def checkout_update(context, request):
db_session = request.db_session
vals = filter_aliquot(context, request, state='pending-checkout')
available_locations = [
(l.id, l.title)
for l in db_session.query(models.Location).order_by('title')]
class CheckoutForm(wtforms.Form):
location_id = wtforms.SelectField(
_('Lab Location'),
description=_('The location of the aliquot'),
choices=available_locations,
coerce=int,
validators=[
wtforms.validators.DataRequired()])
sent_date = DateField(
_(u'Sent Date'),
description=_(u'Date sent for analysis.'),
validators=[
wtforms.validators.Optional(),
DateRange(min=date(1900, 1, 1))
])
sent_name = wtforms.StringField(
_(u'Sent Name '),
description=_(u'The name of the aliquot\'s receiver.'),
validators=[wtforms.validators.Optional()])
sent_notes = wtforms.TextAreaField(
_(u'Sent Notes '),
description=_(u'Notes about this aliquot\'s destination'),
validators=[wtforms.validators.Optional()])
form = CheckoutForm(request.POST, location_id=context.id)
if request.method == 'POST' and check_csrf_token(request):
if 'save' in request.POST and form.validate():
for sample in vals['full_query']:
apply_changes(form, sample)
request.session.flash(_(u'Changed saved'), 'success')
return HTTPOk(json={
'__next__': request.current_route_path(
_route_name='lims.checkout')
})
vals.update({
'form': form
})
return vals
def checkout_update(context, request):
db_session = request.db_session
vals = filter_aliquot(context, request, state='pending-checkout')
available_locations = [
(l.id, l.title)
for l in db_session.query(models.Location).order_by('title')
]
class CheckoutForm(wtforms.Form):
location_id = wtforms.SelectField(
_('Lab Location'),
description=_('The location of the aliquot'),
choices=available_locations,
coerce=int,
validators=[wtforms.validators.DataRequired()])
sent_date = DateField(_(u'Sent Date'),
description=_(u'Date sent for analysis.'),
validators=[
wtforms.validators.Optional(),
DateRange(min=date(1900, 1, 1))
])
sent_name = wtforms.StringField(
_(u'Sent Name '),
description=_(u'The name of the aliquot\'s receiver.'),
validators=[wtforms.validators.Optional()])
sent_notes = wtforms.TextAreaField(
_(u'Sent Notes '),
description=_(u'Notes about this aliquot\'s destination'),
validators=[wtforms.validators.Optional()])
form = CheckoutForm(request.POST, location_id=context.id)
if request.method == 'POST' and check_csrf_token(request):
if 'save' in request.POST and form.validate():
for sample in vals['full_query']:
apply_changes(form, sample)
request.session.flash(_(u'Changed saved'), 'success')
return HTTPOk(
json={
'__next__':
request.current_route_path(_route_name='lims.checkout')
})
vals.update({'form': form})
return vals
def checked_in(context, request):
db_session = request.db_session
vals = filter_aliquot(context, request, state='checked-in')
aliquot = vals['aliquot']
available_locations = [
(l.id, l.title)
for l in db_session.query(models.Location).order_by('title')
]
if 'checkout' in request.POST:
conditionally_required = required_if('ui_selected')
else:
conditionally_required = wtforms.validators.optional()
class CheckoutForm(wtforms.Form):
ui_selected = wtforms.BooleanField()
id = wtforms.IntegerField(widget=wtforms.widgets.HiddenInput())
amount = wtforms.DecimalField(places=1,
validators=[conditionally_required])
freezer = wtforms.StringField(
validators=[wtforms.validators.optional()])
rack = wtforms.StringField(validators=[wtforms.validators.optional()])
box = wtforms.StringField(validators=[wtforms.validators.optional()])
thawed_num = wtforms.IntegerField(
validators=[wtforms.validators.optional()])
location_id = wtforms.SelectField(
choices=available_locations,
coerce=int,
validators=[wtforms.validators.optional()])
notes = wtforms.TextAreaField(
validators=[wtforms.validators.optional()])
class CrudForm(wtforms.Form):
aliquot = wtforms.FieldList(wtforms.FormField(CheckoutForm))
form = CrudForm(request.POST, aliquot=aliquot)
if request.method == 'POST' and check_csrf_token(request):
if 'save' in request.POST and form.validate():
for i, entry in enumerate(form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
request.session.flash(_(u'Changed saved'), 'success')
return HTTPFound(location=request.current_route_path())
elif 'pending-checkout' in request.POST and form.validate():
state = (db_session.query(
models.AliquotState).filter_by(name='pending-checkout').one())
updated_count = 0
for i, entry in enumerate(form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
if entry.ui_selected.data:
aliquot[i].location = context
aliquot[i].state = state
updated_count += 1
db_session.flush()
if updated_count:
request.session.flash(
_(
u'${count} aliquot have been changed to the status of '
u'${state}',
mapping={
'count': updated_count,
'state': state.title
}), 'success')
else:
request.session.flash(_(u'Please select Aliquot'), 'warning')
return HTTPFound(location=request.current_route_path())
vals.update({
'form': form,
})
return vals
def aliquot(context, request):
db_session = request.db_session
specimen_vals = filter_specimen(context,
request,
page_key='specimenpage',
state='pending-aliquot')
specimen = specimen_vals['specimen']
template_values = [{
'specimen': s,
'collect_date': date.today()
} for s in specimen]
aliquot_vals = filter_aliquot(context,
request,
page_key='aliquotpage',
state='pending')
aliquot = aliquot_vals['aliquot']
label_queue = request.session.setdefault(ALIQUOT_LABEL_QUEUE, set())
class AliquotForm(wtforms.Form):
ui_selected = wtforms.BooleanField()
id = wtforms.IntegerField(widget=wtforms.widgets.HiddenInput())
amount = wtforms.DecimalField(
places=1, validators=[wtforms.validators.required()])
collect_date = DateField(validators=[
wtforms.validators.required(),
DateRange(min=date(1900, 1, 1))
])
collect_time = TimeField(validators=[
wtforms.validators.required(),
])
freezer = wtforms.StringField(
validators=[wtforms.validators.optional()])
rack = wtforms.StringField(validators=[wtforms.validators.optional()])
box = wtforms.StringField(validators=[wtforms.validators.optional()])
notes = wtforms.TextAreaField(
validators=[wtforms.validators.optional()])
class SpecimenAliquotForm(AliquotForm):
count = wtforms.IntegerField(validators=[
required_if('ui_selected'),
wtforms.validators.optional()
])
aliquot_type_id = wtforms.SelectField(
coerce=int, validators=[required_if('ui_selected')])
def __init__(self, *args, **kw):
super(AliquotForm, self).__init__(*args, **kw)
if 'obj' in kw:
obj = kw['obj']
if isinstance(obj, models.Specimen):
