def make_executive(portal):
if 'executive' in portal:
return
ex1 = create(portal, 'Folder', 'executive', 'Executive')
ex2 = create(ex1, 'Folder', 'reports', 'Reports')
disallow_default_contenttypes(ex1)
disallow_default_contenttypes(ex2)
ex1.setLayout('folder_contents')
ex2.setLayout('folder_contents')
ex1.manage_permission(AddLIMSRoot, [], 0)
ex1.manage_permission(permissions.AddFolder, [], 0)
ex1.manage_permission(View, ['LabManager', 'Executive'], 0)
ex1.manage_permission(AccessContentsInformation,
['LabManager', 'Executive'], 0)
ex1.manage_permission(ListFolderContents, ['LabManager', 'Executive'], 0)
ex1.manage_permission(ModifyPortalContent, ['LabManager', 'Executive'], 0)
ex2.manage_permission(AddLIMSRoot, [], 0)
ex2.manage_permission(permissions.AddFolder, [], 0)
ex2.manage_permission(View, ['LabManager', 'Executive'], 0)
ex2.manage_permission(AccessContentsInformation,
['LabManager', 'Executive'], 0)
ex2.manage_permission(ListFolderContents, ['LabManager', 'Executive'], 0)
ex2.manage_permission(ModifyPortalContent, ['LabManager', 'Executive'], 0)
def create_structure(lims):
for x in [
[lims, 'Folder', 'sites', 'Sites', ISites],
[lims, 'Folder', 'samples', 'Samples', ISamples],
[lims, 'Folder', 'materials', 'Materials', IMaterials],
[lims, 'Folder', 'solutions', 'Solutions', ISolutions],
[lims, 'Folder', 'ichiplots', 'iChip Lots', IiChipLots],
[lims, 'Folder', 'testruns', 'Test Runs', ITestRuns],
[lims, 'Folder', 'nce', 'Non Conformance Events', INonConformanceEvents],
[lims, 'Folder', 'inventory', 'Inventory', IInventory],
[lims, 'Folder', 'patients', 'Patients', IPatients],
[lims, 'Folder', 'providers', 'Providers', IProviders],
[lims, 'Folder', 'ichipassay', 'iChip Assays', IiChipAssays],
[lims, 'Folder', 'configuration', 'Configuration', IConfiguration],
]:
obj = create(container=x[0], type=x[1], id=x[2], title=x[3])
obj.setLayout('folder_contents')
disallow_default_contenttypes(obj)
alsoProvides(obj, x[4])
# Create configuration after other stuff, so that it's at the bottom of nav
configuration = lims.configuration
for x in [
[configuration, 'Folder', 'aliquoting', 'Aliquoting'],
[configuration, 'Folder', 'departments', 'Departments'],
[configuration, 'Folder', 'contacts', 'Contacts'],
[configuration, 'Folder', 'samplepoints', 'Sample Points'],
[configuration, 'Folder', 'sampletypes', 'Sample Types'],
[configuration, 'Folder', 'analysisservices', 'Analysis Services'],
[configuration, 'Folder', 'calculations', 'Calculations'],
]:
instance = create(container=x[0], type=x[1], id=x[2], title=x[3])
instance.setLayout('folder_contents')
disallow_default_contenttypes(instance)
def AssayBillingRequest(assaybillingrequest, event):
"""A new assay billing request been created!
"""
assaybillingrequest.manage_permission(delete_objects, [], 0)
assaybillingrequest.manage_permission(AddNCE, ['LabManager', 'LabClerk','BillingExec'], 0)
# Don't allow assay request to be nested in each other!
assaybillingrequest.manage_permission(AddAssayRequest, [], 0)
assaybillingrequest.manage_permission(AddClinicalAliquot, [], 0)
assaybillingrequest.manage_permission(AddAssayBillingRequest, [], 0)
disallow_default_contenttypes(assaybillingrequest)
def RandDAliquotAdded(randdaliquot, event):
randdaliquot.manage_permission(AddRandDAliquot, ['Manager', 'LabManager', 'LabClerk', 'Owner','RandDLabClerk', 'RandDLabManager'], 0)
# Don't allow samples to be nested in each other!
randdaliquot.manage_permission(AddClinicalSample, [], 0)
randdaliquot.manage_permission(AddRandDSample, [], 0)
randdaliquot.manage_permission(AddQCSample, [], 0)
# Don't allow other aliquots to be added (only R&D Aliquots should be added)
randdaliquot.manage_permission(AddClinicalAliquot, [], 0)
randdaliquot.manage_permission(AddQCAliquot, [], 0)
randdaliquot.manage_permission(permissions.AddImage, ['LabManager', 'LabClerk'], 0)
disallow_default_contenttypes(randdaliquot)
def AssayBillingRequest(assaybillingrequest, event):
"""A new assay billing request been created!
