happened"),
required=False,
)
current_date_time = schema.Datetime(
title=_(u"Datetime of NCE"),
description=_(u"Datetime of NCE"),
defaultFactory=currentTime,
required=True,
)
category_primary = schema.Choice(
title=_(u"Category - Primary"),
description=_(u"Category - Primary"),
vocabulary='immunarray.lims.vocabularies.nce.PrimaryNCEVocabulary',
required=False,
)
category_secondary = schema.Choice(
title=_(u"Category - Secondary"),
description=_(u"Category - Secondary"),
vocabulary='immunarray.lims.vocabularies.nce.SecondaryNCEVocabulary',
required=False,
)
category_tertiary = schema.Choice(
title=_(u"Category - Tertiary"),
description=_(u"Category - Tertiary"),
vocabulary='immunarray.lims.vocabularies.nce.TertiaryNCEVocabulary',
required=False,
)
risk_score = schema.Choice(
title=_(u"Risk Score"),
description=_(u"Risk Score"),
values=[_(u'Lowest'), _(u'Intermediate'),
_(u'High')],
required=False,
)
initial_finding = schema.Text(
title=_(u"Initial Finding"),
description=_(u"Initial Finding"),
required=False,
)
first_occurrence = schema.Bool(
title=_(u"First Occurrence"),
description=_(u"First Occurrence"),
required=True,
default=False,
)
persons_involved = schema.TextLine(
title=_(u"Persons Involved"),
description=_(u"Persons Involved"),
required=False,
)
remedial_action_type = schema.Choice(
title=_(u"Remedial Action Type"),
description=_(u"Remedial Action Type"),
values=[_(u'Corrective'),
_(u'Preventive'),
_(u'Process Improve')],
required=False,
)
remedial_action = schema.Text(
title=_(u"Remedial Action"),
description=_(u"Remedial Action"),
required=False,
)
is_follow_up_needed = schema.Bool(
title=_(u"Is Follow Up Needed?"),
description=_(u"Is Follow Up Needed?"),
required=True,
default=False,
)
investigation_needed = schema.Bool(
title=_(u"Investigation Needed"),
description=_(u"Investigation Needed"),
required=True,
default=False,
)
Investigation_tracking_number = schema.TextLine(
title=_(u"Investigation Tracking Number"),
description=_(u"Investigation Tracking Number"),
required=False,
)
nce_status = schema.Choice(
title=_(u"Status"),
description=_(u"Status"),
values=[_(u'Closed'),
_(u'In Process'),
_(u'Non Resolvable')],
required=False,
)
date_closed = schema.Date(
title=_(u"Date NCE Closed"),
description=_(u"Date NCE Closed"),
required=False,
)
class IiChipLot(BaseModel):
"""An iChip Lot that will contain iChip objects.
"""
lot_id = schema.TextLine(
title=_(u"iChip Lot ID"),
description=_(u"Used when naming iChips created in this lot"),
required=True,
)
print_date = schema.Date(
title=_(u"iChip Lot Print Date"),
description=_(u"Print Date of iChip Lot"),
required=True,
)
arrival_date = schema.Date(
title=_(u"iChip Lot Arrival Date"),
description=_(u"Arrival Date of iChip Lot"),
required=True,
)
ship_date = schema.Date(
title=_(u"iChip Lot Shipped Date"),
description=_(u"iChip Lot Shipped Date"),
required=True,
)
ichip_lot_expiration_date = schema.Date(
title=_(u"iChip Lot Expiration Date"),
description=_(u"Expiration Date of iChip Lot"),
required=True,
)
nr_ichips = schema.Int(
title=_(u"Number of iChips"),
description=_(u"Number of iChips contained in this lot."),
required=True,
constraint=NonZeroConstraint,
)
# XXX This should be a Text input, same as iChipAssay's framecount
# and the two should match: refactor ichip.I*ChipsInUSVocabulary
frames = schema.Choice(
title=_(u"iChip Frame Layout"),
description=_(u"iChip Frame Layout"),
values=[_(u"1"), _(u"3"), _(u"8")],
required=True,
)
# XXX Allow mutiple selections!
# XXX Need to connect this to iChipAssay.name
form.widget(intended_assay=CheckBoxFieldWidget)
intended_assay = schema.List(
title=_(u"Intended Assay(s)"),
description=_(u"Intended Assay(s)"),
required=True,
value_type=schema.Choice(source=IChipAssayListVocabulary),
)
temp_log = NamedFile(
title=_(u"iChip Lot Travel Temperature Log"),
description=_(u"Travel Temperature Log of iChip Lot"),
required=False,
)
cofa = NamedFile(
title=_(u"iChip Certificate of Analysis"),
description=_(u"Certificate of Analysis of iChip Lot"),
required=False,
)
batch_release = NamedFile(
title=_(u"iChip Batch Release Document"),
description=_(u"Batch Release Document of iChip Lot"),
required=False,
)
gal_file = NamedFile(
title=_(u"Gal File (.gal)"),
description=_(u"Gal File (.gal)"),
required=False,
)
shipping_box_integrity_maintained = schema.Choice(
title=_(u"iChip Shipping Box Integrity Maintained"),
description=_(u"iChip Shipping Box Integrity Maintained"),
values=[_(u"Yes"), _(u"No")],
required=True,
)
product_container_integrity_maintained = schema.Choice(
title=_(u"Product Container Integrity Maintained"),
description=_(u"Product Container Integrity Maintained"),
values=[_(u"Yes"), _(u"No")],
required=True,
)
other_damage = schema.TextLine(
title=_(u"Other Damage"),
description=_(u"Other Damage"),
required=False,
)
temp_on_arrival = schema.Float(
title=_(u"Temperature of iChips on Arrival"),
description=_(u"Temperature of iChips on Arrival"),
required=False,
)
temp_on_arrival_acceptable_limit = schema.Choice(
title=_(u"Temperature of iChips on Arrival Within Acceptable Limit"),
description=_(
u"Temperature of iChips on Arrival Within Acceptable Limit"),
values=[_(u"Yes"), _(u"No")],
required=True,
)
class IAssayBillingRequest(BaseModel):
"""Object that will be attached to sample. It will be the instance object
that has a workflow that can be tracked in the LIMS.