specimen = obj
elif isinstance(obj, models.Aliquot):
specimen = obj.specimen
else:
try:
specimen = kw['specimen']
except KeyError:
specimen = None
if specimen:
self.aliquot_type_id.choices = [
(t.id, t.title)
for t in specimen.specimen_type.aliquot_types.values()
]
else:
self.aliquot_type_id.choices = []
class SpecimenCrudForm(wtforms.Form):
specimen = wtforms.FieldList(wtforms.FormField(SpecimenAliquotForm))
class AliquotCrudForm(wtforms.Form):
aliquot = wtforms.FieldList(wtforms.FormField(AliquotForm))
# Accomodate WTForm's inability to process multiple forms on the same page
# by only passing in the appropriate formdata to the target form
if 'template-form' in request.POST:
specimen_formdata = request.POST
else:
specimen_formdata = None
if 'aliquot-form' in request.POST:
aliquot_formdata = request.POST
else:
aliquot_formdata = None
specimen_form = SpecimenCrudForm(specimen_formdata,
specimen=template_values)
aliquot_form = AliquotCrudForm(aliquot_formdata, aliquot=aliquot)
def update_print_queue():
queued = 0
for entry in aliquot_form.aliquot.entries:
subform = entry.form
if subform.ui_selected.data:
id = subform.id.data
if id in label_queue:
label_queue.discard(id)
else:
queued += 1
label_queue.add(id)
request.session.changed()
return queued
if request.method == 'POST' and check_csrf_token(request):
if not request.has_permission('process'):
raise HTTPForbidden
if 'create' in request.POST and specimen_form.validate():
state = (db_session.query(
models.AliquotState).filter_by(name='pending').one())
location = context
processed_count = 0
for i, entry in enumerate(specimen_form.specimen.entries):
subform = entry.form
# Yes, you are reading this correctly, the original
# code said it needs to be selected AND set
if not (subform.ui_selected.data and subform.count.data):
continue
kw = subform.data
kw['specimen'] = specimen[i]
kw['state'] = state
kw['location'] = location
kw['inventory_date'] = kw['collect_date']
kw['previous_location'] = location
# clean up the dictionary
for field in ['id', 'ui_selected', 'count']:
if field in kw.keys():
del kw[field]
count = subform.count.data
samples = [models.Aliquot(**kw) for i in range(count)]
db_session.add_all(aliquot)
db_session.flush()
processed_count += len(samples)
if processed_count:
request.session.changed()
request.session.flash(
_(u'Successfully created %d Aliquot' % processed_count),
'success')
else:
request.session.flash(_(u'No Aliquot created.'), 'warning')
return HTTPFound(location=request.current_route_path())
elif 'pending-draw' in request.POST:
state_name = 'pending-draw'
state = (db_session.query(
models.SpecimenState).filter_by(name=state_name).one())
transitioned_count = 0
for i, subform in enumerate(specimen_form.specimen.entries):
if subform.ui_selected.data:
specimen[i].state = state
transitioned_count += 1
if transitioned_count:
db_session.flush()
request.session.flash(
_(
u'${count} specimen have been changed to the '
u'status of ${state}.',
mapping={
'count': transitioned_count,
'state': state.title
}), 'success')
else:
request.session.flash(u'Please select specimen', 'warning')
return HTTPFound(location=request.current_route_path())
elif 'aliquoted' in request.POST:
state_name = 'aliquoted'
state = (db_session.query(
models.SpecimenState).filter_by(name=state_name).one())
transitioned_count = 0
for i, subform in enumerate(specimen_form.specimen.entries):
if subform.ui_selected.data:
specimen[i].state = state
transitioned_count += 1
if transitioned_count:
db_session.flush()
request.session.flash(
_(
u'${count} specimen have been changed to the '
u'status of ${state}.',
mapping={
'count': transitioned_count,
'state': state.title
}), 'success')
else:
request.session.flash(u'Please select specimen', 'warning')
return HTTPFound(location=request.current_route_path())
elif 'save' in request.POST and aliquot_form.validate():
updated_count = 0
for i, entry in enumerate(aliquot_form.aliquot.entries):
if apply_changes(entry.form, aliquot[i]):
updated_count += 1
if updated_count:
request.session.flash(
_(u'Updated ${count} aliquot',
mapping={'count': updated_count}), 'success')
else:
request.session.flash(_(u'No changes made'), 'warning')
return HTTPFound(location=request.current_route_path())
elif 'queue' in request.POST and aliquot_form.validate():
for i, subform in enumerate(aliquot_form.aliquot.entries):
apply_changes(subform.form, aliquot[i])
queue_count = update_print_queue()
if queue_count:
request.session.flash(u'Aliquot print queue has changed.',
'success')
else:
request.session.flash(u'Please select aliquot', 'warning')
return HTTPFound(location=request.current_route_path())
elif 'checkin' in request.POST and aliquot_form.validate():
transitioned_count = 0
state = (db_session.query(
models.AliquotState).filter_by(name='checked-in').one())
for i, entry in enumerate(aliquot_form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
if entry.ui_selected.data:
aliquot[i].state = state
transitioned_count += 1
update_print_queue()
if transitioned_count > 0:
request.session.flash(
_(
u'${count} aliquot have been changed to the status '
u'of ${state}.',
mapping={
'count': transitioned_count,
'state': state.title
}), 'success')
else:
request.session.flash(u'Please select aliquot', 'warning')
return HTTPFound(location=request.current_route_path())
elif 'delete' in request.POST and aliquot_form.validate():
deleted_count = 0
for i, entry in enumerate(aliquot_form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
if entry.ui_selected.data:
deleted_count += 1
db_session.delete(aliquot[i])
update_print_queue()
if deleted_count > 0:
request.session.flash(
_(u'${count} aliquot have been deleted.',
mapping={'count': deleted_count}), 'success')
else:
request.session.flash(_(u'Please select Aliquot'), 'warning')
return HTTPFound(location=request.current_route_path())
return {
'filter_form': aliquot_vals['filter_form'],
'has_aliquot': aliquot_vals['has_aliquot'],
'aliquot': aliquot_vals['aliquot'],
'aliquot_pager': aliquot_vals['pager'],
'aliquot_form': aliquot_form,
'has_labels_queued': len(label_queue),
'label_queue': label_queue,
'has_specimen': specimen_vals['has_specimen'],
'specimen': specimen_vals['specimen'],
'specimen_pager': specimen_vals['pager'],
'specimen_form': specimen_form,
}
def checkout(context, request):
db_session = request.db_session
vals = filter_aliquot(context, request, state='pending-checkout')
aliquot = vals['aliquot']
available_locations = [
(l.id, l.title)
for l in db_session.query(models.Location).order_by('title')
]
