def get_task(task_uid):
"""Resolves the task for the given task uid
"""
if not capi.is_uid(task_uid) or task_uid == "0":
# 400 Bad Request, wrong task uid
_fail(412, "Task uid empty or no valid format")
task = api.get_queue().get_task(task_uid)
if not task:
_fail(404, "Task {}".format(task_uid))
if not capi.is_uid(task.context_uid):
_fail(500, "Task's context uid is not valid")
return task
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 _process_value(value):
"""Convert the value into a human readable diff string
"""
if not value:
value = _("Not set")
# handle strings
elif isinstance(value, basestring):
# XXX: bad data, e.g. in AS Method field
if value == "None":
value = _("Not set")
# 0 is detected as the portal UID
elif value == "0":
value = "0"
# handle physical paths
elif value.startswith("/"):
# remove the portal path to reduce noise in virtual hostings
portal_path = api.get_path(api.get_portal())
value = value.replace(portal_path, "", 1)
elif api.is_uid(value):
value = _get_title_or_id_from_uid(value)
# handle dictionaries
elif isinstance(value, (dict)):
value = json.dumps(sorted(value.items()), indent=1)
# handle lists and tuples
elif isinstance(value, (list, tuple)):
value = sorted(map(_process_value, value))
value = "; ".join(value)
# handle unicodes
if isinstance(value, unicode):
value = api.safe_unicode(value).encode("utf8")
return str(value)
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 is_result_range_compliant(analysis):
"""Returns whether the result range from the analysis matches with the
result range for the service counterpart defined in the Sample
"""
if not IRequestAnalysis.providedBy(analysis):
return True
if IDuplicateAnalysis.providedBy(analysis):
# Does not make sense to apply compliance to a duplicate, cause its
# valid range depends on the result of the original analysis
return True
rr = analysis.getResultsRange()
service_uid = rr.get("uid", None)
if not api.is_uid(service_uid):
return True
# Compare with Sample
sample = analysis.getRequest()
# If no Specification is set, assume is compliant
specification = sample.getRawSpecification()
if not specification:
return True
# Compare with the Specification that was initially set to the Sample
sample_rr = sample.getResultsRange(search_by=service_uid)
if not sample_rr:
# This service is not defined in Sample's ResultsRange, we
# assume this *does not* break the compliance
return True
return rr == sample_rr
def get_object_at(self, row, column):
"""Returns an object this container contains at the given position
"""
uid = self.get_uid_at(row, column)
if not api.is_uid(uid):
return None
return api.get_object_by_uid(uid, default=None)
def _get_object(context, value):
"""Resolve a UID to an object.
:param context: context is the object containing the field's schema.
:type context: BaseContent
:param value: A UID.
:type value: string
:return: Returns a Content object or None.
:rtype: BaseContent
"""
if not value:
return None
if api.is_brain(value):
return api.get_object(value)
if api.is_object(value):
return value
if api.is_uid(value):
uc = api.get_tool('uid_catalog', context=context)
brains = uc(UID=value)
if len(brains) == 0:
# Broken Reference!
logger.warn("Reference on {} with UID {} is broken!"
