def update_sample(content, record):
"""
Custom code for updating a sample because of special requirements for storage location and sample type.
:param content: The sample object that has to be modified
:param record: This object has a dictionary, items, that has the values that are to be changed.
:return: The updated sample object
"""
# set and unset the storage locations
for k, v in record.items():
if k == 'StorageLocation':
storage_location_results = search(portal_type='StoragePosition',
Title=v)
if not storage_location_results:
storage_location_results = search(
portal_type='StoragePosition', uid=v)
storage_location = storage_location_results and get_object(
storage_location_results[0]) or None
wf_tool = get_tool("portal_workflow")
location_status = wf_tool.getStatusOf(
'bika_storageposition_workflow', storage_location)
if location_status and location_status.get("review_state",
None) == "available":
current_location = content.getStorageLocation()
if current_location:
doActionFor(current_location, 'liberate')
# assign the sample to the storage location
content.setStorageLocation(storage_location)
sample_status = wf_tool.getStatusOf('bika_sample_workflow',
content)
if sample_status and sample_status.get(
"review_state", None) == "sample_received":
doActionFor(storage_location, 'occupy')
else:
doActionFor(storage_location, 'reserve')
if k == 'SampleType':
sample_type_results = search(portal_type="SampleType", title=v)
if not sample_type_results:
sample_type_results = search(portal_type="SampleType", uid=v)
sample_type = sample_type_results and get_object(
sample_type_results[0]) or None
if isinstance(sample_type, tuple):
sample_type = sample_type[0]
content.setSampleType(sample_type)
return content
def create_project(container, portal_type, **data):
"""
Create a project via API
"""
container = get_object(container)
title = data.get("title", "")
if not title:
fail(404, "Title is required.")
obj = bika_create_object(container, portal_type, **data)
st_titles = data.get("SampleType", "")
st_uids = []
if st_titles and type(st_titles) is list:
for st_title in st_titles:
brains = search(portal_type="SampleType", title=st_title)
if brains:
st_uids.append(brains[0].UID)
if st_uids:
obj.setSampleType(st_uids)
return obj
def create_sample(container, **data):
"""
create a sample from here that doesnt go via api create
:param container:
:param data:
:return: Sample object
"""
container = get_object(container)
request = req.get_request()
# we need to resolve the SampleType to a full object
sample_type = data.get("SampleType", None)
if sample_type is None:
fail(400, "Please provide a SampleType")
# TODO We should handle the same values as in the DataManager for this field
# (UID, path, objects, dictionaries ...)
sample_type_results = search(portal_type="SampleType", title=sample_type)
if not sample_type_results:
sample_type_results = search(portal_type="SampleType", uid=sample_type)
# StorageLocation
storage_location = data.get("StorageLocation", None)
if storage_location is None:
fail(400, "Please provide a StorageLocation")
linked_sample_list = search(portal_type="Sample",
title=data.get('LinkedSample', ''))
linked_sample = linked_sample_list and linked_sample_list[0].getObject(
) or None
try:
volume = str(data.get('Volume'))
float_volume = float(volume)
if not float_volume:
fail(400, "Please provide a correct Volume")
except:
raise
# TODO We should handle the same values as in the DataManager for this field
# (UID, path, objects, dictionaries ...)
storage_location_results = search(portal_type='StoragePosition',
Title=storage_location)
if not storage_location_results:
storage_location_results = search(portal_type='StoragePosition',
uid=storage_location)
# set the values and call the create function
values = {
"title":
data.get('title', ''),
"description":
data.get("description", ""),
"Project":
container, #because the container is in fact the project this sample belongs to.
"AllowSharing":
data.get('AllowSharing', 0),
"StorageLocation":
storage_location_results and get_object(storage_location_results[0])
or None,
"SampleType":
sample_type_results and get_object(sample_type_results[0]) or None,
"SubjectID":
data.get("SubjectID", ""),
"Barcode":
data.get("Barcode", ""),
"Volume":
volume,
"Unit":
data.get("Unit", ""),
"LinkedSample":
linked_sample,
"DateCreated":
data.get("DateCreated", ""),
}
api_source = data.get('APISource', None)
if api_source:
values['APISource'] = api_source
return create_smp(container, request, values)
def create_storage(container, portal_type, **data):
"""
Create a storage unit and (un-)managed storage via API
"""
def set_inputs_into_schema(instance, temperature, department, unit_type):
# Set field values across each object if possible
schema = instance.Schema()
if temperature and 'Temperature' in schema:
instance.Schema()['Temperature'].set(instance, temperature)
if department and 'Department' in schema:
instance.Schema()['Department'].set(instance, department)
if unit_type and 'UnitType' in schema:
instance.Schema()['UnitType'].set(instance, unit_type)
def set_storage_types(instance, storage_interfaces):
schema = instance.Schema()
if storage_interfaces and 'StorageTypes' in schema:
instance.Schema()['StorageTypes'].set(instance, storage_interfaces)
for storage_interface in storage_interfaces:
inter = resolve(storage_interface)
alsoProvides(instance, inter)
container = get_object(container)
# variables for storage unit
department_title = data.get("department", "")
temperature = data.get("temperature", "")
unit_type = data.get("unit_type", "")
department = None
if container.portal_type == "StorageUnit":
department = container.getDepartment()
temperature = container.getTemperature()
else:
brains = search(portal_type="Department", title=department_title)
if not brains:
department = brains[0].getObject()
# variables for managed storage
if portal_type == "ManagedStorage":
number_positions = data.get("number_positions", "")
x_axis = data.get("x_axis", "")
y_axis = data.get("y_axis", "")
try:
x_axis = x_axis and int(x_axis) or ''
y_axis = y_axis and int(y_axis) or ''
number_positions = number_positions and int(number_positions) or ''
except ValueError:
fail(401, "Number positions, X axis and Y axis must be integers.")
if not number_positions or not x_axis or not y_axis:
fail(
400,
"Number positions, X axis and Y axis are required to create storage positions."