# TODO: the values in this form really should be in the crud form
# since the receipt depends on the sent loation being unique.
# If we ever do this, "bulk update" button won't be needed anymore
class CheckoutForm(wtforms.Form):
ui_selected = wtforms.BooleanField()
id = wtforms.IntegerField(widget=wtforms.widgets.HiddenInput())
location_id = wtforms.SelectField(
choices=available_locations,
coerce=int,
validators=[wtforms.validators.DataRequired()])
sent_date = DateField(validators=[wtforms.validators.Optional()])
sent_name = wtforms.StringField(
validators=[wtforms.validators.Optional()])
sent_notes = wtforms.TextAreaField(
validators=[wtforms.validators.Optional()])
class CrudForm(wtforms.Form):
aliquot = wtforms.FieldList(wtforms.FormField(CheckoutForm))
form = CrudForm(request.POST, aliquot=aliquot)
if request.method == 'POST' and check_csrf_token(request):
if 'save' in request.POST and form.validate():
for i, entry in enumerate(form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
request.session.flash(_(u'Changed saved'), 'success')
return HTTPFound(location=request.current_route_path())
elif 'return' in request.POST and form.validate():
state = (db_session.query(
models.AliquotState).filter_by(name='checked-in').one())
updated_count = 0
for i, entry in enumerate(form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
if entry.ui_selected.data:
aliquot[i].location = context
aliquot[i].state = state
updated_count += 1
db_session.flush()
if updated_count:
request.session.flash(
_(
u'${count} aliquot have been changed to the status '
u'of ${state}',
mapping={
'count': updated_count,
'state': state.title
}), 'success')
else:
request.session.flash(_(u'Please select Aliquot'), 'warning')
return HTTPFound(location=request.current_route_path())
elif 'complete' in request.POST and form.validate():
state = (db_session.query(
models.AliquotState).filter_by(name='checked-out').one())
updated_count = 0
for i, entry in enumerate(form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
if entry.ui_selected.data:
aliquot[i].state = state
updated_count += 1
db_session.flush()
if updated_count:
request.session.flash(
_(
u'${count} aliquot have been changed to the status '
u'of ${state}',
mapping={
'count': updated_count,
'state': state.title
}), 'success')
else:
request.session.flash(_(u'Please select Aliquot'), 'warning')
return HTTPFound(location=request.current_route_path())
vals.update({
'form': form,
})
return vals
def aliquot(context, request):
db_session = request.db_session
specimen_vals = filter_specimen(
context, request, page_key='specimenpage', state='pending-aliquot')
specimen = specimen_vals['specimen']
template_values = [
{'specimen': s, 'collect_date': date.today()}
for s in specimen
]
aliquot_vals = filter_aliquot(
context, request, page_key='aliquotpage', state='pending')
aliquot = aliquot_vals['aliquot']
label_queue = request.session.setdefault(ALIQUOT_LABEL_QUEUE, set())
class AliquotForm(wtforms.Form):
ui_selected = wtforms.BooleanField()
id = wtforms.IntegerField(
widget=wtforms.widgets.HiddenInput())
amount = wtforms.DecimalField(
places=1,
validators=[wtforms.validators.required()])
collect_date = DateField(
validators=[
wtforms.validators.required(),
DateRange(min=date(1900, 1, 1))
])
collect_time = TimeField(
validators=[
wtforms.validators.required(),
])
freezer = wtforms.StringField(
validators=[wtforms.validators.optional()])
rack = wtforms.StringField(
validators=[wtforms.validators.optional()])
box = wtforms.StringField(
validators=[wtforms.validators.optional()])
notes = wtforms.TextAreaField(
validators=[wtforms.validators.optional()])
class SpecimenAliquotForm(wtforms.Form):
"""
Similar form to Aliquot, except the fields are conditionally required
if they are selected
"""
ui_selected = wtforms.BooleanField()
id = wtforms.IntegerField(
widget=wtforms.widgets.HiddenInput())
amount = wtforms.DecimalField(
places=1,
validators=[required_if('ui_selected')])
collect_date = DateField(
validators=[
required_if('ui_selected'),
DateRange(min=date(1900, 1, 1))
])
collect_time = TimeField(
validators=[required_if('ui_selected')])
freezer = wtforms.StringField(
validators=[wtforms.validators.optional()])
rack = wtforms.StringField(
validators=[wtforms.validators.optional()])
box = wtforms.StringField(
validators=[wtforms.validators.optional()])
notes = wtforms.TextAreaField(
validators=[wtforms.validators.optional()])
count = wtforms.IntegerField(
validators=[
required_if('ui_selected'),
wtforms.validators.optional()
]
)
aliquot_type_id = wtforms.SelectField(
coerce=int,
validators=[required_if('ui_selected')]
)
def __init__(self, *args, **kw):
super(SpecimenAliquotForm, self).__init__(*args, **kw)
specimen = None
if 'obj' in kw:
obj = kw['obj']
if isinstance(obj, models.Specimen):
specimen = obj
elif isinstance(obj, models.Aliquot):
specimen = obj.specimen
elif 'specimen' in kw:
specimen = kw['specimen']
if specimen:
self.aliquot_type_id.choices = [
(t.id, t.title)
for t in specimen.specimen_type.aliquot_types.values()]
else:
self.aliquot_type_id.choices = []
class SpecimenCrudForm(wtforms.Form):
specimen = wtforms.FieldList(wtforms.FormField(SpecimenAliquotForm))
class AliquotCrudForm(wtforms.Form):
aliquot = wtforms.FieldList(wtforms.FormField(AliquotForm))
# Accomodate WTForm's inability to process multiple forms on the same page
# by only passing in the appropriate formdata to the target form
if 'template-form' in request.POST:
specimen_formdata = request.POST
else:
specimen_formdata = None
if 'aliquot-form' in request.POST:
aliquot_formdata = request.POST
else:
aliquot_formdata = None