"""
assaybillingrequest.manage_permission(delete_objects, [], 0)
assaybillingrequest.manage_permission(
AddNCE, ['LabManager', 'LabClerk', 'BillingExec'], 0)
# Don't allow assay request to be nested in each other!
assaybillingrequest.manage_permission(AddAssayRequest, [], 0)
assaybillingrequest.manage_permission(AddClinicalAliquot, [], 0)
assaybillingrequest.manage_permission(AddAssayBillingRequest, [], 0)
disallow_default_contenttypes(assaybillingrequest)
def QCSampleAdded(qcsample, event):
qcsample.manage_permission(AddQCAliquot, ['LabManager', 'LabClerk'], 0)
qcsample.manage_permission(AddAssayRequest, ['LabManager', 'LabClerk'], 0)
qcsample.manage_permission(AddNCE, ['LabManager', 'LabClerk'], 0)
# Don't allow samples to be nested in each other!
qcsample.manage_permission(AddRandDSample, [], 0)
qcsample.manage_permission(AddQCSample, [], 0)
qcsample.manage_permission(AddClinicalSample, [], 0)
# Don't allow other aliquots to be added (only QC Aliquots should be added)
qcsample.manage_permission(AddClinicalAliquot, [], 0)
qcsample.manage_permission(AddRandDAliquot, [], 0)
qcsample.manage_permission(permissions.AddImage, ['LabManager', 'LabClerk'], 0)
disallow_default_contenttypes(qcsample)
def ClinicalAliquotAdded(clinicalaliquot, event):
"""A new Clinical Sample has been created!
"""
clinicalaliquot.manage_permission(delete_objects, [], 0)
clinicalaliquot.manage_permission(AddClinicalAliquot, ['Manager', 'LabManager', 'LabClerk', 'Owner'], 0)
# Don't allow samples to be nested in each other!
clinicalaliquot.manage_permission(AddQCSample, [], 0)
clinicalaliquot.manage_permission(AddRandDSample, [], 0)
clinicalaliquot.manage_permission(AddClinicalSample, [], 0)
# Don't allow other aliquots to be added (only R&D Aliquots should be added)
clinicalaliquot.manage_permission(AddRandDAliquot, [], 0)
clinicalaliquot.manage_permission(AddQCAliquot, [], 0)
clinicalaliquot.manage_permission(permissions.AddImage, ['LabManager', 'LabClerk'], 0)
disallow_default_contenttypes(clinicalaliquot)
def RandDAliquotAdded(randdaliquot, event):
randdaliquot.manage_permission(AddRandDAliquot, [
'Manager', 'LabManager', 'LabClerk', 'Owner', 'RandDLabClerk',
'RandDLabManager'
], 0)
# Don't allow samples to be nested in each other!
randdaliquot.manage_permission(AddClinicalSample, [], 0)
randdaliquot.manage_permission(AddRandDSample, [], 0)
randdaliquot.manage_permission(AddQCSample, [], 0)
# Don't allow other aliquots to be added (only R&D Aliquots should be added)
randdaliquot.manage_permission(AddClinicalAliquot, [], 0)
randdaliquot.manage_permission(AddQCAliquot, [], 0)
randdaliquot.manage_permission(permissions.AddImage,
['LabManager', 'LabClerk'], 0)
disallow_default_contenttypes(randdaliquot)
def ClinicalSampleAdded(clinicalsample, event):
"""A new Clinical Sample has been created!
"""
clinicalsample.manage_permission(AddClinicalAliquot, ['LabManager', 'LabClerk'], 0)
clinicalsample.manage_permission(AddAssayRequest, ['LabManager', 'LabClerk'], 0)
clinicalsample.manage_permission(AddNCE, ['LabManager', 'LabClerk'], 0)
# Don't allow samples to be nested in each other!
clinicalsample.manage_permission(AddQCSample, [], 0)
clinicalsample.manage_permission(AddRandDSample, [], 0)
clinicalsample.manage_permission(AddClinicalSample, [], 0)
# Don't allow other aliquots to be added (only R&D Aliquots should be added)
clinicalsample.manage_permission(AddRandDAliquot, [], 0)
clinicalsample.manage_permission(AddQCAliquot, [], 0)
clinicalsample.manage_permission(permissions.AddImage, ['LabManager', 'LabClerk'], 0)
disallow_default_contenttypes(clinicalsample)
def ClinicalAliquotAdded(clinicalaliquot, event):
"""A new Clinical Sample has been created!