"""
assay_name = schema.Choice(title=_(u"Assay to be Billed"),
description=_(u"Assay to be Billed"),
source=IChipAssayListVocabulary,
required=True)
billing_program = schema.Choice(title=_(u"Billing Program"),
description=_(u"Billing Program"),
source=BillingProgramsVocabulary,
required=True)
# Need to make content file and title from sampleid and assay name
sample_id = schema.TextLine(
title=_(u"Billing Sample ID"),
description=_(u"Billing Sample ID"),
required=False,
)
date_ordered = schema.Date(
title=_(u"Date Billing Requste was added to LIMS"),
description=_(u"Date Billing Requste was added to LIMS"),
defaultFactory=currentDate,
required=True,
)
date_resulted = schema.Date(
title=_(u"Assay Billing Resolved Date"),
description=_(u"Assay Billing Resolved Date"),
required=False,
)
date_billed = schema.Date(
title=_(u"Assay Billed on Date"),
description=_(u"Assay Billed on Date"),
required=False,
)
form.widget(diagnosis_code=CheckBoxFieldWidget)
diagnosis_code = schema.List(
title=_(u"Diagnosis & ICD-10 Codes"),
description=_(u"Diagnosis & ICD-10 Codes"),
required=False,
value_type=schema.Choice(values=[
_(u"D89.89"),
_(u"D89.9"),
_(u"L93.2"),
_(u"M32.10"),
_(u"M35.9"),
_(u"Other, please specify")
]),
)
diagnosis_code_other = schema.List(
title=_(u"Other Diagnosis Code(s)"),
description=_(u"Other Diagnosis Code(s) Enter one Per Line"),
missing_value=None,
required=False,
value_type=schema.TextLine())
primary_insurance_name = schema.TextLine(
title=_(u"Primary Insurance Name"),
description=_(u"Primary Insurance Name"),
required=False,
)
primary_insurance_payerID = schema.TextLine(
title=_(u"Primary Insurance Payer ID"),
description=_(u"Primary Insurance Payer ID"),
required=False,
)
primary_insurance_policy_number = schema.TextLine(
title=_(u"Primary Insurance Policy Number"),
description=_(u"Primary Insurance Policy Number"),
required=False,
)
primary_insurance_plan_number = schema.TextLine(
title=_(u"Primary Insurance Plan Number"),
description=_(u"Primary Insurance Plan Number"),
required=False,
)
primary_insurance_authorization_precertificate = schema.TextLine(
title=_(u"Primary Insurance Authorization"),
description=_(u"Primary Insurance Authorization"),
required=False,
)
primary_insurance_subscriber_name = schema.TextLine(
title=_(u"Primary Insurance Subscriber Name"),
description=_(u"Primary Insurance Subscriber Name"),
required=False,
)
"""directives.widget(level=RadioFieldWidget)"""
primary_insurance_relation_to_insured = schema.Choice(
title=_(u"Primary Insurance Relation to Insured"),
description=_(u"Primary Insurance Relation to Insured"),
values=[_(u"Self"), _(u"Spouse"),
_(u"Child"),
_(u"Other")],
required=False,
)
primary_insurance_subscriber_DOB = schema.Date(
title=_(u"Primary Insurance Subscriber DOB"),
description=_(u"Primary Insurance Subscriber DOB"),
required=False,
)
primary_insurance_effective_date = schema.Date(
title=_(u"Primary Insurance Effective Date"),
description=_(u"Primary Insurance Effective Date"),
required=False,
)
primary_insurance_address = schema.TextLine(
title=_(u"Primary Insurance Address"),
description=_(u"Primary Insurance Address"),
required=False,
)
primary_city = schema.TextLine(
title=_(u"Primary Insurance City"),
description=_(u"Primary Insurance City"),
required=False,
)
primary_state = schema.TextLine(
title=_(u"Primary Insurance State"),
description=_(u"Primary Insurance State"),
required=False,
)
primary_insurance_zip_code = schema.TextLine(
title=_(u"Primary Insurance Zip Code"),
description=_(u"Primary Insurance Zip Code"),
required=False,
)
secondary_insurance_name = schema.TextLine(
title=_(u"Secondary Insurance Name"),
description=_(u"Secondary Insurance Name"),
required=False,
)
secondary_insurance_payerID = schema.TextLine(
title=_(u"Secondary Insurance Payer ID"),
description=_(u"Secondary Insurance Payer ID"),
required=False,
)
secondary_insurance_policy_number = schema.TextLine(
title=_(u"Secondary Insurance Policy Number"),
description=_(u"Secondary Insurance Policy Number"),
required=False,
)
secondary_insurance_plan_number = schema.TextLine(
title=_(u"Secondary Insurance Plan Number"),
description=_(u"Secondary Insurance Plan Number"),
required=False,
)
secondary_insurance_authorization_precertificate = schema.TextLine(
title=_(u"Secondary Insurance Authorization"),
description=_(u"Secondary Insurance Authorization"),