specimen_form = SpecimenCrudForm(specimen_formdata, specimen=template_values)
aliquot_form = AliquotCrudForm(aliquot_formdata, aliquot=aliquot)
def update_print_queue():
queued = 0
for entry in aliquot_form.aliquot.entries:
subform = entry.form
if subform.ui_selected.data:
id = subform.id.data
if id in label_queue:
label_queue.discard(id)
else:
queued += 1
label_queue.add(id)
request.session.changed()
return queued
if request.method == 'POST' and check_csrf_token(request):
if not request.has_permission('process'):
raise HTTPForbidden
if 'create' in request.POST and specimen_form.validate():
state = (
db_session.query(models.AliquotState)
.filter_by(name='pending')
.one())
location = context
processed_count = 0
for i, entry in enumerate(specimen_form.specimen.entries):
subform = entry.form
# Yes, you are reading this correctly, the original
# code said it needs to be selected AND set
if not (subform.ui_selected.data and subform.count.data):
continue
kw = subform.data
kw['specimen'] = specimen[i]
kw['state'] = state
kw['location'] = location
kw['inventory_date'] = kw['collect_date']
kw['previous_location'] = location
# clean up the dictionary
for field in ['id', 'ui_selected', 'count']:
if field in kw.keys():
del kw[field]
count = subform.count.data
samples = [models.Aliquot(**kw) for i in range(count)]
db_session.add_all(aliquot)
db_session.flush()
processed_count += len(samples)
if processed_count:
request.session.changed()
request.session.flash(
_(u'Successfully created %d Aliquot' % processed_count),
'success')
else:
request.session.flash(_(u'No Aliquot created.'), 'warning')
return HTTPFound(location=request.current_route_path())
elif 'pending-draw' in request.POST:
state_name = 'pending-draw'
state = (
db_session.query(models.SpecimenState)
.filter_by(name=state_name)
.one())
transitioned_count = 0
for i, subform in enumerate(specimen_form.specimen.entries):
if subform.ui_selected.data:
specimen[i].state = state
transitioned_count += 1
if transitioned_count:
db_session.flush()
request.session.flash(
_(u'${count} specimen have been changed to the '
u'status of ${state}.',
mapping={'count': transitioned_count,
'state': state.title}),
'success')
else:
request.session.flash(u'Please select specimen', 'warning')
return HTTPFound(location=request.current_route_path())
elif 'aliquoted' in request.POST:
state_name = 'aliquoted'
state = (
db_session.query(models.SpecimenState)
.filter_by(name=state_name)
.one())
transitioned_count = 0
for i, subform in enumerate(specimen_form.specimen.entries):
if subform.ui_selected.data:
specimen[i].state = state
transitioned_count += 1
if transitioned_count:
db_session.flush()
request.session.flash(
_(u'${count} specimen have been changed to the '
u'status of ${state}.',
mapping={'count': transitioned_count,
'state': state.title}),
'success')
else:
request.session.flash(u'Please select specimen', 'warning')
return HTTPFound(location=request.current_route_path())
elif 'save' in request.POST and aliquot_form.validate():
updated_count = 0
for i, entry in enumerate(aliquot_form.aliquot.entries):
if apply_changes(entry.form, aliquot[i]):
updated_count += 1
if updated_count:
request.session.flash(
_(u'Updated ${count} aliquot',
mapping={'count': updated_count}),
'success')
else:
request.session.flash(_(u'No changes made'), 'warning')
return HTTPFound(location=request.current_route_path())
elif 'queue' in request.POST and aliquot_form.validate():
for i, subform in enumerate(aliquot_form.aliquot.entries):
apply_changes(subform.form, aliquot[i])
queue_count = update_print_queue()
if queue_count:
request.session.flash(
u'Aliquot print queue has changed.', 'success')
else:
request.session.flash(u'Please select aliquot', 'warning')
return HTTPFound(location=request.current_route_path())
elif 'checkin' in request.POST and aliquot_form.validate():
transitioned_count = 0
state = (
db_session.query(models.AliquotState)
.filter_by(name='checked-in')
.one())
for i, entry in enumerate(aliquot_form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
if entry.ui_selected.data:
aliquot[i].state = state
transitioned_count += 1
update_print_queue()
if transitioned_count > 0:
request.session.flash(
_(u'${count} aliquot have been changed to the status '
u'of ${state}.',
mapping={'count': transitioned_count,
'state': state.title}),
'success')
else:
request.session.flash(u'Please select aliquot', 'warning')
return HTTPFound(location=request.current_route_path())
elif 'delete' in request.POST and aliquot_form.validate():
deleted_count = 0
for i, entry in enumerate(aliquot_form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
if entry.ui_selected.data:
deleted_count += 1
db_session.delete(aliquot[i])
update_print_queue()
if deleted_count > 0:
request.session.flash(
_(u'${count} aliquot have been deleted.',
mapping={'count': deleted_count}),
'success')
else:
request.session.flash(
_(u'Please select Aliquot'),
'warning')
return HTTPFound(location=request.current_route_path())
return {
'filter_form': aliquot_vals['filter_form'],
'has_aliquot': aliquot_vals['has_aliquot'],
'aliquot': aliquot_vals['aliquot'],
'aliquot_pager': aliquot_vals['pager'],
'aliquot_form': aliquot_form,
'has_labels_queued': len(label_queue),
'label_queue': label_queue,
'has_specimen': specimen_vals['has_specimen'],
'specimen': specimen_vals['specimen'],
'specimen_pager': specimen_vals['pager'],
'specimen_form': specimen_form,
}
def checkout(context, request):
db_session = request.db_session
vals = filter_aliquot(context, request, state='pending-checkout')
aliquot = vals['aliquot']
available_locations = [
(l.id, l.title)
for l in db_session.query(models.Location).order_by('title')]