.format(repr(context), value))
return None
return brains[0].getObject()
return None
def metadata_to_searchable_text(self, brain, key, value):
"""Parse the given metadata to text
:param brain: ZCatalog Brain
:param key: The name of the metadata column
:param value: The raw value of the metadata column
:returns: Searchable and translated unicode value or None
"""
if not value:
return u""
if value is Missing.Value:
return u""
if api.is_uid(value):
return u""
if isinstance(value, (bool)):
return u""
if isinstance(value, (list, tuple)):
for v in value:
return self.metadata_to_searchable_text(brain, key, v)
if isinstance(value, (dict)):
for k, v in value.items():
return self.metadata_to_searchable_text(brain, k, v)
if self.is_date(value):
return self.to_str_date(value)
if "state" in key.lower():
return self.translate_review_state(value,
api.get_portal_type(brain))
if not isinstance(value, basestring):
value = str(value)
return safe_unicode(value)
def guard(self, action):
"""Returns False if the sample is queued or contains queued analyses
"""
# Check if this current request life-cycle is handled by a consumer
request = capi.get_request()
queue_task_uid = request.get("queue_tuid", "")
if capi.is_uid(queue_task_uid):
ctx_id = capi.get_id(self.context)
logger.info("Skip guard for {}: {}".format(ctx_id, action))
return True
# Don't do anything if senaite.queue is not enabled
if not api.is_queue_enabled():
return True
# Check if the sample is queued
if api.is_queued(self.context, status=["queued"]):
return False
# Check whether the sample contains queued analyses
for brain in self.context.getAnalyses():
if api.is_queued(brain, status=["queued"]):
return False
return True
def process_value(self, value):
"""Process publication value
"""
# UID -> SuperModel
if api.is_uid(value):
# Do not process "0" as the portal object
# -> Side effect in specifications when the value is "0"
if value == "0":
return "0"
return self.to_super_model(value)
# Content -> SuperModel
elif api.is_object(value):
return self.to_super_model(value)
# String -> Unicode
elif isinstance(value, basestring):
return safe_unicode(value).encode("utf-8")
# DateTime -> DateTime
elif isinstance(value, DateTime):
return value
# Process list values
elif isinstance(value, (LazyMap, list, tuple)):
return map(self.process_value, value)
# Process dict values
elif isinstance(value, (dict)):
return {k: self.process_value(v) for k, v in value.iteritems()}
# Process function
elif safe_callable(value):
return self.process_value(value())
# Always return the unprocessed value last
return value
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 get_brain(self, uid, catalog):
if not api.is_uid(uid):
return None
query = dict(UID=uid)
brains = api.search(query, catalog)
if brains and len(brains) == 1:
return brains[0]
return None
def get_brain(self, uid, catalog):
if not api.is_uid(uid):
return None
query = dict(UID=uid)
brains = api.search(query, catalog)
if brains and len(brains) == 1:
return brains[0]
return None
def to_super_model(self, thing):
"""Wraps an object into a Super Model
"""
if api.is_uid(thing):
return SuperModel(thing)
if not api.is_object(thing):
raise TypeError("Expected a portal object, got '{}'".format(
type(thing)))
return thing
def get_object(self, brain_or_object_or_uid):
"""Get the full content object. Returns None if the param passed in is
not a valid, not a valid object or not found
:param brain_or_object_or_uid: UID/Catalog brain/content object
:returns: content object
"""
if api.is_uid(brain_or_object_or_uid):
return api.get_object_by_uid(brain_or_object_or_uid, default=None)
if api.is_object(brain_or_object_or_uid):
return api.get_object(brain_or_object_or_uid)
return None
def get_task(task_uid):
"""Resolves the task for the given task uid
"""
if not api.is_uid(task_uid) or task_uid == "0":
# 400 Bad Request, wrong task uid
_fail(412, "Task uid empty or no valid format")
task = qapi.get_queue().get_task(task_uid)
if not task:
_fail(404, "Task {}".format(task_uid))
return task
def addDepartment(self, dep):
"""Adds a department
:param dep: UID or department object
:returns: True when the department was added
"""
if api.is_uid(dep):
dep = api.get_object_by_uid(dep)
deps = self.getDepartments()
if dep not in deps:
return False
deps.append(dep)
self.setDepartments(deps)
return True
def __call__(self):
form = self.request.form
# Form submit toggle
form_submitted = form.get("submitted", False)
form_store = form.get("button_store", False)
form_cancel = form.get("button_cancel", False)
# Get the container
container = self.get_container()
if not container:
return self.redirect(message=_s("No items selected"),
level="warning")
if not IStorageSamplesContainer.providedBy(container):
logger.warn("Not a samples container: {}").format(repr(container))
self.redirect(redirect_url=self.get_next_url())
# If container is full, there is no way to add more samples there
if container.is_full():
message = _("Cannot store samples. Samples container {} is full")
return self.redirect(message=message.format(api.get_id(container)),
level="warning")
# Handle store
if form_submitted and form_store:
alpha_position = form.get("position")
sample_uid = form.get("sample_uid")
if not alpha_position or not api.is_uid(sample_uid):
message = _("No position or not valid sample selected")
return self.redirect(message=message)
sample = api.get_object(sample_uid)
logger.info("Storing sample {} in {} at {}".format(
api.get_id(sample), api.get_id(container), alpha_position))
# Store
position = container.alpha_to_position(alpha_position)
if container.add_object_at(sample, position[0], position[1]):
message = _("Stored sample {} at position {}").format(
api.get_id(sample), alpha_position)
if container.is_full():
return self.redirect(redirect_url=self.get_next_url())
return self.redirect(redirect_url=self.get_fallback_url(),
message=message)
# Handle cancel
if form_submitted and form_cancel:
return self.redirect(message=_("Sample storing canceled"))
return self.template()
def removeDepartment(self, dep):
"""Removes a department
:param dep: UID or department object
:returns: True when the department was removed
"""
if api.is_uid(dep):
dep = api.get_object_by_uid(dep)
deps = self.getDepartments()
if dep not in deps:
return False
deps.remove(dep)
self.setDepartments(deps)
return True
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 __init__(self, thing):
# Type based initializers
if isinstance(thing, basestring) and thing == "0":
self.init_with_instance(api.get_portal())
elif api.is_uid(thing):
self.init_with_uid(thing)
elif api.is_brain(thing):
self.init_with_brain(thing)
elif api.is_object(thing):
self.init_with_instance(thing)
else:
raise TypeError("Can not initialize a SuperModel with '{}'".format(
repr(thing)))
def process(self, task):
"""Transition the objects from the task
"""
# The worksheet is the context
worksheet = self.context
uids = task.get("uids", [])
slots = task.get("slots", [])
# Sanitize the slots list and pad with empties
slots = map(lambda s: _api.to_int(s, None) or "", slots)
slots += [""] * abs(len(uids) - len(slots))
# Sort analyses so those with an assigned slot are added first
# Note numeric values get precedence over strings, empty strings here
uids_slots = zip(uids, slots)
uids_slots = sorted(uids_slots, key=lambda i: i[1])
# Remove those with no valid uids
uids_slots = filter(lambda us: _api.is_uid(us[0]), uids_slots)
# Remove duplicate uids while keeping the order
seen = set()
uids_slots = filter(lambda us: not (us[0] in seen or seen.add(us[0])),
uids_slots)
# Remove uids that are already in the worksheet (just in case)
layout = filter(None, worksheet.getLayout() or [])
existing = map(lambda r: r.get("analysis_uid"), layout)
uids_slots = filter(lambda us: us[0] not in existing, uids_slots)
# If there are too many objects to process, split them in chunks to
# prevent the task to take too much time to complete
chunks = get_chunks_for(task, items=uids_slots)
# Process the first chunk
for uid, slot in chunks[0]:
# Add the analysis
slot = slot or None
analysis = _api.get_object_by_uid(uid)
worksheet.addAnalysis(analysis, slot)
# Reindex the worksheet
worksheet.reindexObject()
if chunks[1]:
# Unpack the remaining analyses-slots and add them to the queue
uids, slots = zip(*chunks[1])
api.add_assign_task(worksheet, analyses=uids, slots=slots)
def get_client_from_query(self, query, purge=False):
"""Resolves the client from the query passed-in
"""
keys = ["getPrimaryReferrerUID", "getClientUID", "getParentUID", "UID"]
for key in keys:
uid = query.get(key)
if not api.is_uid(uid) or uid == "0":
continue
client = api.get_object_by_uid(uid)
if IClient.providedBy(client):
if purge:
# Remove the key:value from the query
del (query[key])
return client
return None
def get_task_uid(task_or_uid, default=_marker):
"""Returns the task unique identifier
:param task_or_uid: QueueTask/task uid/dict
:param default: (Optional) fallback value
:return: the task's unique identifier
"""
if api.is_uid(task_or_uid) and task_or_uid != "0":
return task_or_uid
if isinstance(task_or_uid, QueueTask):
return get_task_uid(task_or_uid.task_uid, default=default)
if isinstance(task_or_uid, dict):
