def to_service_uid(uid_brain_obj_str):
"""Resolves the passed in element to a valid uid. Returns None if the value
cannot be resolved to a valid uid
"""
if api.is_uid(uid_brain_obj_str) and uid_brain_obj_str != "0":
return uid_brain_obj_str
if api.is_object(uid_brain_obj_str):
obj = api.get_object(uid_brain_obj_str)
if IAnalysisService.providedBy(obj):
return api.get_uid(obj)
elif IRoutineAnalysis.providedBy(obj):
return obj.getServiceUID()
else:
logger.error("Type not supported: {}".format(obj.portal_type))
return None
if isinstance(uid_brain_obj_str, six.string_types):
# Maybe is a keyword?
query = dict(portal_type="AnalysisService",
getKeyword=uid_brain_obj_str)
brains = api.search(query, SETUP_CATALOG)
if len(brains) == 1:
return api.get_uid(brains[0])
# Or maybe a title
query = dict(portal_type="AnalysisService", title=uid_brain_obj_str)
brains = api.search(query, SETUP_CATALOG)
if len(brains) == 1:
return api.get_uid(brains[0])
return None
def _to_service(self, thing):
"""Convert to Analysis Service
:param thing: UID/Catalog Brain/Object/Something
:returns: Analysis Service object or None
"""
# Convert UIDs to objects
if api.is_uid(thing):
thing = api.get_object_by_uid(thing, None)
# Bail out if the thing is not a valid object
if not api.is_object(thing):
logger.warn("'{}' is not a valid object!".format(repr(thing)))
return None
# Ensure we have an object here and not a brain
obj = api.get_object(thing)
if IAnalysisService.providedBy(obj):
return obj
if IAnalysis.providedBy(obj):
return obj.getAnalysisService()
# An object, but neither an Analysis nor AnalysisService?
# This should never happen.
portal_type = api.get_portal_type(obj)
logger.error("ARAnalysesField doesn't accept objects from {} type. "
"The object will be dismissed.".format(portal_type))
return None
def _to_service(self, thing):
"""Convert to Analysis Service
:param thing: UID/Catalog Brain/Object/Something
:returns: Analysis Service object or None
"""
# Convert UIDs to objects
if api.is_uid(thing):
thing = api.get_object_by_uid(thing, None)
# Bail out if the thing is not a valid object
if not api.is_object(thing):
logger.warn("'{}' is not a valid object!".format(repr(thing)))
return None
# Ensure we have an object here and not a brain
obj = api.get_object(thing)
if IAnalysisService.providedBy(obj):
return obj
if IAnalysis.providedBy(obj):
return obj.getAnalysisService()
# An object, but neither an Analysis nor AnalysisService?
# This should never happen.
msg = "ARAnalysesField doesn't accept objects from {} type. " \
"The object will be dismissed.".format(api.get_portal_type(obj))
logger.warn(msg)
return None
def create_analysis(context, source, **kwargs):
"""Create a new Analysis. The source can be an Analysis Service or
an existing Analysis, and all possible field values will be set to the
values found in the source object.
:param context: The analysis will be created inside this object.
:param source: The schema of this object will be used to populate analysis.
:param kwargs: The values of any keys which match schema fieldnames will
be inserted into the corrosponding fields in the new analysis.
:returns: Analysis object that was created
:rtype: Analysis
"""
an_id = kwargs.get('id', source.getKeyword())
analysis = _createObjectByType("Analysis", context, an_id)
copy_analysis_field_values(source, analysis, **kwargs)
# AnalysisService field is not present on actual AnalysisServices.
if IAnalysisService.providedBy(source):
analysis.setAnalysisService(source)
else:
analysis.setAnalysisService(source.getAnalysisService())
# Set the interims from the Service
service_interims = analysis.getAnalysisService().getInterimFields()
# Avoid references from the analysis interims to the service interims
service_interims = copy.deepcopy(service_interims)
analysis.setInterimFields(service_interims)
analysis.unmarkCreationFlag()
zope.event.notify(ObjectInitializedEvent(analysis))
return analysis
def addReferenceAnalysis(self, service):
"""
Creates a new Reference Analysis object based on this Sample
Reference, with the type passed in and associates the newly
created object to the Analysis Service passed in.