required=False,
)
secondary_insurance_subscriber_name = schema.TextLine(
title=_(u"Secondary Insurance Subscriber Name"),
description=_(u"Secondary Insurance Subscriber Name"),
required=False,
)
"""directives.widget(level=RadioFieldWidget)"""
secondary_insurance_relation_to_insured = schema.Choice(
title=_(u"Secondary Insurance Relation to Insured"),
description=_(u"Secondary Insurance Relation to Insured"),
values=[_(u"Self"), _(u"Spouse"),
_(u"Child"),
_(u"Other")],
required=False,
)
secondary_insurance_subscriber_DOB = schema.Datetime(
title=_(u"Secondary Insurance Subscriber DOB"),
description=_(u"Secondary Insurance Subscriber DOB"),
required=False,
)
secondary_insurance_effective_date = schema.Datetime(
title=_(u"Secondary Insurance Effective Date"),
description=_(u"Secondary Insurance Effective Date"),
required=False,
)
secondary_insurance_address = schema.TextLine(
title=_(u"Secondary Insurance Address"),
description=_(u"Secondary Insurance Address"),
required=False,
)
secondary_city = schema.TextLine(
title=_(u"Secondary Insurance City"),
description=_(u"Secondary Insurance City"),
required=False,
)
secondary_state = schema.TextLine(
title=_(u"Secondary Insurance State"),
description=_(u"Secondary Insurance State"),
required=False,
)
secondary_insurance_zip_code = schema.TextLine(
title=_(u"Secondary Insurance Zip Code"),
description=_(u"Secondary Insurance Zip Code"),
required=False,
)
assignment_of_benefits_patient_name = schema.TextLine(
title=_(u"Assignment of Benefits Patient Name"),
description=_(u"Assignment of Benefits Patient Name"),
required=False,
)
release_signed = schema.Bool(
title=_(u"Release Signed"),
description=_(u"Release Signed"),
)
assignment_of_benefits_signature_date = schema.Date(
title=_(u"Assignment of Benefits Signature Date"),
description=_(u"Assignment of Benefits Signature Date"),
required=False,
default=datetime.date.today(),
)
authorization_signature_patient_name = schema.TextLine(
title=_(u"Authorization Signature Patient Name"),
description=_(u"Authorization Signature Patient Name"),
required=False,
)
payment_signed = schema.Bool(
title=_(u"Payment Signed"),
description=_(u"Payment Signed"),
)
authorization_signature_date = schema.Date(
title=_(u"Authorization Signature Date"),
description=_(u"Authorization Signature Date"),
required=False,
default=datetime.date.today(),
)
comment = schema.Text(
title=_(u"Any Notes or Comments About the Assay Billing Request"),
description=_(
u"Any Notes or Comments About the Assay Billing Request"),
required=False,
)
class ISite(IOrganisation):
""" Commercial Site
"""
therapak_id = schema.TextLine(
title=_(u"Therapak ID"),
description=_(u"Therapak ID"),
default=u'',
required=False,
)
site_name = schema.TextLine(
title=_(u"Site Name"),
description=_(u"Site Name"),
required=True,
)
sales_rep = schema.Bool(
title=_(u"Sales Representative"),
description=_(u"Site is a Sales Representative"),
default=False,
)
setup_by = schema.TextLine(
title=_(u"Setup By"),
description=_(u"Setup By"),
required=False,
)
primary_provider = schema.TextLine(
title=_(u"Primary Provider"),
description=_(u"Primary Provider"),
required=False,
)
fax_number = schema.TextLine(
title=_(u"Fax Number"),
description=_(u"Fax Number"),
required=False,
)
fax_confirmed = schema.Bool(
title=_(u"Fax Number Confirmed"),
description=_(u"Fax Number Confirmed"),
required=False,
default=False,
)
megapractice_id = schema.TextLine(
title=_(u"Mega Practice ID"),
description=_(u"Link multiple sites together"),
required=False,
)
inbound_shipping_method = schema.Choice(
title=_(u"Inbound Shipping Method"),
description=_(u"Inbound Shipping Method"),
values=[(u'FedEx'), (u'UPS')],
required=False,
)
kits_on_site = schema.Int(
title=_(u"Kits on Site"),
description=_(u"Kits on Site"),
default=0,
required=False,
)
free_kits_left = schema.Int(
title=_(u"Free Kits Left"),
description=_(u"Free Kits Left"),
default=0,
required=False,
)
primary_contact = schema.TextLine(
title=_(u"Primary Site Contact"),
description=_(u"Primary Site Contact"),
required=False,
)
primary_contact_phone = schema.TextLine(
title=_(u"Primary Office Contact Phone Number"),
description=_(u"Primary Office Contact Phone Number"),
required=False,
)
site_notes = schema.Text(
title=_(u"Site Notes"),
description=_(u"Site Notes"),
required=False,
)
class IQCSample(ISample):
"""QC Sample!