"""
clinicalaliquot.manage_permission(delete_objects, [], 0)
clinicalaliquot.manage_permission(
AddClinicalAliquot, ['Manager', 'LabManager', 'LabClerk', 'Owner'], 0)
# Don't allow samples to be nested in each other!
clinicalaliquot.manage_permission(AddQCSample, [], 0)
clinicalaliquot.manage_permission(AddRandDSample, [], 0)
clinicalaliquot.manage_permission(AddClinicalSample, [], 0)
# Don't allow other aliquots to be added (only R&D Aliquots should be added)
clinicalaliquot.manage_permission(AddRandDAliquot, [], 0)
clinicalaliquot.manage_permission(AddQCAliquot, [], 0)
clinicalaliquot.manage_permission(permissions.AddImage,
['LabManager', 'LabClerk'], 0)
disallow_default_contenttypes(clinicalaliquot)
def MakePatient(self, pt, dob, marital_status, gender,
ssn, mrn, consent_acquired, ethnicity):
#set permission for new patient record
pt.manage_permission(
AddPatient, ['Manager', 'LabManager', 'LabClerk', 'Owner'], 0)
disallow_default_contenttypes(pt)
patient = api.content.create(container=pt,
type = 'Patient',
dob = dob,
marital_status = marital_status,
gender = gender,
ssn = ssn,
medical_record_number = mrn,
research_consent = consent_acquired,
race = ethnicity,
)
def CommercialBoxAdded(instance, event):
"""A new commercial box has been created
"""
# Permit Aliquots to be added here
instance.manage_permission(AddAliquot, [], 0)
# Prevent adding box in a box
instance.manage_permission(AddCommercialBox, [], 0)
instance.manage_permission(AddRandDBox, [], 0)
instance.manage_permission(AddQCBox, [], 0)
disallow_default_contenttypes(instance)
# name box
instance.setTitle(
"%s - %s - %s" %
(instance.box_number, instance.box_type, instance.Type()))
# reindex for title to work
instance.reindexObject(idxs=['Title', 'sortable_title', 'title'])
def MakePatient(self, pt, dob, marital_status, gender, ssn, mrn,
consent_acquired, ethnicity):
#set permission for new patient record
pt.manage_permission(AddPatient,
['Manager', 'LabManager', 'LabClerk', 'Owner'], 0)
disallow_default_contenttypes(pt)
patient = api.content.create(
container=pt,
type='Patient',
dob=dob,
marital_status=marital_status,
gender=gender,
ssn=ssn,
medical_record_number=mrn,
research_consent=consent_acquired,
race=ethnicity,
)
def iChipLotAdded(instance, event):
"""iChipLot has been added, some configuration and permissions
to set on the new folder
"""
# Set default permissions for a new ichiplot
instance.manage_permission(delete_objects, [], 0)
instance.manage_permission(AddiChip, ['LabManager', 'LabClerk'], 0)
disallow_default_contenttypes(instance)
# I want to create X amount of iChips from form value.
for x in range(1, instance.nr_ichips + 1):
ichip = create(container=instance,
title="{0}_{1:03d}".format(instance.title, x),
type='iChip',
ichip_id="{0}_{1:03d}".format(instance.title, x))
# Configure each ichip to reflect the parent's settings
ichip.frames = instance.frames
def iChipLotAdded(instance, event):
"""iChipLot has been added, some configuration and permissions
to set on the new folder
"""
# Set default permissions for a new ichiplot
instance.manage_permission(delete_objects, [], 0)
instance.manage_permission(AddiChip, ['LabManager', 'LabClerk'], 0)
disallow_default_contenttypes(instance)
# I want to create X amount of iChips from form value.
for x in range(1, instance.nr_ichips + 1):
ichip = create(container=instance,
title = "{0}_{1:03d}".format(instance.title, x),
type='iChip',
ichip_id="{0}_{1:03d}".format(instance.title, x))
# Configure each ichip to reflect the parent's settings
ichip.frames = instance.frames
def RackAdded(instance, event):
"""A new Rack has been created!