:param service: Object, brain or UID of the Analysis Service
:param reference_type: type of ReferenceAnalysis, where 'b' is is
Blank and 'c' is Control
:type reference_type: A String
:returns: the newly created Reference Analysis
:rtype: string
"""
if api.is_uid(service) or api.is_brain(service):
return self.addReferenceAnalysis(api.get_object(service))
if not IAnalysisService.providedBy(service):
return None
interim_fields = service.getInterimFields()
analysis = _createObjectByType("ReferenceAnalysis", self, id=tmpID())
# Copy all the values from the schema
# TODO Add Service as a param in ReferenceAnalysis constructor and do
# this logic there instead of here
discard = [
'id',
]
keys = service.Schema().keys()
for key in keys:
if key in discard:
continue
if key not in analysis.Schema().keys():
continue
val = service.getField(key).get(service)
# Campbell's mental note:never ever use '.set()' directly to a
# field. If you can't use the setter, then use the mutator in order
# to give the value. We have realized that in some cases using
# 'set' when the value is a string, it saves the value
# as unicode instead of plain string.
# analysis.getField(key).set(analysis, val)
mutator_name = analysis.getField(key).mutator
mutator = getattr(analysis, mutator_name)
mutator(val)
analysis.setAnalysisService(service)
ref_type = self.getBlank() and 'b' or 'c'
analysis.setReferenceType(ref_type)
analysis.setInterimFields(interim_fields)
analysis.unmarkCreationFlag()
renameAfterCreation(analysis)
return analysis
def _resolve_items_to_service_uids(items):
portal = api.portal.get()
# We need to send a list of service UIDS to setAnalyses function.
# But we may have received one, or a list of:
# AnalysisService instances
# Analysis instances
# service titles
# service UIDs
# service Keywords
service_uids = []
# Maybe only a single item was passed
if type(items) not in (list, tuple):
items = [
items,
]
for item in items:
uid = False
# service objects
if IAnalysisService.providedBy(item):
uid = item.UID()
service_uids.append(uid)
# Analysis objects (shortcut for eg copying analyses from other AR)
if IAnalysis.providedBy(item):
uid = item.getService().UID()
service_uids.append(uid)
# Maybe object UID.
bsc = getToolByName(portal, 'bika_setup_catalog')
brains = bsc(UID=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
# Maybe service Title
bsc = getToolByName(portal, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', title=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
# Maybe service Title
bsc = getToolByName(portal, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', getKeyword=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
if not uid:
raise RuntimeError(
str(item) + " should be the UID, title, keyword "
" or title of an AnalysisService.")
return service_uids
def get(self, instance, **kwargs):
an_interims = RecordsField.get(self, instance, **kwargs) or []
if not IAnalysisService.providedBy(instance):
return an_interims
# This instance implements IAnalysisService
calculation = instance.getCalculation()
if not calculation:
return an_interims
# Ensure the service includes the interims from the calculation
an_keys = map(lambda interim: interim['keyword'], an_interims)
# Avoid references from the service interims to the calculation interims
calc_interims = copy.deepcopy(calculation.getInterimFields())
calc_interims = filter(lambda inter: inter['keyword'] not in an_keys,
calc_interims)
return an_interims + calc_interims
def _resolve_items_to_service_uids(items):
portal = api.portal.get()
# We need to send a list of service UIDS to setAnalyses function.
# But we may have received one, or a list of:
# AnalysisService instances
# Analysis instances
# service titles
# service UIDs
# service Keywords
service_uids = []
# Maybe only a single item was passed
if type(items) not in (list, tuple):
items = [items, ]
for item in items:
uid = False
# service objects
if IAnalysisService.providedBy(item):
uid = item.UID()
service_uids.append(uid)
# Analysis objects (shortcut for eg copying analyses from other AR)
if IAnalysis.providedBy(item):
uid = item.getService().UID()
service_uids.append(uid)
# Maybe object UID.
bsc = getToolByName(portal, 'bika_setup_catalog')
brains = bsc(UID=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
# Maybe service Title
bsc = getToolByName(portal, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', title=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
# Maybe service Keyword
bsc = getToolByName(portal, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', getKeyword=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
if not uid:
raise RuntimeError(
str(item) + " should be the UID, title, keyword "
" or title of an AnalysisService.")