"""
# Unlike Clinical Samples which store this value in "usn" field,
# RandD/QC samples have a dedicated veracis_id field.
veracis_id = schema.TextLine(
title=_(u"QC Veracis Sample ID"),
description=_(u"QC Veracis Sample ID"),
defaultFactory=assignVeracisId(),
required=True,
)
source_id_one = schema.TextLine(
title=_(u"Primary QC Source Sample ID"),
description=_(u"Primary QC Source Sample ID"),
required=True,
)
source_id_two = schema.TextLine(
title=_(u"Secondary QC Source Sample ID"),
description=_(u"Secondary QC Source Sample ID"),
required=False,
)
source_id_three = schema.TextLine(
title=_(u"Tertiary QC Source Sample ID"),
description=_(u"Tertiary QC Source Sample ID"),
required=False,
)
date_added = schema.Date(
title=_(u"Date QC Sample was added to LIMS"),
description=_(u"Date QC Sample was added to LIMS"),
defaultFactory=currentDate,
required=True,
)
added_by = schema.Choice(
title=_(u"Operator that Added QC Sample to LIMS"),
description=_(u"Operator that Added QC Sample to LIMS"),
vocabulary=u"plone.principalsource.Users",
required=False,
)
source = schema.TextLine(
title=_(u"Source of QC Sample"),
description=_(u"Source of QC Sample"),
required=False,
)
description = schema.TextLine(
title=_(u"Description of QC Sample"),
description=_(u"Description of QC Sample"),
required=False,
)
fluid_type = schema.Choice(
title=_(u"QC Fluid Type"),
description=_(u"QC Fluid Type"),
values=[_(u"Serum"),
_(u"Plasma"),
_(u"CSF"), _(u"Tissue")],
required=True,
)
date_received = schema.Date(
title=_(u"Date QC Sample was Received"),
description=_(u"Date QC Sample was Received"),
required=True,
)
comment = schema.Text(
title=_(u"Any Notes or Comments About the QC Sample"),
description=_(u"Any Notes or Comments About the QC Sample"),
required=False,
)
class ISolution(BaseModel):
"""Base Solution schema fields
"""
solution_name = schema.TextLine(
title=_(u"Solution Name"),
description=_(u"Solution Name"),
required=True,
)
batch_number = schema.TextLine(
title=_(u"Batch Number"),
description=_(u"Batch Number"),
required=True,
)
make_date = schema.Date(
title=_(u"Date Made"),
description=_(u"Date Made"),
required=True,
)
expiration_date = schema.Date(
title=_(u"Expiration Date"),
description=_(u"Expiration Date"),
required=True,
)
initial_amount = Amount(
title=_(u"Initial amount made"),
description=_(u"Enter a decimal number"),
required=True,
)
remaining_amount = Amount(
title=_(u"Amount remaining"),
description=_(u"You should not need to edit this value"),
)
unit = schema.TextLine(
title=_(u"Unit"),
description=_("Enter the unit in which the amounts are measured"),
required=True,
)
made_by = schema.Choice(
title=_(u"Made By"),
description=_(u"The operator created the material lot"),
source=UserVocabulary,
required=True)
materials_used = schema.Dict(title=_(u"Materials Used"),
key_type=schema.Choice(
title=_(u"Material"),
source=MaterialsVocabulary,
required=False),
value_type=Amount(title=u"Amount Used",
required=False),
required=False)
solutions_used = schema.Dict(
title=_(u"Solution(s) Used"),
key_type=schema.Choice(title=_(u"Solution"),
source=SolutionBatchesForTestRunsVocabulary,
required=False),
value_type=Amount(title=u"Amount Used", required=False),
required=False)
viability = schema.Int(
title=_(u"Solution Viability"),
description=_(u"Viability of solution in hours. "
u"Leave blank if solution does not expire."),
required=False,
)
completed_solution_prep_form = NamedFile(
title=_(u"Completed Solution Preperation Form"),
required=False,
)
class ITestRun(IVeracisRunBase):
# Serum Addition
serum_time_start = schema.Datetime(
title=_(u"Start Time of Serum Addition"),
description=_(u"Start Time of Serum Addition"),
required=False,
)
serum_humidity_start = schema.Float(
title=_(u"Humidity at Serum Addition Start"),
description=_(u"Humidity at Serum Addition Start"),
required=False,
)
serum_room_temperature_start = schema.Float(
title=_(u"Room Temperature at Serum Addition Start"),
description=_(u"Room Temperature at Serum Addition Start"),
required=False,
)
serum_time_end = schema.Datetime(
title=_(u"End Time of Serum Addition"),
description=_(u"End Time of Serum Addition"),
required=False,
)
serum_humidity_end = schema.Float(
title=_(u"Humidity at Serum Addition End"),
description=_(u"Humidity at Serum Addition End"),
required=False,
)
serum_room_temperature_end = schema.Float(
title=_(u"Room Temperature at Serum Addition End"),
description=_(u"Room Temperature at Serum Addition End"),
required=False,
)
# Choice of lab tech/lab manager
serum_witness_name = schema.TextLine(
title=_(u"Witness for Serum Addition"),
description=_(u"Witness for Serum Addition"),
required=False,
)
serum_witness_date = schema.Date(
title=_(u"Aliquot Consume Date"),
description=_(u"Aliquot Consume Date"),
required=False,
)
# Antibody Prep
# Antibody Addition
antibody_time_start = schema.Datetime(
title=_(u"Start Time of Antibody Addition"),
description=_(u"Start Time of Antibody Addition"),
required=False,
)
antibody_humidity_start = schema.Float(
title=_(u"Humidity at Antibody Addition Start"),
description=_(u"Humidity at Antibody Addition Start"),
required=False,
)
antibody_room_temperature_start = schema.Float(
title=_(u"Room Temperature at Antibody Addition Start"),
description=_(u"Room Temperature at Antibody Addition Start"),
required=False,
)
antibody_time_end = schema.Datetime(
title=_(u"End Time of Antibody Addition"),
description=_(u"End Time of Antibody Addition"),
required=False,
)
antibody_humidity_end = schema.Float(
title=_(u"Humidity at Antibody Addition End"),
description=_(u"Humidity at Antibody Addition End"),
required=False,
)
antibody_room_temperature_end = schema.Float(
title=_(u"Room Temperature at Antibody Addition End"),
description=_(u"Room Temperature at Antibody Addition End"),
required=False,
)
# Choice of labtech/labmanager
antibody_witness_name = schema.TextLine(
title=_(u"Witness for Antibody Addition"),
description=_(u"Witness for Antibody Addition"),
required=False,
)
antibody_witness_date = schema.Date(
title=_(u"Aliquot Consume Date"),
description=_(u"Aliquot Consume Date"),
required=False,
)
assay_uid = Attribute("""Assay UID
Link directly back to the iChipAssay so that the edit form has a copy
when required. Also used to link QC aliquots back to the HQC and LQC
of the selected Assay.