"""
# Permit Commercial Boxes to be added here
# @formatter:off
instance.manage_permission(AddCommercialBox,
['Manager', 'LabManager', 'LabClerk', 'Owner'],
0)
instance.manage_permission(
AddRandDBox,
['Manager', 'LabManager', 'RandDLabClerk', 'RandDLabManager', 'Owner'],
0)
instance.manage_permission(
AddQCBox,
['Manager', 'LabManager', 'RandDLabClerk', 'RandDLabManager', 'Owner'],
0)
# @formatter:on
# Prevent adding Rack in a rack!
instance.manage_permission(AddRack, [], 0)
disallow_default_contenttypes(instance)
def make_executive(portal):
if 'executive' in portal:
return
ex1 = create(portal, 'Folder', 'executive', 'Executive')
ex2 = create(ex1, 'Folder', 'reports', 'Reports')
disallow_default_contenttypes(ex1)
disallow_default_contenttypes(ex2)
ex1.setLayout('folder_contents')
ex2.setLayout('folder_contents')
ex1.manage_permission(AddLIMSRoot, [], 0)
ex1.manage_permission(
permissions.AddFolder, [], 0)
ex1.manage_permission(
View, ['LabManager', 'Executive'], 0)
ex1.manage_permission(
AccessContentsInformation, ['LabManager', 'Executive'], 0)
ex1.manage_permission(
ListFolderContents, ['LabManager', 'Executive'], 0)
ex1.manage_permission(
ModifyPortalContent, ['LabManager', 'Executive'], 0)
ex2.manage_permission(AddLIMSRoot, [], 0)
ex2.manage_permission(
permissions.AddFolder, [], 0)
ex2.manage_permission(
View, ['LabManager', 'Executive'], 0)
ex2.manage_permission(
AccessContentsInformation, ['LabManager', 'Executive'], 0)
ex2.manage_permission(
ListFolderContents, ['LabManager', 'Executive'], 0)
ex2.manage_permission(
ModifyPortalContent, ['LabManager', 'Executive'], 0)
def make_billing(portal):
if 'billing' in portal:
return
b1 = create(portal, 'Folder', 'billing', 'Billing')
b2 = create(b1, 'Folder', 'assaybillingrequests', 'Assay Billing Requests')
b3 = create(b1, 'Folder', 'billingProgram_workflow', 'Billing Programs')
disallow_default_contenttypes(b1)
disallow_default_contenttypes(b2)
disallow_default_contenttypes(b3)
b1.setLayout('folder_contents')
b2.setLayout('folder_contents')
b3.setLayout('folder_contents')
# @formatter:off
b1.manage_permission(AddLIMSRoot, [], 0)
b1.manage_permission(permissions.AddFolder, [], 0)
b1.manage_permission(View, ['LabManager', 'BillingExec'], 0)
b1.manage_permission(AccessContentsInformation,
['LabManager', 'BillingExec'], 0)
b1.manage_permission(ListFolderContents, ['LabManager', 'BillingExec'], 0)
b1.manage_permission(AddAssayBillingRequest, ['LabManager', 'BillingExec'],
0)
b1.manage_permission(ModifyPortalContent, ['LabManager', 'BillingExec'], 0)
b1.manage_permission(AddAssayBillingRequest, [], 0)
b1.manage_permission(AddBillingProgram, [], 0)
b1.manage_permission(AddAliquotPlate, [], 0)
b2.manage_permission(AddLIMSRoot, [], 0)
b2.manage_permission(permissions.AddFolder, [], 0)
b2.manage_permission(View, ['LabManager', 'BillingExec'], 0)
b2.manage_permission(AccessContentsInformation,
['LabManager', 'BillingExec'], 0)
b2.manage_permission(ListFolderContents, ['LabManager', 'BillingExec'], 0)
b2.manage_permission(ModifyPortalContent, ['LabManager', 'BillingExec'], 0)
b2.manage_permission(AddAssayBillingRequest, ['LabManager', 'BillingExec'],
0)
b2.manage_permission(AddBillingProgram, [], 0)
b2.manage_permission(AddAliquotPlate, [], 0)
b2.manage_permission(AddLIMSRoot, [], 0)
b3.manage_permission(permissions.AddFolder, [], 0)
b3.manage_permission(View, ['LabManager', 'BillingExec'], 0)
b3.manage_permission(AccessContentsInformation,
['LabManager', 'BillingExec'], 0)
b3.manage_permission(ListFolderContents, ['LabManager', 'BillingExec'], 0)
b3.manage_permission(AddBillingProgram, ['LabManager', 'BillingExec'], 0)
b3.manage_permission(ModifyPortalContent, ['LabManager', 'BillingExec'], 0)
b3.manage_permission(AddAssayBillingRequest, [], 0)
b3.manage_permission(AddAliquotPlate, [], 0)
def make_billing(portal):
if 'billing' in portal:
return
b1 = create(portal, 'Folder', 'billing', 'Billing')
b2 = create(b1, 'Folder', 'assaybillingrequests', 'Assay Billing Requests')
b3 = create(b1, 'Folder', 'billingProgram_workflow', 'Billing Programs')
disallow_default_contenttypes(b1)