return service_uids
def resolve_to_uid(item):
if api.is_uid(item):
return item
elif IAnalysisService.providedBy(item):
return item.UID()
elif IRoutineAnalysis.providedBy(item):
return item.getServiceUID()
bsc = api.get_tool("bika_setup_catalog")
brains = bsc(portal_type='AnalysisService', getKeyword=item)
if brains:
return brains[0].UID
brains = bsc(portal_type='AnalysisService', title=item)
if brains:
return brains[0].UID
raise RuntimeError(
str(item) + " should be the UID, title, keyword "
" or title of an AnalysisService.")
def _get_service_uid(self, item):
if api.is_uid(item):
return item
if not api.is_object(item):
logger.warn("Not an UID: {}".format(item))
return None
obj = api.get_object(item)
if IAnalysisService.providedBy(obj):
return api.get_uid(obj)
if IAnalysis.providedBy(obj) and IRequestAnalysis.providedBy(obj):
return obj.getServiceUID()
# An object, but neither an Analysis nor AnalysisService?
# This should never happen.
msg = "ARAnalysesField doesn't accept objects from {} type. " \
"The object will be dismissed."
logger.warn(msg.format(api.get_portal_type(obj)))
return None
def create_analysis(context, source, **kwargs):
"""Create a new Analysis. The source can be an Analysis Service or
an existing Analysis, and all possible field values will be set to the
values found in the source object.
:param context: The analysis will be created inside this object.
:param source: The schema of this object will be used to populate analysis.
:param kwargs: The values of any keys which match schema fieldnames will
be inserted into the corrosponding fields in the new analysis.
:returns: Analysis object that was created
:rtype: Analysis
"""
an_id = kwargs.get('id', source.getKeyword())
analysis = _createObjectByType("Analysis", context, an_id)
copy_analysis_field_values(source, analysis, **kwargs)
# AnalysisService field is not present on actual AnalysisServices.
if IAnalysisService.providedBy(source):
analysis.setAnalysisService(source)
else:
analysis.setAnalysisService(source.getAnalysisService())
analysis.unmarkCreationFlag()
zope.event.notify(ObjectInitializedEvent(analysis))
return analysis
def _resolve_items_to_service_uids(items):
""" Returns a list of service uids without duplicates based on the items
:param items:
A list (or one object) of service-related info items. The list can be
heterogeneous and each item can be:
- Analysis Service instance
- Analysis instance
- Analysis Service title
- Analysis Service UID
- Analysis Service Keyword
If an item that doesn't match any of the criterias above is found, the
function will raise a RuntimeError
"""
portal = None
bsc = None
service_uids = []
# Maybe only a single item was passed
if type(items) not in (list, tuple):
items = [items, ]
for item in items:
# service objects
if IAnalysisService.providedBy(item):
uid = item.UID()
service_uids.append(uid)
continue
# Analysis objects (shortcut for eg copying analyses from other AR)
if IAnalysis.providedBy(item):
uid = item.getService().UID()
service_uids.append(uid)
continue
# An object UID already there?
if (item in service_uids):
continue
# Maybe object UID.
portal = portal if portal else api.portal.get()
bsc = bsc if bsc else getToolByName(portal, 'bika_setup_catalog')
brains = bsc(UID=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
continue
# Maybe service Title
brains = bsc(portal_type='AnalysisService', title=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
continue
# Maybe service Keyword
brains = bsc(portal_type='AnalysisService', getKeyword=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
continue
raise RuntimeError(
str(item) + " should be the UID, title, keyword "
" or title of an AnalysisService.")
return list(set(service_uids))
def _resolve_items_to_service_uids(items):
""" Returns a list of service uids without duplicates based on the items
:param items:
A list (or one object) of service-related info items. The list can be
heterogeneous and each item can be:
- Analysis Service instance
- Analysis instance
- Analysis Service title
- Analysis Service UID
- Analysis Service Keyword
If an item that doesn't match any of the criterias above is found, the
function will raise a RuntimeError
"""
portal = None
bsc = None
service_uids = []
# Maybe only a single item was passed
if type(items) not in (list, tuple):
items = [
items,
]
for item in items:
# service objects
if IAnalysisService.providedBy(item):
uid = item.UID()
service_uids.append(uid)
continue
# Analysis objects (shortcut for eg copying analyses from other AR)
if IAnalysis.providedBy(item):
uid = item.getService().UID()
service_uids.append(uid)
