def __init__(self, context, request):
SE.__init__(self, context, request)
if IAliquot.providedBy(context):
self.icon = self.portal_url + \
"/++resource++bika.sanbi.images/aliquot_big.png"
elif IBiospecimen.providedBy(context):
self.icon = self.portal_url + \
"/++resource++bika.sanbi.images/biospecimen_big.png"
self.allow_edit = True
def biospecimens(self):
""" Return samples providing IBiospecimen of the current project
"""
items = []
w_tool = getToolByName(self.context, 'portal_workflow')
samples = self.context.objectValues('Sample')
for sample in samples:
if IBiospecimen.providedBy(sample):
st1 = w_tool.getStatusOf("bika_sample_workflow", sample)
st2 = w_tool.getStatusOf("bika_cancellation_workflow", sample)
if st1.get('review_state', None) == 'sample_received' and \
st2.get('cancellation_state', None) == 'active':
items.append({'uid': sample.UID(), 'title': sample.Title()})
items.sort(lambda x, y: cmp(x['title'], y['title']))
return items
def __init__(self, context):
self.context = context
self.sort = 10
self.random = 4
if IAliquot.providedBy(context):
self.hidden_fields = ['Kit', 'SubjectID',
'Barcode', 'Sampling Date',
'ScheduledSamplingSampler',
'PreparationWorkflow',
'SamplePoint', 'Sampler']
if IBiospecimen.providedBy(context):
self.hidden_fields = ['Sampling Date',
'LinkedSample',
'ScheduledSamplingSampler',
'PreparationWorkflow',
'SamplePoint', 'Sampler']
def biospecimens(self):
""" Return samples providing IBiospecimen of the current project
"""
items = []
w_tool = getToolByName(self.context, 'portal_workflow')
samples = self.context.objectValues('Sample')
for sample in samples:
if IBiospecimen.providedBy(sample):
st1 = w_tool.getStatusOf("bika_sample_workflow", sample)
st2 = w_tool.getStatusOf("bika_cancellation_workflow", sample)
if st1.get('review_state', None) == 'sample_received' and \
st2.get('cancellation_state', None) == 'active':
items.append({
'uid': sample.UID(),
'title': sample.Title()
})
items.sort(lambda x, y: cmp(x['title'], y['title']))
return items
def folderitems(self, full_objects=False):
items = BikaListingView.folderitems(self)
bsc = getToolByName(self.context, 'bika_setup_catalog')
brains = bsc(portal_type='SampleType', inactive_state='active')
biospecimen_types = [{
'ResultValue': brain.UID,
'ResultText': brain.title
} for brain in brains]
ret = []
for x, item in enumerate(items):
if not items[x].has_key('obj'):
continue
obj = items[x]['obj']
if not IBiospecimen.providedBy(obj):
continue
items[x]['Type'] = obj.getSampleType() and obj.getSampleType(
).Title() or ''
items[x]['Volume'] = obj.getField('Volume').get(obj)
items[x]['Unit'] = VOLUME_UNITS[0]['ResultText']
items[x]['SubjectID'] = obj.getField('SubjectID').get(obj)
kit = obj.getField('Kit').get(obj)
items[x]['Kit'] = kit
items[x]['Project'] = obj.aq_parent
if kit:
items[x]['replace']['Kit'] = \
'<a href="%s">%s</a>' % (kit.absolute_url(), kit.Title())
items[x]['replace']['Project'] = \
'<a href="%s">%s</a>' % (kit.aq_parent.absolute_url(),
kit.aq_parent.Title())
items[x]['Barcode'] = obj.getField('Barcode').get(obj)
items[x]['replace']['Title'] = "<a href='%s'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
# TODO: SPECIFY OBJ STATES WHERE USER CAN EDIT BARCODE
if self.allow_edit and isActive(self.context) and \