# TODO: the values in this form really should be in the crud form
# since the receipt depends on the sent loation being unique.
# If we ever do this, "bulk update" button won't be needed anymore
class CheckoutForm(wtforms.Form):
ui_selected = wtforms.BooleanField()
id = wtforms.IntegerField(
widget=wtforms.widgets.HiddenInput())
location_id = wtforms.SelectField(
choices=available_locations,
coerce=int,
validators=[
wtforms.validators.DataRequired()])
sent_date = DateField(
validators=[
wtforms.validators.Optional(),
DateRange(min=date(1900, 1, 1))
])
sent_name = wtforms.StringField(
validators=[wtforms.validators.Optional()])
sent_notes = wtforms.TextAreaField(
validators=[wtforms.validators.Optional()])
class CrudForm(wtforms.Form):
aliquot = wtforms.FieldList(wtforms.FormField(CheckoutForm))
form = CrudForm(request.POST, aliquot=aliquot)
if request.method == 'POST' and check_csrf_token(request):
if 'save' in request.POST and form.validate():
for i, entry in enumerate(form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
request.session.flash(_(u'Changed saved'), 'success')
return HTTPFound(location=request.current_route_path())
elif 'return' in request.POST and form.validate():
state = (
db_session.query(models.AliquotState)
.filter_by(name='checked-in')
.one())
updated_count = 0
for i, entry in enumerate(form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
if entry.ui_selected.data:
aliquot[i].location = context
aliquot[i].state = state
updated_count += 1
db_session.flush()
if updated_count:
request.session.flash(
_(u'${count} aliquot have been changed to the status '
u'of ${state}',
mapping={
'count': updated_count,
'state': state.title
}),
'success')
else:
request.session.flash(_(u'Please select Aliquot'), 'warning')
return HTTPFound(location=request.current_route_path())
elif 'complete' in request.POST and form.validate():
state = (
db_session.query(models.AliquotState)
.filter_by(name='checked-out')
.one())
updated_count = 0
for i, entry in enumerate(form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
if entry.ui_selected.data:
aliquot[i].state = state
updated_count += 1
db_session.flush()
if updated_count:
request.session.flash(
_(u'${count} aliquot have been changed to the status '
u'of ${state}',
mapping={
'count': updated_count,
'state': state.title
}),
'success')
else:
request.session.flash(_(u'Please select Aliquot'), 'warning')
return HTTPFound(location=request.current_route_path())
vals.update({
'form': form,
})
return vals
def checkin(context, request):
db_session = request.db_session
vals = filter_aliquot(context, request, state='checked-out')
aliquot = vals['aliquot']
available_locations = [
(l.id, l.title)
for l in db_session.query(models.Location).order_by('title')]
if 'checkin' in request.POST:
conditionally_required = required_if('ui_selected')
else:
conditionally_required = wtforms.validators.optional()
class CheckinForm(wtforms.Form):
ui_selected = wtforms.BooleanField()
id = wtforms.IntegerField(
widget=wtforms.widgets.HiddenInput())
amount = wtforms.DecimalField(
places=1,
validators=[conditionally_required])
freezer = wtforms.StringField(
validators=[wtforms.validators.optional()])
rack = wtforms.StringField(
validators=[wtforms.validators.optional()])
box = wtforms.StringField(
validators=[wtforms.validators.optional()])
thawed_num = wtforms.IntegerField(
validators=[wtforms.validators.optional()])
location_id = wtforms.SelectField(
choices=available_locations,
coerce=int,
validators=[wtforms.validators.optional()])
notes = wtforms.TextAreaField(
validators=[wtforms.validators.optional()])
class CrudForm(wtforms.Form):
aliquot = wtforms.FieldList(wtforms.FormField(CheckinForm))
form = CrudForm(request.POST, aliquot=aliquot)
if request.method == 'POST' and check_csrf_token(request):
if 'save' in request.POST and form.validate():
for i, entry in enumerate(form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
request.session.flash(_(u'Changed saved'), 'success')
return HTTPFound(location=request.current_route_path())
elif 'checkin' in request.POST and form.validate():
state = (
db_session.query(models.AliquotState)
.filter_by(name='checked-in')
.one())
updated_count = 0
for i, entry in enumerate(form.aliquot.entries):
apply_changes(entry.form, aliquot[i])
if entry.ui_selected.data:
aliquot[i].location = context
aliquot[i].state = state
updated_count += 1
db_session.flush()
if updated_count:
request.session.flash(
_(u'${count} aliquot have been changed to the status of '
u'${state}',
mapping={
'count': updated_count,
'state': state.title
}),
'success')
else:
request.session.flash(_(u'Please select Aliquot'), 'warning')
return HTTPFound(location=request.current_route_path())
vals.update({
'form': form,
})
return vals
def settings(context, request):
"""
Manages application-wide settings
"""
if request.method == 'POST':
check_csrf_token(request)
db_session = request.db_session
specimen_types = (db_session.query(models.SpecimenType).order_by(
models.SpecimenType.title).all())
specimen_types_count = len(specimen_types)
aliquot_types = (db_session.query(models.AliquotType).options(
orm.joinedload('specimen_type')).join(
models.AliquotType.specimen_type).order_by(
models.SpecimenType.title, models.AliquotType.title).all())
aliquot_types_count = len(specimen_types)
labs_types = (db_session.query(models.Location).order_by(
models.Location.title).all())
class SpecimenTypeForm(wtforms.Form):
ui_selected = wtforms.BooleanField()
id = wtforms.HiddenField()
title = wtforms.StringField(label=_(u'Title'),
description=_(u'The displayed label'),
validators=[
wtforms.validators.input_required(),
])
description = wtforms.TextAreaField(
label=_(u'Description'),
validators=[wtforms.validators.optional()])
tube_type = wtforms.StringField(
label=_(u'Tube Type'), validators=[wtforms.validators.optional()])
default_tubes = wtforms.IntegerField(
label=_(u'Default Amount'),
description=_(u'Default amount to use by default when '
u'a new specimen'),
validators=[wtforms.validators.optional()])
def validate_title(self, field):
query = (db_session.query(
models.SpecimenType).filter_by(name=slugify(field.data)))
# apparently the removed field remains as None...
if self.id and self.id.data:
query = query.filter(models.SpecimenType.id != self.id.data)
(exists, ) = db_session.query(query.exists()).one()
if exists:
raise wtforms.validators.ValidationError(
_('A type with a similar name already exists'))
class SpecimenTypeCrudForm(wtforms.Form):
types = wtforms.FieldList(wtforms.FormField(SpecimenTypeForm))
class AliquotTypeForm(wtforms.Form):
ui_selected = wtforms.BooleanField()
id = wtforms.HiddenField()
specimen_type_id = wtforms.SelectField(
label=_(u'Specimen Type'),
description=_(
u'The specimen type this sample type can processed from'),
choices=[(t.id, t.title) for t in specimen_types],
coerce=int,
validators=[wtforms.validators.input_required()])
title = wtforms.StringField(label=_(u'Title'),
validators=[
wtforms.validators.input_required(),
])
description = wtforms.TextAreaField(
label=_(u'Description'),
validators=[wtforms.validators.optional()])
units = wtforms.StringField(
label=_(u'Measuring Units'),
description=_(u'The unit of measurement per-sample of this type'),
validators=[wtforms.validators.input_required()])
def validate_title(self, field):
query = (db_session.query(
models.AliquotType).filter_by(name=slugify(field.data)))