continue
# An object UID already there?
if (item in service_uids):
continue
# Maybe object UID.
portal = portal if portal else api.portal.get()
bsc = bsc if bsc else getToolByName(portal, 'bika_setup_catalog')
brains = bsc(UID=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
continue
# Maybe service Title
brains = bsc(portal_type='AnalysisService', title=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
continue
# Maybe service Keyword
brains = bsc(portal_type='AnalysisService', getKeyword=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
continue
raise RuntimeError(
str(item) + " should be the UID, title, keyword "
" or title of an AnalysisService.")
return list(set(service_uids))
def doActionToAnalysis(source_analysis, action):
"""
This functions executes the action against the analysis.
:base: a full analysis object. The new analyses will be cloned from it.
:action: a dictionary representing an action row.
[{'action': 'duplicate', ...}, {,}, ...]
:returns: the new analysis
"""
if not IRequestAnalysis.providedBy(source_analysis):
# Only routine analyses (assigned to a Request) are supported
logger.warn("Only IRequestAnalysis are supported in reflex testing")
return None
state = api.get_review_status(source_analysis)
action_id = action.get('action', '')
if action_id == "new_analysis":
# Create a new analysis (different from the original)
service_uid = action.get("new_analysis", "")
if not api.is_uid(service_uid):
logger.error("Not a valid UID: {}".format(service_uid))
return None
service = api.get_object_by_uid(service_uid, None)
if not service or not IAnalysisService.providedBy(service):
logger.error("No valid service for UID {}".format(service_uid))
return None
analysis = create_analysis(source_analysis.aq_parent, service)
analysis.setSamplePartition(source_analysis.getSamplePartition())
changeWorkflowState(analysis, "bika_analysis_workflow",
"sample_received")
elif action_id == 'setvisibility':
target_id = action.get('setvisibilityof', '')
if target_id == "original":
analysis = source_analysis
else:
analysis = _fetch_analysis_for_local_id(source_analysis, target_id)
elif action_id == 'repeat' and state != 'retracted':
# Repeat an analysis consist on cancel it and then create a new
# analysis with the same analysis service used for the canceled
# one (always working with the same sample). It'll do a retract
# action
doActionFor(source_analysis, 'retract')
analysis_request = source_analysis.getRequest()
analysis = analysis_request.getAnalyses(sort_on="created")[-1]
analysis = api.get_object(analysis)
analysis.setResult('')
elif action_id == 'duplicate' or state == 'retracted':
analysis = duplicateAnalysis(source_analysis)
analysis.setResult('')
elif action_id == 'setresult':
target = action.get('setresulton', '')
result_value = action.get('setresultdiscrete', '') or \
action['setresultvalue']
if target == 'original':
analysis = source_analysis.getOriginalReflexedAnalysis()
analysis.setResult(result_value)
elif target == 'new':
# Create a new analysis
analysis = duplicateAnalysis(source_analysis)
analysis.setResult(result_value)
doActionFor(analysis, 'submit')
else:
logger.error("Unknown 'setresulton' directive: {}".format(target))
return None
else:
logger.error("Unknown Reflex Rule action: {}".format(action_id))
return None
analysis.setReflexRuleAction(action_id)
analysis.setIsReflexAnalysis(True)
analysis.setReflexAnalysisOf(source_analysis)
analysis.setReflexRuleActionsTriggered(
source_analysis.getReflexRuleActionsTriggered())
if action.get('showinreport', '') == "invisible":
analysis.setHidden(True)
elif action.get('showinreport', '') == "visible":
analysis.setHidden(False)
# Setting the original reflected analysis
if source_analysis.getOriginalReflexedAnalysis():
analysis.setOriginalReflexedAnalysis(
source_analysis.getOriginalReflexedAnalysis())
else:
analysis.setOriginalReflexedAnalysis(source_analysis)
analysis.setReflexRuleLocalID(action.get('an_result_id', ''))
# Setting the remarks to base analysis
#remarks = get_remarks(action, analysis)
#analysis.setRemarks(remarks)
return analysis