getSecurityManager().checkPermission(ManageAliquots, obj) and \
items[x]['review_state'] == "sample_due":
items[x]['allow_edit'] = [
'Type', 'SubjectID', 'Barcode', 'Volume', 'Unit'
]
items[x]['choices']['Type'] = biospecimen_types
items[x]['choices']['Unit'] = VOLUME_UNITS
ret.append(item)
return ret
def folderitems(self, full_objects=False):
items = BikaListingView.folderitems(self)
bsc = getToolByName(self.context, 'bika_setup_catalog')
brains = bsc(portal_type='SampleType', inactive_state='active')
biospecimen_types = [
{
'ResultValue': brain.UID,
'ResultText': brain.title
}
for brain in brains
]
ret = []
for x, item in enumerate(items):
if not items[x].has_key('obj'):
continue
obj = items[x]['obj']
if not IBiospecimen.providedBy(obj):
continue
items[x]['Type'] = obj.getSampleType() and obj.getSampleType().Title() or ''
items[x]['Volume'] = obj.getField('Volume').get(obj)
items[x]['Unit'] = VOLUME_UNITS[0]['ResultText']
items[x]['SubjectID'] = obj.getField('SubjectID').get(obj)
kit = obj.getField('Kit').get(obj)
items[x]['Kit'] = kit
items[x]['Project'] = obj.aq_parent
if kit:
items[x]['replace']['Kit'] = \
'<a href="%s">%s</a>' % (kit.absolute_url(), kit.Title())
items[x]['replace']['Project'] = \
'<a href="%s">%s</a>' % (kit.aq_parent.absolute_url(),
kit.aq_parent.Title())
items[x]['Barcode'] = obj.getField('Barcode').get(obj)
items[x]['replace']['Title'] = "<a href='%s'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
# TODO: SPECIFY OBJ STATES WHERE USER CAN EDIT BARCODE
if self.allow_edit and isActive(self.context) and \
getSecurityManager().checkPermission(ManageAliquots, obj) and \
items[x]['review_state'] == "sample_due":
items[x]['allow_edit'] = ['Type', 'SubjectID', 'Barcode', 'Volume', 'Unit']
items[x]['choices']['Type'] = biospecimen_types
items[x]['choices']['Unit'] = VOLUME_UNITS
ret.append(item)
return ret
def objects_between_two_uids(context, uid_1, uid_2, portal_type, wf_1, wf_2, state):
"""Retrieve the objects of type portal_type between two ordered objects
using their uids.
"""
w_tool = getToolByName(context, 'portal_workflow')
uc = getToolByName(context, 'uid_catalog')
first_id = uc(UID=uid_1)[0].id
last_id = uc(UID=uid_2)[0].id
objects = context.objectValues(portal_type)
# Filter objects by workflow state active
items = []
for obj in objects:
if IBiospecimen.providedBy(obj):
st1 = w_tool.getStatusOf(wf_1, obj)
st2 = w_tool.getStatusOf(wf_2, obj)
if st1.get('review_state', None) == state and \
st2.get('cancellation_state', None) == 'active' and \
first_id <= obj.getId() <= last_id:
items.append(obj)
return items
def objects_between_two_uids(context, uid_1, uid_2, portal_type, wf_1, wf_2,
state):
"""Retrieve the objects of type portal_type between two ordered objects
using their uids.
"""
w_tool = getToolByName(context, 'portal_workflow')
uc = getToolByName(context, 'uid_catalog')
first_id = uc(UID=uid_1)[0].id
last_id = uc(UID=uid_2)[0].id
objects = context.objectValues(portal_type)
# Filter objects by workflow state active
items = []
for obj in objects:
if IBiospecimen.providedBy(obj):
st1 = w_tool.getStatusOf(wf_1, obj)
st2 = w_tool.getStatusOf(wf_2, obj)
if st1.get('review_state', None) == state and \
st2.get('cancellation_state', None) == 'active' and \
first_id <= obj.getId() <= last_id:
items.append(obj)
return items