)
# common variables
prefix = data.get("prefix", "")
leading_zeros = data.get("leading_zeros", "")
if not prefix or not leading_zeros:
fail(
400,
"Prefix and leading_zeros are required to construct storage unit title and Id."
)
number_items = data.get("number_items", "")
try:
number_items = number_items and int(number_items) or 1
except ValueError:
fail(401, "Number items must be integer.")
seq_start = data.get("seq_start", "")
try:
seq_start = seq_start and int(seq_start) or 1
except ValueError:
fail(401, "Id sequence start must be integer.")
sequence = range(seq_start, seq_start + number_items)
units = []
for x in sequence:
id_obj = prefix + '-' + str(x).zfill(len(leading_zeros) + 1)
title_obj = prefix + ' ' + str(x).zfill(len(leading_zeros) + 1)
instance = api.content.create(container=container,
type=portal_type,
id=id_obj,
title=title_obj)
if instance.portal_type == "StorageUnit":
set_inputs_into_schema(instance, temperature, department,
unit_type)
elif instance.portal_type == "UnmanagedStorage":
set_storage_types(instance,
["baobab.lims.interfaces.IStockItemStorage"])
elif instance.portal_type == "ManagedStorage":
instance.setXAxis(x_axis)
instance.setYAxis(y_axis)
set_storage_types(
instance, ["baobab.lims.interfaces.ISampleStorageLocation"])
positions = storage_positions(instance, number_positions)
for position in positions:
set_storage_types(
position,
["baobab.lims.interfaces.ISampleStorageLocation"])
position.reindexObject()
instance.reindexObject()
units.append(instance)
return units
def set(self, instance, value, **kw): # noqa
"""Set the value of the refernce field
"""
ref = []
# The value is an UID
if api.is_uid(value):
ref.append(api.get_object_by_uid(value))
# The value is already an object
if api.is_at_content(value):
ref.append(value)
# The value is a dictionary
# -> handle it like a catalog query
if u.is_dict(value):
results = api.search(portal_type=self.allowed_types, **value)
ref = map(api.get_object, results)
# The value is a list
if u.is_list(value):
for item in value:
# uid
if api.is_uid(item):
ref.append(api.get_object_by_uid(item))
continue
# object
if api.is_at_content(item):
ref.append(api.get_object(item))
continue
# path
if api.is_path(item):
ref.append(api.get_object_by_path(item))
continue
# dict (catalog query)
if u.is_dict(item):
results = api.search(portal_type=self.allowed_types, **item)
objs = map(api.get_object, results)
ref.extend(objs)
continue
# Plain string
# -> do a catalog query for title
if isinstance(item, basestring):
results = api.search(portal_type=self.allowed_types, title=item)
objs = map(api.get_object, results)
ref.extend(objs)
continue
# The value is a physical path
if api.is_path(value):
ref.append(api.get_object_by_path(value))
# Handle non multi valued fields
if not self.multi_valued and len(ref) > 1:
raise ValueError("Multiple values given for single valued field {}"
.format(self.field))
return self._set(instance, ref, **kw)
def set(self, instance, value, **kw): # noqa
"""Set the value of the refernce field
"""
ref = []
# The value is an UID
if api.is_uid(value):
ref.append(api.get_object_by_uid(value))
# The value is already an object
if api.is_at_content(value):
ref.append(value)
# The value is a dictionary
# -> handle it like a catalog query
if u.is_dict(value):
results = api.search(portal_type=self.allowed_types, **value)
ref = map(api.get_object, results)
# The value is a list
if u.is_list(value):
for item in value:
# uid
if api.is_uid(item):
ref.append(api.get_object_by_uid(item))
continue
# object
if api.is_at_content(item):
ref.append(api.get_object(item))
continue
# path
if api.is_path(item):
ref.append(api.get_object_by_path(item))
continue
# dict (catalog query)
if u.is_dict(item):
results = api.search(portal_type=self.allowed_types,
**item)
objs = map(api.get_object, results)
ref.extend(objs)
continue
# Plain string
# -> do a catalog query for title
if isinstance(item, basestring):
results = api.search(portal_type=self.allowed_types,
title=item)
objs = map(api.get_object, results)
ref.extend(objs)
continue
# The value is a physical path
if api.is_path(value):
ref.append(api.get_object_by_path(value))
# Handle non multi valued fields
if not self.multi_valued and len(ref) > 1:
raise ValueError(
"Multiple values given for single valued field {}".format(
self.field))
return self._set(instance, ref, **kw)