""")
assay_name = Attribute("""Assay Name
For convenience, I'll store the assay_name too, but it should not be used
for lookup.
""")
plates = Attribute("""Plates
A map of aliquots/ichips/wells per plate is stored here as a list
of dictionaries. The format matches what is excpected by the form,
which is the same as the data returned when creating a new test run.
The format of each plate looks like this:
{'chip-1_well-1': UID,
'chip-1_well-X': UID,
'chip-2_well-1': UID,
'chip-2_well-X': UID,
'chip-3_well-1': UID,
'chip-3_well-X': UID,
'chip-4_well-1': UID,
'chip-4_well-X': UID,
'chip-id-1': UID,
'chip-id-2': UID,
'chip-id-3': UID,
'chip-id-4': UID,
'comments-ichip-1': '',
'comments-ichip-2': '',
'comments-ichip-3': '',
'comments-ichip-4': '',
'scan-slot-1': '',
'scan-slot-2': '',
'scan-slot-3': '',
'scan-slot-4': '',
'comments': ''
}
""")
solutions = Attribute("""Solution batches in use
Details of all solution batches selected for use in this run, stored
as a list of lists like this:
[list of solution batch ids]
""")
ichip_humidity = Attribute("""iChip Humidity
Humidity is logged before and after each ichip is prepared.
""")
import_log = Attribute("""TestRun result import log.
""")
class IiChipAssay(BaseModel):
""" Interface that will allow for creation of new iChip Assays"""
name = schema.TextLine(
title=_(u"iChip Assay"),
required=True,
)
description = schema.TextLine(
title=_(u"Description"),
description=_(u"Description"),
required=False,
)
framecount = schema.Int(
title=_(u"Frame Layout"),
description=_(u"No Well = 1, Eight Well = 8"),
required=True,
)
number_of_unique_ichips_lots_needed = schema.Int(
title=_(u"Number of Unique iChip Lots Needed"),
description=_(u"Number of Unique iChip Lots Needed"),
required=True,
default=2,
)
number_of_same_lot_replication_needed = schema.Int(
title=_(u"Same Lot Replication Needed For Samples"),
description=_(u"Same Lot Replication Needed For Samples"),
required=True,
default=2,
)
number_of_high_value_controls = schema.Int(
title=_(u"Number of High/Positive Controls"),
description=_(u"Number of High/Positive Controls"),
required=True,
default=2,
)
qc_high_choice = schema.Choice(
title=_(u"Select High/Positive QC Veracis ID"),
description=_(u"Select High/Positive QC Veracis ID"),
source=InUseQCListVocabulary,
required=False,
)
number_of_low_value_controls = schema.Int(
title=_(u"Number of Low/Negative Controls"),
description=_(u"Number of Low/Negative Controls"),
required=True,
default=1,
)
qc_low_choice = schema.Choice(
title=_(u"Select Low/Negative QC Veracis ID"),
description=_(u"Select Low/Negative QC Veracis ID"),
source=InUseQCListVocabulary,
required=False,
)
sample_qc_dilution_factor = schema.Int(
title=_(u"Material Dilution Factor"),
description=_(u"Material Dilution Factor"),
required=True,
default=75,
)
# THere's a vocab for this in vocabs/solutions. XXX showing Types only.
# solutions = schema.List(
# value_type=schema.Choice(
# title=
# source=, required=False)
max_number_of_plates_per_test_run = schema.Int(
title=_(u"Max Number of Plates per Test Run"),
description=_(u"Max Number of Plates per Test Run"),
required=True,
default=8,
)
number_of_working_aliquots_needed = schema.Int(
title=_(u"Number of Working Aliquots Needed"),
description=_(u"Number of Working Aliquots Needed"),
required=True,
default=1,
)
desired_working_aliquot_volume = schema.Int(
title=_(u"Desired Working Aliquot Volume (uL)"),
description=_(u"Desired Working Aliquot Volume (uL)"),
required=True,
default=12,
)
minimum_working_aliquot_volume = schema.Int(
title=_(u"Minimum Working Aliquot Volume (uL)"),
description=_(u"Minimum Working Aliquot Volume (uL)"),
required=True,
default=8,
)
desired_use = schema.Choice(
title=_(u"iChip Assay Status"),
description=_(u"iChip Layout"),
values=[
_(u"Development"),
_(u"Commercial"),
],
required=True,
)
form.widget(needed_solutions=CheckBoxFieldWidget)
needed_solutions = schema.List(
title=_(u"Solutions Needed for Assay"),
description=_(u"Solutions Needed for Assay"),
required=False,
value_type=schema.Choice(source=SolutionsForiChipAssayVocabulary),
)
comments = RichText(
title=_(u"Comments"),
description=_(u"Comments"),
required=False,
)
class IBillingProgram(BaseModel):
"""Object that will be billing programs that can be added to the system,
will be what is used to determin if a billing message needs to be generated,
cost to patient, and message structure to be sent to third party.