# apparently the removed field remains as None...
if self.id and self.id.data:
query = query.filter(models.AliquotType.id != self.id.data)
(exists, ) = db_session.query(query.exists()).one()
if exists:
raise wtforms.validators.ValidationError(
_('A type with a similar name already exists'))
class AliquotTypeCrudForm(wtforms.Form):
types = wtforms.FieldList(wtforms.FormField(AliquotTypeForm))
class LabForm(wtforms.Form):
ui_selected = wtforms.BooleanField()
id = wtforms.HiddenField()
name = wtforms.StringField(label=_(u'Name'),
description=_(u'This is the system name'),
validators=[wtforms.validators.Required()])
title = wtforms.StringField(
label=_(u'Title'),
description=_(u'This is the human readable title'),
validators=[wtforms.validators.Required()])
active = wtforms.BooleanField(description=_(
u'Actives labs will be available in new location dropdowns'),
label=_(u'Active'))
is_enabled = wtforms.BooleanField(
description=_(u'Enabled labs will be available on Lims homepage'),
label=_(u'Enabled'))
class LabsTypeCrudForm(wtforms.Form):
types = wtforms.FieldList(wtforms.FormField(LabForm))
# We need to accomodate WTForm's inability to process multiple forms
# in the same page by adding a hidden value to check which form
# was submitted
lab_type_crud_form = LabsTypeCrudForm(
request.POST if 'lab-type-crud-form' in request.POST else None,
types=labs_types,
)
lab_add_form = LabForm(request.POST if 'lab-add-form' in
request.POST else None)
del lab_add_form.id
del lab_add_form.ui_selected
specimen_type_add_form = SpecimenTypeForm(
request.POST if 'specimen-type-add-form' in request.POST else None, )
del specimen_type_add_form.id
del specimen_type_add_form.ui_selected
specimen_type_crud_form = SpecimenTypeCrudForm(
request.POST if 'specimen-type-crud-form' in request.POST else None,
types=specimen_types,
)
aliquot_type_add_form = AliquotTypeForm(
request.POST if 'aliquot-type-add-form' in request.POST else None)
del aliquot_type_add_form.id
del aliquot_type_add_form.ui_selected
aliquot_type_crud_form = AliquotTypeCrudForm(
request.POST if 'aliquot-type-crud-form' in request.POST else None,
types=aliquot_types,
)
if 'specimen-type-add-form' in request.POST:
if specimen_type_add_form.validate():
data = specimen_type_add_form.data
data['name'] = slugify(data['title'])
db_session.add(models.SpecimenType(**data))
request.session.flash(_(u'Sucessfully added specimen type'),
'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(_(u'Form errors, please revise below'),
'danger')
elif 'specimen-type-crud-form' in request.POST and 'save' in request.POST:
if specimen_type_crud_form.validate():
for i, entry in enumerate(specimen_type_crud_form.types.entries):
del entry.form.id
apply_changes(entry.form, specimen_types[i])
db_session.flush()
request.session.flash(_(u'Sucessfully updated specimen types'),
'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(_(u'Form errors, please revise below'),
'danger')
elif 'specimen-type-crud-form' in request.POST \
and 'delete' in request.POST:
ids = [
e.form.id.object_data
for e in specimen_type_crud_form.types.entries
if e.form.ui_selected.data
]
if not ids:
request.session.flash(_(u'No specimen types selected'), 'warning')
(exists, ) = (db_session.query(
db_session.query(models.Specimen).filter(
models.Specimen.specimen_type_id.in_(ids)).exists()).one())
if not exists:
count = (db_session.query(models.SpecimenType).filter(
models.SpecimenType.id.in_(ids)).delete(
synchronize_session=False))
db_session.flush()
request.session.flash(
_(u'Deleted {0} specimen types'.format(count)), 'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(
_(u'Selected types already have specimen collected'), 'danger')
elif 'aliquot-type-add-form' in request.POST:
if aliquot_type_add_form.validate():
data = aliquot_type_add_form.data
data['name'] = slugify(data['title'])
db_session.add(models.AliquotType(**data))
request.session.flash(_(u'Sucessfully added aliquot type'),
'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(_(u'Form errors, please revise below'),
'danger')
elif 'aliquot-type-crud-form' in request.POST and 'save' in request.POST:
if aliquot_type_crud_form.validate():
for i, entry in enumerate(aliquot_type_crud_form.types.entries):
del entry.form.id
apply_changes(entry.form, aliquot_types[i])
db_session.flush()
request.session.flash(_(u'Sucessfully updated aliquot types'),
'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(_(u'Form errors, please revise below'),
'danger')
elif 'aliquot-type-crud-form' in request.POST and 'delete' in request.POST:
ids = [
e.form.id.object_data for e in aliquot_type_crud_form.types.entries
if e.form.ui_selected.data
]
if not ids:
request.session.flash(_(u'No aliquot types selected'), 'warning')
(exists, ) = (db_session.query(
db_session.query(models.Aliquot).filter(
models.Aliquot.aliquot_type_id.in_(ids)).exists()).one())
if not exists:
count = (db_session.query(models.AliquotType).filter(
models.AliquotType.id.in_(ids)).delete(
synchronize_session=False))
request.session.flash(
_(u'Deleted {0} aliquot types'.format(count)), 'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(
_(u'Selected types already have aliquot collected'), 'danger')
elif 'lab-add-form' in request.POST:
if lab_add_form.validate():
db_session.add(models.Location(**lab_add_form.data))
db_session.flush()
request.session.flash(
_(u'Sucessfully added lab: {}'.format(
lab_add_form.data['title'])), 'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(_(u'Form errors, please revise below'),
'danger')
elif 'lab-type-crud-form' in request.POST and 'save' in request.POST:
if lab_type_crud_form.validate():
for i, entry in enumerate(lab_type_crud_form.types.entries):
del entry.form.id
apply_changes(entry.form, labs_types[i])
db_session.flush()
request.session.flash(_(u'Sucessfully updated labs'), 'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(_(u'Form errors, please revise below'),
'danger')
elif 'lab-type-crud-form' in request.POST and 'delete' in request.POST:
ids = [
e.form.id.object_data for e in lab_type_crud_form.types.entries
if e.form.ui_selected.data
]
titles = [
e.data['title'] for e in lab_type_crud_form.types.entries
if e.form.ui_selected.data
]
if not ids:
request.session.flash(_(u'No labs selected'), 'warning')
(exists, ) = (db_session.query(
db_session.query(models.Location).filter(
models.Location.id.in_(ids)).exists()).one())
if exists:
count = (db_session.query(models.Location).filter(
models.Location.id.in_(ids)).delete(synchronize_session=False))
db_session.flush()
request.session.flash(
_(u'Sucessfully deleted labs: {}'.format(', '.join(titles))),
'success')
return HTTPFound(location=request.current_route_path())
query = (db_session.query(models.Location).order_by(models.Location.title))
return {
'specimen_types': specimen_types,
'specimen_types_count': specimen_types_count,
'specimen_type_add_form': specimen_type_add_form,
'specimen_type_crud_form': specimen_type_crud_form,
'aliquot_types': aliquot_types,
'aliquot_types_count': aliquot_types_count,
'aliquot_type_add_form': aliquot_type_add_form,
'aliquot_type_crud_form': aliquot_type_crud_form,
'labs_types': labs_types,
'lab_type_crud_form': lab_type_crud_form,
'lab_add_form': lab_add_form,
'labs': query
}
def settings(context, request):
"""
Manages application-wide settings
"""
if request.method == 'POST':
check_csrf_token(request)
db_session = request.db_session
specimen_types = (
db_session.query(models.SpecimenType)
.order_by(models.SpecimenType.title)
.all())
specimen_types_count = len(specimen_types)
aliquot_types = (
db_session.query(models.AliquotType)
.options(orm.joinedload('specimen_type'))
.join(models.AliquotType.specimen_type)
.order_by(
models.SpecimenType.title,
models.AliquotType.title)
.all())
aliquot_types_count = len(specimen_types)
labs_types = (
db_session.query(models.Location)
.order_by(models.Location.title)
.all())
class SpecimenTypeForm(wtforms.Form):
ui_selected = wtforms.BooleanField()
id = wtforms.HiddenField()
title = wtforms.StringField(
label=_(u'Title'),
description=_(u'The displayed label'),
validators=[
wtforms.validators.input_required(),
])
description = wtforms.TextAreaField(
label=_(u'Description'),
validators=[wtforms.validators.optional()])
tube_type = wtforms.StringField(
label=_(u'Tube Type'),
validators=[wtforms.validators.optional()])
default_tubes = wtforms.IntegerField(
label=_(u'Default Amount'),
description=_(
u'Default amount to use by default when '
u'a new specimen'),
validators=[wtforms.validators.optional()])
def validate_title(self, field):
query = (
db_session.query(models.SpecimenType)
.filter_by(name=slugify(field.data)))