disallow_default_contenttypes(b2)
disallow_default_contenttypes(b3)
b1.setLayout('folder_contents')
b2.setLayout('folder_contents')
b3.setLayout('folder_contents')
# @formatter:off
b1.manage_permission(AddLIMSRoot, [], 0)
b1.manage_permission(permissions.AddFolder, [], 0)
b1.manage_permission(View, ['LabManager', 'BillingExec'], 0)
b1.manage_permission(AccessContentsInformation, ['LabManager', 'BillingExec'], 0)
b1.manage_permission(ListFolderContents, ['LabManager', 'BillingExec'], 0)
b1.manage_permission(AddAssayBillingRequest, ['LabManager', 'BillingExec'], 0)
b1.manage_permission(ModifyPortalContent, ['LabManager', 'BillingExec'], 0)
b1.manage_permission(AddAssayBillingRequest,[],0)
b1.manage_permission(AddBillingProgram,[],0)
b1.manage_permission(AddAliquotPlate,[],0)
b2.manage_permission(AddLIMSRoot, [], 0)
b2.manage_permission(permissions.AddFolder, [], 0)
b2.manage_permission(View, ['LabManager', 'BillingExec'], 0)
b2.manage_permission(AccessContentsInformation, ['LabManager', 'BillingExec'], 0)
b2.manage_permission(ListFolderContents, ['LabManager', 'BillingExec'], 0)
b2.manage_permission(ModifyPortalContent, ['LabManager', 'BillingExec'], 0)
b2.manage_permission(AddAssayBillingRequest, ['LabManager', 'BillingExec'], 0)
b2.manage_permission(AddBillingProgram,[],0)
b2.manage_permission(AddAliquotPlate,[],0)
b2.manage_permission(AddLIMSRoot, [], 0)
b3.manage_permission(permissions.AddFolder, [], 0)
b3.manage_permission(View, ['LabManager', 'BillingExec'], 0)
b3.manage_permission(AccessContentsInformation, ['LabManager', 'BillingExec'], 0)
b3.manage_permission(ListFolderContents, ['LabManager', 'BillingExec'], 0)
b3.manage_permission(AddBillingProgram, ['LabManager', 'BillingExec'], 0)
b3.manage_permission(ModifyPortalContent, ['LabManager', 'BillingExec'], 0)
b3.manage_permission(AddAssayBillingRequest, [],0)
b3.manage_permission(AddAliquotPlate,[],0)
def make_customer_service(portal):
if 'customerservice' in portal:
return
cs1 = create(portal, 'Folder', 'customerservice', 'Customer Service')
cs2 = create(cs1, 'Folder', 'customercalls', 'Customer Calls')
cs3 = create(cs1, 'Folder', 'providercalls', 'Provider Calls')
disallow_default_contenttypes(cs1)
disallow_default_contenttypes(cs2)
disallow_default_contenttypes(cs3)
cs1.setLayout('folder_contents')
cs2.setLayout('folder_contents')
cs3.setLayout('folder_contents')
# @formatter:off
cs1.manage_permission(AddLIMSRoot, [], 0)
cs1.manage_permission(permissions.AddFolder, [], 0)
cs1.manage_permission(View, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs1.manage_permission(AccessContentsInformation, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs1.manage_permission(ListFolderContents, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs1.manage_permission(AddAssayBillingRequest, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs1.manage_permission(ModifyPortalContent, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs2.manage_permission(AddLIMSRoot, [], 0)
cs2.manage_permission(permissions.AddFolder, [], 0)
cs2.manage_permission(View, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs2.manage_permission(AccessContentsInformation, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs2.manage_permission(ListFolderContents, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs2.manage_permission(AddCustomerServiceCall, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs2.manage_permission(ModifyPortalContent, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs3.manage_permission(AddLIMSRoot, [], 0)
cs3.manage_permission(permissions.AddFolder, [], 0)
cs3.manage_permission(View, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs3.manage_permission(AccessContentsInformation, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs3.manage_permission(ListFolderContents, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs3.manage_permission(AddBillingProgram, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs3.manage_permission(ModifyPortalContent, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
def ProviderAdded(instance, event):
"""A new material has been created!