"""
program_name = schema.TextLine(
title=_(u"Name of Billing Program"),
description=_(u"Name of Billing Program"),
required=False,
)
assay_name = schema.Choice(title=_(u"Assay to be Billed"),
description=_(u"Assay to be Billed"),
source=IChipAssayListVocabulary,
required=True)
cost_of_assay = schema.Float(
title=_(u"Full Cost of Assay"),
description=_(u"Full Cost of Assay"),
required=True,
)
max_cost_to_patient = schema.Float(
title=_(u"Max Cost to Patient"),
description=_(u"Max Cost to Patient"),
required=True,
)
discount_to_patient = schema.Float(
title=_(u"Discout to Patient"),
description=_(u"Discout to Patient"),
default=0.0,
required=True,
)
allow_balance_bill = schema.Bool(title=_(u"Allow Balance Billing"),
description=_(u"Allow Balance Billing"))
class IVeracisRunBase(BaseModel):
"""Object that will be the base of all veracis runs
"""
run_number = schema.Int(
title=_(u"Veracis Run Number"),
description=_(u"Veracis Run Number"),
required=True,
)
run_planner = schema.TextLine(
title=_(u"Veracis Run Planner"),
description=_(u"Veracis Run Operator"),
required=True,
)
run_operator = schema.TextLine(
title=_(u"Veracis Run Operator"),
description=_(u"Veracis Run Operator"),
required=True,
)
run_date = schema.Date(
title=_(u"Veracis Test Run Date"),
description=_(u"Veracis Test Run Date (MM/DD/YYYY)"),
default=date.today(),
)
test_scan_date = schema.Date(
title=_(u"Veracis Test Scan Date"),
description=_(u"Veracis Test Scan Date (MM/DD/YYYYY)"),
default=date.today(),
)
pdf_veracis_run = NamedBlobImage(
title=_(u"PDF Upload of Test Form"),
description=_(u"PDF Upload of Test Form"),
required=False,
)
class IiChip(BaseModel):
"""An iChip Lot that will be the container class object
"""
ichip_id = schema.TextLine(
title=_(u"iChip ID"),
required=True,
)
ichip_run_date = schema.TextLine(
title=_(u"iChip Run Date"),
description=_(u"Run Date of iChip (Read only)"),
readonly=True,
required=False,
)
# Image name to actual image (zip image file before upload)
image = schema.Dict(
key_type=schema.TextLine(
title=_(u"Image Title (ie Agilent Red)"),
description=_(u"Image Title (ie Agilent Red)"),
required=False,
),
value_type=NamedBlobImage(
title=_(u"iChip Agilent Image"),
description=_(u"Agilent Image of iChip (.tiff)"),
required=False),
)
# Image extraction name to extraction
image_extractions = schema.Dict(
key_type=schema.TextLine(
title=_(u"Image Extraction Title (ie Agilent Red)"),
description=_(u"Image Extraction Title (ie Agilent Red)"),
required=False,
),
value_type=NamedBlobFile(
title=_(u"iChip Agilent Image Extraction"),
description=_(u"Agilent Image Extraction of iChip (.tiff)"),
required=False),
)
# update to have vocabulary tied to choices
storage_location = schema.Choice(
title=_(u"iChip Storage Location"),
description=_(u"Storage Location of iChip"),
values=[_('EQ-76'), _('EQ-Unknown')],
required=False,
)
# well to aliquot ID tested on it
well_to_aliquot = schema.Dict(
key_type=schema.TextLine(
title=_(u"Well ID"),
description=_(u"Well ID"),
required=False,
),
value_type=schema.TextLine(
title=_(u"Aliquot ID"),
description=_(u"Aliquot ID"),
required=False,
),
)
comment = RichText(
title=_(u"iChip Comment"),
description=_(u"Comments about iChip"),
required=False,
)
class ICommercialBox(BaseModel):
"""Boxes can hold either 100 sampels or 81 samples"""
#tmp_box_number = assignBoxNumber()
box_number = schema.TextLine(
title=_(u'R&D Box Number'),
description=_(u'R&D Box Number'),
defaultFactory=assignBoxNumber(),
#default=assignBoxNumber(),
required=True,
)
box_type = schema.Choice(
title=_(u"Sample Type"),
description=_(u"Sample Type"),
values=[_(u"Bulk"), _(u"Working")],
required=True,
)
max_samples = schema.Int(
title=_(u'Max Number of Samples'),
description=_(u'Max Number of Samples'),
default=81,
)
remaining_volume = schema.Int(
title=_(u"Remaining Aliquot Spaces"),
description=_(u"Remaining Aliquot Spaces"),
required=True,
)
aliquot_dic = schema.Dict(title=_(u'Box Count to Aliquot ID'),
required=False,
key_type=schema.TextLine(
title=_(u"Box Count"),
description=_(u"Box Count"),
required=False,
),
value_type=List(
title=_(u"Aliquot ID, UID"),
description=_(u"Aliquot ID, UID"),
required=False,
))
class IClinicalAliquot(IAliquot):
title = schema.TextLine(
title=_(u"Aliquot Name"),
description=_(u"Aliquot Name/ID"),
required=False,
)
sample_id = schema.TextLine(
title=_(u"Parent ID"),
description=_(u"Parent ID"),
required=False,
)
aliquot_type = schema.Choice(
title=_(u"Aliquot Type"),
description=_(u"Aliquot Type"),
required=True,
values=[_(u'Bulk'), _(u'Working')],
)
pour_date = schema.Date(
title=_(u"Aliquot Pour Date"),
description=_(u"Aliquot Pour Date"),
required=False,
default=date.today(),
)
consume_date = schema.Date(
title=_(u"Aliquot Consume Date"),
description=_(u"Aliquot Consume Date"),
required=False,
)
numeric_result = schema.Float(
title=_(u"Numeric Result"),