task_uid = task_or_uid.get("task_uid", None)
return get_task_uid(task_uid, default=default)
if default is _marker:
raise ValueError("{} is not supported".format(repr(task_or_uid)))
return default
def getResultRange(self, values, uid_keyword_service):
if not uid_keyword_service:
return None
if api.is_object(uid_keyword_service):
uid_keyword_service = api.get_uid(uid_keyword_service)
key = "keyword"
if api.is_uid(uid_keyword_service) and uid_keyword_service != "0":
# We always assume a uid of "0" refers to portal
key = "uid"
# Find out the item for the given uid/keyword
from bika.lims.content.analysisspec import ResultsRangeDict
value = filter(lambda v: v.get(key) == uid_keyword_service, values)
return value and ResultsRangeDict(dict(value[0].items())) or None
def __init__(self, name, request, context, *arg, **kw):
super(QueueTask, self).__init__(*arg, **kw)
if api.is_uid(context):
context_uid = context
context_path = kw.get("context_path")
if not context_path:
raise ValueError("context_path is missing")
elif api.is_object(context):
context_uid = api.get_uid(context)
context_path = api.get_path(context)
else:
raise TypeError("No valid context object")
# Set defaults
kw = kw or {}
task_uid = str(kw.get("task_uid", tmpID()))
uids = map(str, kw.get("uids", []))
created = api.to_float(kw.get("created"), default=time.time())
status = kw.get("status", None)
min_sec = api.to_int(kw.get("min_seconds"), default=get_min_seconds())
max_sec = api.to_int(kw.get("max_seconds"), default=get_max_seconds())
priority = api.to_int(kw.get("priority"), default=10)
retries = api.to_int(kw.get("retries"), default=get_max_retries())
unique = self._is_true(kw.get("unique", False))
chunks = api.to_int(kw.get("chunk_size"), default=get_chunk_size(name))
username = kw.get("username", self._get_authenticated_user(request))
err_message = kw.get("error_message", None)
self.update({
"task_uid": task_uid,
"name": name,
"context_uid": context_uid,
"context_path": context_path,
"uids": uids,
"created": created,
"status": status and str(status) or None,
"error_message": err_message and str(err_message) or None,
"min_seconds": min_sec,
"max_seconds": max_sec,
"priority": priority,
"retries": retries,
"unique": unique,
"chunk_size": chunks,
"username": str(username),
})
def resolve_uid(self, result_range):
"""Resolves the uid key for the result_range passed in if it does not
exist when contains a keyword
"""
value = result_range.copy()
uid = value.get("uid")
if api.is_uid(uid) and uid != "0":
return value
# uid key does not exist or is not valid, try to infere from keyword
keyword = value.get("keyword")
if keyword:
query = dict(portal_type="AnalysisService", getKeyword=keyword)
brains = api.search(query, SETUP_CATALOG)
if len(brains) == 1:
uid = api.get_uid(brains[0])
value["uid"] = uid
return value
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 resolve_uid(self, raw_dict):
"""Returns a copy of the raw dictionary passed in, but with additional
key "uid". It's value is inferred from "keyword" if present
"""
value = raw_dict.copy()
uid = value.get("uid")
if api.is_uid(uid) and uid != "0":
return value
# uid key does not exist or is not valid, try to infere from keyword
keyword = value.get("keyword")
if keyword:
query = dict(portal_type="AnalysisService", getKeyword=keyword)
brains = api.search(query, SETUP_CATALOG)
if len(brains) == 1:
uid = api.get_uid(brains[0])
value["uid"] = uid
return value
def get_form_value(self, form_key, object_brain_uid, default=None):
"""Returns a value from the request's form for the given uid, if any
"""
if form_key not in self.request.form:
return default
uid = object_brain_uid
if not api.is_uid(uid):
uid = api.get_uid(object_brain_uid)
values = self.request.form.get(form_key)
if isinstance(values, list):
if len(values) == 0:
return default
if len(values) > 1:
logger.warn("Multiple set of values for {}".format(form_key))
values = values[0]
return values.get(uid, default)
def _process_value(value):
"""Convert the value into a human readable diff string
"""
if not value:
value = _("Not set")
# XXX: bad data, e.g. in AS Method field
elif value == "None":
value = _("Not set")
# 0 is detected as the portal UID
elif value == "0":
pass
elif api.is_uid(value):
value = _get_title_or_id_from_uid(value)
elif isinstance(value, (dict)):
value = json.dumps(sorted(value.items()), indent=1)
elif isinstance(value, (list, tuple)):
value = sorted(map(_process_value, value))
value = "; ".join(value)
elif isinstance(value, unicode):
value = api.safe_unicode(value).encode("utf8")
return str(value)
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