# apparently the removed field remains as None...
if self.id and self.id.data:
query = query.filter(models.SpecimenType.id != self.id.data)
(exists,) = db_session.query(query.exists()).one()
if exists:
raise wtforms.validators.ValidationError(_(
'A type with a similar name already exists'))
class SpecimenTypeCrudForm(wtforms.Form):
types = wtforms.FieldList(wtforms.FormField(SpecimenTypeForm))
class AliquotTypeForm(wtforms.Form):
ui_selected = wtforms.BooleanField()
id = wtforms.HiddenField()
specimen_type_id = wtforms.SelectField(
label=_(u'Specimen Type'),
description=_(
u'The specimen type this sample type can processed from'),
choices=[(t.id, t.title) for t in specimen_types],
coerce=int,
validators=[
wtforms.validators.input_required()
])
title = wtforms.StringField(
label=_(u'Title'),
validators=[
wtforms.validators.input_required(),
])
description = wtforms.TextAreaField(
label=_(u'Description'),
validators=[wtforms.validators.optional()])
units = wtforms.StringField(
label=_(u'Measuring Units'),
description=_(u'The unit of measurement per-sample of this type'),
validators=[wtforms.validators.input_required()])
def validate_title(self, field):
query = (
db_session.query(models.AliquotType)
.filter_by(name=slugify(field.data)))
# apparently the removed field remains as None...
if self.id and self.id.data:
query = query.filter(models.AliquotType.id != self.id.data)
(exists,) = db_session.query(query.exists()).one()
if exists:
raise wtforms.validators.ValidationError(_(
'A type with a similar name already exists'))
class AliquotTypeCrudForm(wtforms.Form):
types = wtforms.FieldList(wtforms.FormField(AliquotTypeForm))
class LabForm(wtforms.Form):
ui_selected = wtforms.BooleanField()
id = wtforms.HiddenField()
name = wtforms.StringField(
label=_(u'Name'),
description=_(
u'This is the system name'),
validators=[wtforms.validators.Required()])
title = wtforms.StringField(
label=_(u'Title'),
description=_(
u'This is the human readable title'),
validators=[wtforms.validators.Required()])
active = wtforms.BooleanField(
description=_(
u'Actives labs will be available in new location dropdowns'),
label=_(u'Active'))
is_enabled = wtforms.BooleanField(
description=_(
u'Enabled labs will be available on Lims homepage'),
label=_(u'Enabled'))
class LabsTypeCrudForm(wtforms.Form):
types = wtforms.FieldList(wtforms.FormField(LabForm))
# We need to accomodate WTForm's inability to process multiple forms
# in the same page by adding a hidden value to check which form
# was submitted
lab_type_crud_form = LabsTypeCrudForm(
request.POST if 'lab-type-crud-form' in request.POST else None,
types=labs_types,
)
lab_add_form = LabForm(
request.POST if 'lab-add-form' in request.POST else None)
del lab_add_form.id
del lab_add_form.ui_selected
specimen_type_add_form = SpecimenTypeForm(
request.POST if 'specimen-type-add-form' in request.POST else None,
)
del specimen_type_add_form.id
del specimen_type_add_form.ui_selected
specimen_type_crud_form = SpecimenTypeCrudForm(
request.POST if 'specimen-type-crud-form' in request.POST else None,
types=specimen_types,
)
aliquot_type_add_form = AliquotTypeForm(
request.POST if 'aliquot-type-add-form' in request.POST else None
)
del aliquot_type_add_form.id
del aliquot_type_add_form.ui_selected
aliquot_type_crud_form = AliquotTypeCrudForm(
request.POST if 'aliquot-type-crud-form' in request.POST else None,
types=aliquot_types,
)
if 'specimen-type-add-form' in request.POST:
if specimen_type_add_form.validate():
data = specimen_type_add_form.data
data['name'] = slugify(data['title'])
db_session.add(models.SpecimenType(**data))
request.session.flash(
_(u'Sucessfully added specimen type'), 'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(
_(u'Form errors, please revise below'), 'danger')
elif 'specimen-type-crud-form' in request.POST and 'save' in request.POST:
if specimen_type_crud_form.validate():
for i, entry in enumerate(specimen_type_crud_form.types.entries):
del entry.form.id
apply_changes(entry.form, specimen_types[i])
db_session.flush()
request.session.flash(
_(u'Sucessfully updated specimen types'), 'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(
_(u'Form errors, please revise below'), 'danger')
elif 'specimen-type-crud-form' in request.POST \
and 'delete' in request.POST:
ids = [
e.form.id.object_data
for e in specimen_type_crud_form.types.entries
if e.form.ui_selected.data]
if not ids:
request.session.flash(_(u'No specimen types selected'), 'warning')
(exists,) = (
db_session.query(
db_session.query(models.Specimen)
.filter(models.Specimen.specimen_type_id.in_(ids))
.exists())
.one())
if not exists:
count = (
db_session.query(models.SpecimenType)
.filter(models.SpecimenType.id.in_(ids))
.delete(synchronize_session=False))
db_session.flush()
request.session.flash(
_(u'Deleted {0} specimen types'.format(count)), 'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(
_(u'Selected types already have specimen collected'),
'danger')
elif 'aliquot-type-add-form' in request.POST:
if aliquot_type_add_form.validate():
data = aliquot_type_add_form.data
data['name'] = slugify(data['title'])
db_session.add(models.AliquotType(**data))
request.session.flash(
_(u'Sucessfully added aliquot type'), 'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(
_(u'Form errors, please revise below'), 'danger')
elif 'aliquot-type-crud-form' in request.POST and 'save' in request.POST:
if aliquot_type_crud_form.validate():
for i, entry in enumerate(aliquot_type_crud_form.types.entries):
del entry.form.id
apply_changes(entry.form, aliquot_types[i])
db_session.flush()
request.session.flash(
_(u'Sucessfully updated aliquot types'), 'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(
_(u'Form errors, please revise below'), 'danger')
elif 'aliquot-type-crud-form' in request.POST and 'delete' in request.POST:
ids = [
e.form.id.object_data
for e in aliquot_type_crud_form.types.entries
if e.form.ui_selected.data]
if not ids:
request.session.flash(_(u'No aliquot types selected'), 'warning')