description=_(u"SLE_key_Score"),
required=False,
)
text_result = schema.TextLine(
title=_(u"Text Result"),
description=_(u"SLE_key_Classification"),
required=False,
)
class IPatient(IPerson):
"""Patient record
"""
dob = schema.Date(
title=_(u"Date of Birth"),
description=_(u"Date of Birth"),
required=True,
)
marital_status = schema.Choice(
title=_(u"Marital Status"),
description=_(u"Marital Status"),
values=[_(u'Single'), _(u'Married'),
_(u'Other')],
required=False,
)
gender = schema.Choice(
title=_(u"Gender"),
description=_(u"Gender"),
values=[_(u'Male'), _(u'Female'),
_(u'Other')],
required=False,
)
ssn = schema.TextLine(
title=_(u"Social Security Number"),
description=_(u"Social Security Number"),
required=False,
)
medical_record_number = schema.TextLine(
title=_(u"Medical Record Number"),
description=_(u"Medical Record Number"),
required=False,
)
ethnicity = schema.Choice(
title=_(u"Patient Race"),
description=_(u"Patient Race"),
values=[
_(u'African American or Black'),
_(u'Asian Indian Middle Eastern'),
_(u'Caucasian'),
_(u'Hispanic or Latino'),
_(u'Other')
],
required=False,
)
ethnicity_other = schema.TextLine(
title=_(u"Ethnicity Other"),
description=_(u"Ethnicity Other"),
required=False,
)
# append to this list to track the sample run on a particular patient
tested_unique_sample_ids = schema.List(
title=_(u"List of Unique Sample Numbers"),
description=_(u"List of Unique Sample Numbers"),
required=False,
value_type=schema.TextLine())
class ICustomerServiceCall(BaseModel):
"""Interface for Customer Service Call objects CSC
"""
csc_client = schema.Choice(
title=_(u"Client"),
description=_(u"Client"),
required=True,
values=[_(u'Quarantined'), _(u'Released')],
)
csc_instance = schema.Choice(
title=_(u"Instance Type"),
description=_(u"Instance Type"),
required=True,
values=[_(u'Quarantined'), _(u'Released')],
)
csc_datetime = schema.Datetime(
title=_(u"Date and Time of Instance"),
description=_(u"Date and Time of Instance"),
required=False,
)
csc_follow_up_needed = schema.Bool(
title=_(u"Is Follow Up Needed"),
description=_(u"Is Follow Up Needed"),
required=False,
)
csc_status = schema.Choice(
title=_(u"Status of CSI"),
description=_(u"Status of CSI"),
required=True,
values=[_(u'Open'), _(u'Closed'), _(u'Held')],
)
csc_details = schema.Text(
title=_(u"Details of CSI"),
description=_(u"Details of CSI"),
required=False,
)
class IClinicalSample(ISample):
"""Sample that will contain all the billing info and high level information
that is applicable to all aliquots made from this material, location of
tests ordered on sample
"""
# Clinical Samples "Veracis ID" is stored here, in USN field.
usn = schema.TextLine(
title=_(u"Unique Sample Number"),
description=_(u"Sample ID from the blood draw kit"),
required=False,
)
# want to index this field
sample_serial_number = schema.Int(
title=_(u"Sample Serial Number"),
description=_(u"Sample Serial Number"),
required=False,
)
""" Want to do an n+1 but allow be edited, should be unique"""
# list or tuple? JP 3-14-17, let this be blank for remote order
# option at a later date, need test ordered and status!
# use this to drive a setup handler that will make the lists of what should
# be tested! (jp 4-11-17)
research_consent = schema.Choice(
title=_(u"Patient Consent to Research"),
description=_(u"Patient Gives consent to research use"),
values=[_(u'No'), _(u'Yes')],
required=True,
)
front_end_qa = schema.Choice(
title=_(u"Front End QA Status"),
description=_(u"Front End QA Status"),
required=False,
values=[_(u"Initial"),
_(u"Review Pass"),
_(u"Held"), ],
)
sample_ordering_healthcare_provider = schema.TextLine(
title=_(u"Ordering Healthcare Provider"),
description=_(u"Ordering Healthcare Provider"),
required=False,
)
sample_ordering_healthcare_provider_signature = schema.Bool(
title=_(u"Ordering Healthcare Provider Signature Provided"),
description=_(u"Ordering Healthcare Provider Signature Provided"),
required=False,
)
# directives.widget(primary_healthcare_provider=AutocompleteFieldWidget)
primary_healthcare_provider = schema.TextLine(
title=_(u"Primary Healthcare Provider"),
description=_(u"Primary Healthcare Provider"),
required=False,
)
"""directives.widget(level=RadioFieldWidget)"""
ana_testing = schema.Choice(
title=_(u"ANA Testing Results"),
description=_(u"ANA Testing Results"),
required=True,
values=[_(u'No Response'),
_(u'Not Performed'),
_(u'Negative'),
_(u'Positive')],
)
clinical_impression = schema.Choice(
title=_(u"Clinical Impression of SLE"),
description=_(u"Clinical Impression of SLE"),
required=True,
values=[_(u'Not Specified'),
_(u'Uncertain'),
_(u'Yes'),
_(u'No')],
)
xray_ordered = schema.Bool(
title=_(u"X-Ray Ordered"),
description=_(u"X-Ray Ordered"),
required=False,
)
other_test_ordered = schema.TextLine(
title=_(u"Other Test(s) Ordered"),
description=_(u"Other Test(s) Ordered Enter One Per Line"),
required=False,
)