"""
instance.manage_permission(AddProvider, [], 0)
disallow_default_contenttypes(instance)
def SiteAdded(instance, event):
"""A new material has been created!
"""
instance.manage_permission(AddSite, [], 0)
disallow_default_contenttypes(instance)
def make_clinical_sample(
self, usn_from_form, consent_acquired, ana_testing, clin_rash,
clin_seiz_psych, clin_mouth_sores, clin_hair_loss, clin_joint_pain,
clin_inflam, clin_other, clin_other_specify, diag_D89_89,
diag_M32_10, diag_D89_9, diag_M35_9, diag_L93_2, diag_other,
diag_other_specify, provider_nip_clean, provider_signed,
draw_location, draw_tel, phlebotomist_name, draw_signed,
collection_date, shipment_date, test_other_specify,
clinical_impression, ordering_provider_name, site_id,
assay_selection, other_clinical_symptoms, other_inflam,
other_joint_pain):
"""Make a clinical sample via api, set serial number
Need to add option for assay choice at a later date
"""
# logical test order passed via end user
# assign serial number for sample
sn = api.content.find(context=api.portal.get(),
portal_type='ClinicalSample')
all_sn = []
# list of all serial numbers
sn_uid = [s.UID for s in sn]
for i in sn_uid:
value = api.content.get(UID=i)
all_sn.append(value.sample_serial_number)
if len(all_sn) == 0:
serial_number = 10000
else:
serial_number = max(all_sn) + 1
symptoms_choice = []
if clin_rash is not None:
symptoms_choice.append(unicode(clin_rash, "utf-8"))
if clin_seiz_psych is not None:
symptoms_choice.append(unicode(clin_seiz_psych, "utf-8"))
if clin_mouth_sores is not None:
symptoms_choice.append(unicode(clin_mouth_sores, "utf-8"))
if clin_hair_loss is not None:
symptoms_choice.append(unicode(clin_hair_loss, "utf-8"))
if clin_joint_pain is not None:
symptoms_choice.append(unicode(clin_joint_pain, "utf-8"))
if clin_inflam is not None:
symptoms_choice.append(unicode(clin_inflam, "utf-8"))
if clin_other is not None:
symptoms_choice.append(unicode(clin_other, "utf-8"))
# datetime.datetime.strptime
diagnosis_code = []
if diag_D89_89 is not None:
diagnosis_code.append(unicode(diag_D89_89, "utf-8"))
if diag_M32_10 is not None:
diagnosis_code.append(unicode(diag_M32_10, "utf-8"))
if diag_D89_9 is not None:
diagnosis_code.append(unicode(diag_D89_9, "utf-8"))
if diag_M35_9 is not None:
diagnosis_code.append(unicode(diag_M35_9, "utf-8"))
if diag_L93_2 is not None:
diagnosis_code.append(unicode(diag_L93_2, "utf-8"))
if diag_other is not None:
diagnosis_code.append(unicode(diag_other, "utf-8"))
try:
py_collection_date = \
datetime.datetime.strptime(collection_date, "%Y-%m-%d").date()
except:
py_collection_date = None
try:
py_shipment_date = \
datetime.datetime.strptime(shipment_date, "%Y-%m-%d").date()
except:
py_shipment_date = None
# need to split clin_other_specify on ', '
# if clin_other_specify != "":
# Get primary health care provider from site!
site_objects = api.content.find(context=api.portal.get(),
portal_type='Site')
site_uids = [i.UID for i in site_objects]
primary_provider = "null"
for j in site_uids:
site = api.content.get(UID=j)
if site_id == str(site.title):
primary_provider = site.primary_provider
# set permission for clinical sample
cs = api.portal.get()
sample = cs['lims']['samples']
disallow_default_contenttypes(sample)
clinical_sample = api.content.create(
container=sample,
type='ClinicalSample',
id=usn_from_form,
usn=usn_from_form,
safe_id=True,
sample_serial_number=serial_number,
research_consent=consent_acquired,
sample_ordering_healthcare_provider=ordering_provider_name,
sample_ordering_healthcare_provider_signature=provider_signed,
primary_healthcare_provider=primary_provider,
ana_testing=ana_testing,
clinical_impression=clinical_impression,
other_test_ordered=test_other_specify,
symptoms_choice=symptoms_choice,
symptoms_text=clin_other_specify,
phlebotomist_name=phlebotomist_name,
phlebotomist_signature_provided=draw_signed,
collection_date=py_collection_date,
received_date=py_shipment_date,
joint_pain_text=other_joint_pain,
inflammation_text=other_inflam,
other_symptoms_text=other_clinical_symptoms,
)
clinical_sample_uid = clinical_sample.UID()
# Creates Assay Request Object on Sample Creation, on for each assay
# selected!
for a in assay_selection:
assay_request = api.content.create(
container=clinical_sample,
type='AssayRequest',
title=a,
assay_name=a)
transition(assay_request, to_state='to_be_tested')
# add billing program from rec to object
billing_request = api.content.create(
container=assay_request,
type='AssayBillingRequest',
title=usn_from_form,
safe_id=True,
assay_name=a,
sample_id=usn_from_form,
diagnosis_code=diagnosis_code,
diagnosis_code_other=diag_other_specify)
return clinical_sample_uid
def make_clinical_sample(
self, usn_from_form, consent_acquired, ana_testing, clin_rash,
clin_seiz_psych, clin_mouth_sores, clin_hair_loss, clin_joint_pain,
clin_inflam, clin_other, clin_other_specify, diag_D89_89,
diag_M32_10, diag_D89_9, diag_M35_9, diag_L93_2, diag_other,
diag_other_specify, provider_nip_clean, provider_signed,
draw_location, draw_tel, phlebotomist_name, draw_signed,
collection_date, shipment_date, test_other_specify,
clinical_impression, ordering_provider_name, site_id,
assay_selection, other_clinical_symptoms, other_inflam,
other_joint_pain):
"""Make a clinical sample via api, set serial number
Need to add option for assay choice at a later date
"""
# logical test order passed via end user
# assign serial number for sample
sn = api.content.find(context=api.portal.get(),
portal_type='ClinicalSample')
all_sn = []
# list of all serial numbers
sn_uid = [s.UID for s in sn]
for i in sn_uid:
value = api.content.get(UID=i)
all_sn.append(value.sample_serial_number)
if len(all_sn) == 0:
serial_number = 10000
else:
serial_number = max(all_sn) + 1
symptoms_choice = []
if clin_rash is not None:
symptoms_choice.append(unicode(clin_rash, "utf-8"))
if clin_seiz_psych is not None:
symptoms_choice.append(unicode(clin_seiz_psych, "utf-8"))
if clin_mouth_sores is not None:
symptoms_choice.append(unicode(clin_mouth_sores, "utf-8"))
if clin_hair_loss is not None:
symptoms_choice.append(unicode(clin_hair_loss, "utf-8"))
if clin_joint_pain is not None:
symptoms_choice.append(unicode(clin_joint_pain, "utf-8"))
if clin_inflam is not None:
symptoms_choice.append(unicode(clin_inflam, "utf-8"))
if clin_other is not None:
symptoms_choice.append(unicode(clin_other, "utf-8"))
# datetime.datetime.strptime
diagnosis_code = []
if diag_D89_89 is not None:
diagnosis_code.append(unicode(diag_D89_89, "utf-8"))
if diag_M32_10 is not None:
diagnosis_code.append(unicode(diag_M32_10, "utf-8"))
if diag_D89_9 is not None:
diagnosis_code.append(unicode(diag_D89_9, "utf-8"))
if diag_M35_9 is not None:
diagnosis_code.append(unicode(diag_M35_9, "utf-8"))
if diag_L93_2 is not None:
diagnosis_code.append(unicode(diag_L93_2, "utf-8"))
if diag_other is not None:
diagnosis_code.append(unicode(diag_other, "utf-8"))
try:
py_collection_date = \
datetime.datetime.strptime(collection_date, "%Y-%m-%d").date()
except:
py_collection_date = None
try:
py_shipment_date = \
datetime.datetime.strptime(shipment_date, "%Y-%m-%d").date()
except:
py_shipment_date = None
# need to split clin_other_specify on ', '
# if clin_other_specify != "":
# Get primary health care provider from site!
site_objects = api.content.find(context=api.portal.get(),
portal_type='Site')
site_uids = [i.UID for i in site_objects]
primary_provider = "null"
for j in site_uids:
site = api.content.get(UID=j)
if site_id == str(site.title):
primary_provider = site.primary_provider
# set permission for clinical sample
cs = api.portal.get()
sample = cs['lims']['samples']
disallow_default_contenttypes(sample)
clinical_sample = api.content.create(
container=sample,
type='ClinicalSample',
id=usn_from_form,
usn=usn_from_form,
safe_id=True,
sample_serial_number=serial_number,
research_consent=consent_acquired,
sample_ordering_healthcare_provider=ordering_provider_name,
sample_ordering_healthcare_provider_signature=provider_signed,
primary_healthcare_provider=primary_provider,
ana_testing=ana_testing,
clinical_impression=clinical_impression,
other_test_ordered=test_other_specify,
symptoms_choice=symptoms_choice,
symptoms_text=clin_other_specify,
phlebotomist_name=phlebotomist_name,
phlebotomist_signature_provided=draw_signed,
collection_date=py_collection_date,
received_date=py_shipment_date,
joint_pain_text=other_joint_pain,
inflammation_text=other_inflam,
other_symptoms_text=other_clinical_symptoms,
)
clinical_sample_uid = clinical_sample.UID()
# Creates Assay Request Object on Sample Creation, on for each assay
# selected!
for a in assay_selection:
assay_request = api.content.create(container=clinical_sample,
type='AssayRequest',
title=a,
assay_name=a)
transition(assay_request, to_state='to_be_tested')
# add billing program from rec to object
billing_request = api.content.create(
container=assay_request,
type='AssayBillingRequest',
title=usn_from_form,
safe_id=True,
assay_name=a,
sample_id=usn_from_form,
diagnosis_code=diagnosis_code,
diagnosis_code_other=diag_other_specify)
return clinical_sample_uid
def MaterialModified(instance, event):
"""A new material has been created!
"""
instance.manage_permission(AddMaterial, [], 0)
disallow_default_contenttypes(instance)
def MaterialModified(instance, event):
"""A new material has been created!
"""
instance.manage_permission(AddMaterial, [], 0)
disallow_default_contenttypes(instance)
def SolutionModified(instance, event):
"""A new solution has been created!
"""
instance.manage_permission(AddSolution, [], 0)
disallow_default_contenttypes(instance)
UpdateSourceMaterials(instance, event)
def SolutionModified(instance, event):
"""A new solution has been created!
"""
instance.manage_permission(AddSolution, [], 0)
disallow_default_contenttypes(instance)
UpdateSourceMaterials(instance, event)
def make_customer_service(portal):
if 'customerservice' in portal:
return
cs1 = create(portal, 'Folder', 'customerservice', 'Customer Service')
cs2 = create(cs1, 'Folder', 'customercalls', 'Customer Calls')
cs3 = create(cs1, 'Folder', 'providercalls', 'Provider Calls')
disallow_default_contenttypes(cs1)
disallow_default_contenttypes(cs2)
disallow_default_contenttypes(cs3)
cs1.setLayout('folder_contents')
cs2.setLayout('folder_contents')
cs3.setLayout('folder_contents')
# @formatter:off
cs1.manage_permission(AddLIMSRoot, [], 0)
cs1.manage_permission(permissions.AddFolder, [], 0)
cs1.manage_permission(
View, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs1.manage_permission(
AccessContentsInformation,
['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs1.manage_permission(
ListFolderContents,
['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs1.manage_permission(
AddAssayBillingRequest,
['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs1.manage_permission(
ModifyPortalContent,
['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs2.manage_permission(AddLIMSRoot, [], 0)
cs2.manage_permission(permissions.AddFolder, [], 0)
cs2.manage_permission(
View, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs2.manage_permission(
AccessContentsInformation,
['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs2.manage_permission(
ListFolderContents,
['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs2.manage_permission(
AddCustomerServiceCall,
['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs2.manage_permission(
ModifyPortalContent,
['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs3.manage_permission(AddLIMSRoot, [], 0)
cs3.manage_permission(permissions.AddFolder, [], 0)
cs3.manage_permission(
View, ['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs3.manage_permission(
AccessContentsInformation,
['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs3.manage_permission(
ListFolderContents,
['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs3.manage_permission(
AddBillingProgram,
['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
cs3.manage_permission(
ModifyPortalContent,
['LabManager', 'LabClerk', 'SalesRep', 'BillingExec'], 0)