(exists,) = (
db_session.query(
db_session.query(models.Aliquot)
.filter(models.Aliquot.aliquot_type_id.in_(ids))
.exists())
.one())
if not exists:
count = (
db_session.query(models.AliquotType)
.filter(models.AliquotType.id.in_(ids))
.delete(synchronize_session=False))
request.session.flash(
_(u'Deleted {0} aliquot types'.format(count)), 'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(
_(u'Selected types already have aliquot collected'),
'danger')
elif 'lab-add-form' in request.POST:
if lab_add_form.validate():
db_session.add(models.Location(**lab_add_form.data))
db_session.flush()
request.session.flash(
_(u'Sucessfully added lab: {}'.format(
lab_add_form.data['title'])), 'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(
_(u'Form errors, please revise below'), 'danger')
elif 'lab-type-crud-form' in request.POST and 'save' in request.POST:
if lab_type_crud_form.validate():
for i, entry in enumerate(lab_type_crud_form.types.entries):
del entry.form.id
apply_changes(entry.form, labs_types[i])
db_session.flush()
request.session.flash(
_(u'Sucessfully updated labs'), 'success')
return HTTPFound(location=request.current_route_path())
else:
request.session.flash(
_(u'Form errors, please revise below'), 'danger')
elif 'lab-type-crud-form' in request.POST and 'delete' in request.POST:
ids = [
e.form.id.object_data
for e in lab_type_crud_form.types.entries
if e.form.ui_selected.data]
titles = [
e.data['title']
for e in lab_type_crud_form.types.entries
if e.form.ui_selected.data]
if not ids:
request.session.flash(_(u'No labs selected'), 'warning')
(exists,) = (
db_session.query(
db_session.query(models.Location)
.filter(models.Location.id.in_(ids))
.exists())
.one())
if exists:
count = (
db_session.query(models.Location)
.filter(models.Location.id.in_(ids))
.delete(synchronize_session=False))
db_session.flush()
request.session.flash(
_(u'Sucessfully deleted labs: {}'.format(
', '.join(titles))), 'success')
return HTTPFound(location=request.current_route_path())
query = (
db_session.query(models.Location)
.order_by(models.Location.title))
return {
'specimen_types': specimen_types,
'specimen_types_count': specimen_types_count,
'specimen_type_add_form': specimen_type_add_form,
'specimen_type_crud_form': specimen_type_crud_form,
'aliquot_types': aliquot_types,
'aliquot_types_count': aliquot_types_count,
'aliquot_type_add_form': aliquot_type_add_form,
'aliquot_type_crud_form': aliquot_type_crud_form,
'labs_types': labs_types,
'lab_type_crud_form': lab_type_crud_form,
'lab_add_form': lab_add_form,
'labs': query
}
def specimen(context, request):
db_session = request.db_session
vals = filter_specimen(context, request, state=u'pending-draw')
specimen = vals['specimen']
# Override specimen with default processing locations on save
# This was previosly set in the Plone site content object
# but don't have the resources to properly re-implement this
# functionality, so this will have to do for now.
processing_location_name = None
processing_location = None
if 'aeh' in db_session.bind.url.database:
processing_location_name = {
'richman lab': 'richman lab',
'avrc': 'richman lab'
}.get(context.name)
elif 'cctg' in db_session.bind.url.database:
processing_location_name = {
'harbor-ucla-clinic': 'harbor-ucla-clinic',
'long-beach-clinic': 'long-beach-lab',
'long-beach-lab': 'long-beach-lab',
'usc-clinic': 'usc-lab',
'usc-lab': 'usc-lab',
'avrc': 'avrc',
}.get(context.name)
elif 'mhealth' in db_session.bind.url.database:
processing_location_name = {
'avrc': 'avrc',
}.get(context.name)
else:
processing_location_name = None
if processing_location_name:
processing_location = (
db_session.query(models.Location)
.filter_by(name=processing_location_name)
.one())
overriden_specimen = [{
'id': s.id,
'tubes': s.tubes,
'collect_date': s.collect_date,
'collect_time': s.collect_time,
'location_id': processing_location and processing_location.id,
'notes': s.notes
} for s in specimen if s]
Form = build_crud_form(context, request)
form = Form(request.POST, specimen=overriden_specimen)
label_queue = request.session.setdefault(SPECIMEN_LABEL_QUEUE, set())
if (request.method == 'POST' and
check_csrf_token(request) and
form.validate()):
if not request.has_permission('process'):
raise HTTPForbidden
if 'save' in request.POST:
updated_count = 0
for i, subform in enumerate(form.specimen.entries):
if apply_changes(subform.form, specimen[i]):
updated_count += 1
db_session.flush()
if updated_count:
request.session.flash(u'Changes saved', 'success')
else:
request.session.flash(u'No changes were saved', 'warning')
return HTTPFound(location=request.current_route_path())
if 'queue' in request.POST:
queue_count = 0
for i, subform in enumerate(form.specimen.entries):
apply_changes(subform.form, specimen[i])
if subform.ui_selected.data:
queue_count += 1
specimen_id = subform['id'].data
if specimen_id in label_queue:
label_queue.discard(specimen_id)
else:
label_queue.add(specimen_id)
request.session.changed()
if queue_count:
request.session.flash(
u'Specimen print queue has changed.', 'success')
else:
request.session.flash(u'Please select specimen', 'warning')
return HTTPFound(location=request.current_route_path())
for state_name in ('not-collected', 'pending-aliquot'):
if state_name in request.POST:
state = (
db_session.query(models.SpecimenState)
.filter_by(name=state_name)
.one())
transitioned_count = 0
updated_count = 0
for i, subform in enumerate(form.specimen.entries):
if subform.ui_selected.data:
specimen[i].state = state
transitioned_count += 1
if apply_changes(subform.form, specimen[i]):
updated_count += 1
db_session.flush()
if transitioned_count:
request.session.flash(
u'%d Specimen have been changed to the status of %s.'
% (transitioned_count, state.title),
'success')
else:
request.session.flash(u'Please select specimen', 'warning')
return HTTPFound(location=request.current_route_path())
vals.update({
'form': form,
'has_labels_queued': len(label_queue),
'label_queue': label_queue,
})
return vals