"""working example of multi choice input jp 1-31-17"""
form.widget(symptoms_choice=CheckBoxFieldWidget)
symptoms_choice = schema.List(
title=_(u"Symptoms"),
description=_(u"Symptoms, Select All That Apply"),
required=False,
value_type=schema.Choice(
values=[_(u"Rash"),
_(u"Mouth Sores"),
_(u"Joint Pain"),
_(u"Inflammation"),
_(u"Seizures or Psychosis"),
_(u"Hair Loss")]),
)
joint_pain_text = schema.TextLine(
title=_(u"Joint Pain Specifics"),
description=_(u"Joint Pain Specifics (Enter One Per Line)"),
required=False,
)
inflammation_text = schema.TextLine(
title=_(u"Inflammation Specifics"),
description=_(u"Inflammation Specifics (Enter One Per Line)"),
required=False,
)
other_symptoms_text = schema.TextLine(
title=_(u"Other Symptom(s)"),
description=_(u"Other Symptom(s) Enter One Per Line"),
required=False,
)
phlebotomist_name = schema.TextLine(
title=_(u"Phlebotomist Name"),
description=_(u"Phlebotomist Name"),
required=False,
)
phlebotomist_signature_provided = schema.Bool(
title=_(u"Ordering Healthcare Provider Signature Provided"),
description=_(u"Ordering Healthcare Provider Signature Provided"),
required=False,
)
collection_date = schema.Date(
title=_(u"Sample Collection Date"),
description=_(u"Sample Collection Date"),
required=False,
default=date.today(),
)
received_date = schema.Date(
title=_(u"Sample Received Date"),
description=_(u"Sample Received Date"),
required=False,
default=date.today(),
)
class IMaterial(BaseModel):
"""Base schema fields common to all Material types.
To use these fields, create a new Dexterity type and enable the
IMaterial behaviour for it.
"""
product_name = schema.TextLine(title=_(u"Product Name"),
description=_(u"Product Name"),
required=True)
lot_number = schema.TextLine(title=_(u"Lot"),
description=_(u"The lot number"),
required=True)
bottle_number = schema.Int(
title=_(u"Bottle Number"),
description=_(u"Bottle Number"),
defaultFactory=AssignBottleNumber(),
required=True,
)
vendor = schema.TextLine(
title=_(u"Vendor"),
description=_(u"The vendor that supplied the lot"),
required=True)
catalog_number = schema.TextLine(
title=_(u"Catalog Number"),
description=_(u"The lot's catalog number"),
required=True)
arrival_date = schema.Date(
title=_(u"Arrival Date"),
description=_(u"The date on which the lot arrived"),
required=True)
expiration_date = schema.Date(
title=_(u"Expiration Date"),
description=_(u"The date on which the lot expires"),
required=True)
coa = NamedBlobImage(title=_(u"Certificate of Analysis"),
description=_(u"Certificate of Analysis"),
required=False)
initial_amount = Amount(
title=_(u"Initial Amount"),
description=_(u"Enter a decimal number"),
required=True,
)
remaining_amount = Amount(
title=_(u"Amount Remaining"),
description=_(u"You should not need to edit this value"),
)
unit = schema.TextLine(
title=_(u"Unit"),
description=_("Enter the unit in which the amounts are measured"),
required=True,
)
received_by = schema.Choice(
title=_(u"Received By"),
description=_(u"The operator that received the material lot"),
source=LabUsersUserVocabulary,
required=False # value will be completed by workflow transition
)
opened_by = schema.Choice(
title=_(u"Opened By"),
description=_(u"The operator that Opened the material lot"),
source=LabUsersUserVocabulary,
required=False # value will be completed by workflow transition
)
purchase_order = schema.TextLine(title=_(u"Purchase Order"),
description=_(u"Purchase Order"),
required=False)
shipping_tracking_number = schema.TextLine(
title=_(u"Shipping Tracking Number"),
description=_(u"Shipping Tracking Number"),
required=False)
intended_use = schema.Choice(
title=_(u"Intended Use"),
description=_(u"Intended Use"),
values=[_(u'Commercial'), _(u'Development')],
required=True,
)
meets_raw_material_specifications = schema.Choice(
title=_(u"Meets Raw Material Specifications"),
description=_(u"Meets Raw Material Specifications"),
values=[_(u'Yes'), _(u'No')],
required=False,
)
shipping_box_integrity_maintained = schema.Choice(
title=_(u"Raw Material Box Integrity Maintained"),
description=_(u"Raw Material Box Integrity Maintained"),
values=[_(u"Yes"), _(u"No")],
required=False,
)
product_container_integrity_maintained = schema.Choice(
title=_(u"Product Container Integrity Maintained"),
description=_(u"Product Container Integrity Maintained"),
values=[_(u"Yes"), _(u"No")],
required=False,
)
other_damage = schema.TextLine(
title=_(u"Other Damage"),
description=_(u"Other Damage"),
required=False,
)
temp_on_arrival = schema.TextLine(
title=_(u"Temperature of Raw Material on Arrival"),
description=_(u"Temperature of Raw Material on Arrival"),
required=False,
)
temp_on_arrival_acceptable_limit = schema.Choice(
title=_(u"Temperature of Raw Material on Arrival "
u"Within Acceptable Limit"),
description=_(u"Temperature of Raw Material on Arrival "
u"Within Acceptable Limit"),
values=[_(u"Yes"), _(u"No")],
required=False,
)
