def get_user_contact(user, contact_types=['Contact', 'LabContact']):
"""Returns the associated contact of a Plone user
If the user passed in has no contact associated, return None.
The `contact_types` parameter filter the portal types for the search.
:param: Plone user
:contact_types: List with the contact portal types to search
:returns: Contact associated to the Plone user or None
"""
if not user:
return None
query = {'portal_type': contact_types, 'getUsername': user.id}
brains = search(query, catalog='portal_catalog')
if not brains:
return None
if len(brains) > 1:
# Oops, the user has multiple contacts assigned, return None
contacts = map(lambda c: c.Title, brains)
err_msg = "User '{}' is bound to multiple Contacts '{}'"
err_msg = err_msg.format(user.id, ','.join(contacts))
logger.error(err_msg)
return None
return get_object(brains[0])
def getTransitionUsers(obj, action_id, last_user=False):
"""
This function returns a list with the users who have done the transition.
:action_id: a sring as the transition id.
:last_user: a boolean to return only the last user triggering the
transition or all of them.
:returns: a list of user ids.
"""
workflow = getToolByName(obj, 'portal_workflow')
users = []
try:
# https://jira.bikalabs.com/browse/LIMS-2242:
# Sometimes the workflow history is inexplicably missing!
review_history = list(workflow.getInfoFor(obj, 'review_history'))
except WorkflowException:
logger.error(
"workflow history is inexplicably missing."
" https://jira.bikalabs.com/browse/LIMS-2242")
return users
# invert the list, so we always see the most recent matching event
review_history.reverse()
for event in review_history:
if event.get('action', '') == action_id:
value = event.get('actor', '')
users.append(value)
if last_user:
return users
return users
def get_workflow_actions(self):
""" Compile a list of possible workflow transitions for items
in this Table.
"""
# cbb return empty list if we are unable to select items
if not self.show_select_column:
return []
workflow = getToolByName(self.context, 'portal_workflow')
# get all transitions for all items.
transitions = {}
actions = []
for obj in [i.get('obj', '') for i in self.items]:
# Unresolved error
# LIMS-1861 Recurrent error after managing analysis from an AR
# https://jira.bikalabs.com/browse/LIMS-1861
# Was:
# obj = hasattr(obj, 'getObject') and obj.getObject() or obj
try:
obj = hasattr(obj, 'getObject') and obj.getObject() or obj
except AttributeError, e:
logger.error("Unresolved error LIMS-1861: %s" % str(e))
continue
for it in workflow.getTransitionsFor(obj):
transitions[it['id']] = it
def sendAlertEmail(self):
# Send an alert email
laboratory = self.context.bika_setup.laboratory
subject = self.request.get('subject')
to = self.request.get('to')
body = self.request.get('body')
body = "<br/>".join(body.split("\r\n"))
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = subject
mime_msg['From'] = formataddr(
(encode_header(laboratory.getName()),
laboratory.getEmailAddress()))
mime_msg['To'] = to
msg_txt = MIMEText(safe_unicode(body).encode('utf-8'),
_subtype='html')
mime_msg.preamble = 'This is a multi-part MIME message.'
mime_msg.attach(msg_txt)
succeed = False
try:
host = getToolByName(self.context, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except Exception, msg:
ar = self.context.id
logger.error("Panic level email %s: %s" % (ar, str(msg)))
message = _('Unable to send an email to alert client '
'that some results exceeded the panic levels') \
+ (": %s" % str(msg))
self.addMessage(message, 'warning')
def removeAnalysis(self, analysis):
""" delete an analyses from the worksheet and un-assign it
"""
workflow = getToolByName(self, 'portal_workflow')
# overwrite saved context UID for event subscriber
self.REQUEST['context_uid'] = self.UID()
try:
workflow.doActionFor(analysis, 'unassign')
except WorkflowException as e:
message = str(e)
logger.error(
"Cannot use 'unassign' transition on {}: {}".format(
analysis, message))
# Note: subscriber might unassign the AR and/or promote the worksheet
# remove analysis from context.Analyses *after* unassign,
# (doActionFor requires worksheet in analysis.getBackReferences)
Analyses = self.getAnalyses()
if analysis in Analyses:
Analyses.remove(analysis)
self.setAnalyses(Analyses)
layout = [slot for slot in self.getLayout() if slot['analysis_uid'] != analysis.UID()]
self.setLayout(layout)
if analysis.portal_type == "DuplicateAnalysis":
self._delObject(analysis.id)
def Import(self):
folder = self.context.patients
rows = self.get_rows(3)
for row in rows:
if not row['Firstname'] or not row['PrimaryReferrer']:
continue
pc = getToolByName(self.context, 'portal_catalog')
client = pc(portal_type='Client', Title=row['PrimaryReferrer'])
if len(client) == 0:
raise IndexError("Primary referrer invalid: '%s'" % row['PrimaryReferrer'])
client = client[0].getObject()
_id = folder.invokeFactory('Patient', id=tmpID())
obj = folder[_id]
obj.unmarkCreationFlag()
renameAfterCreation(obj)
Fullname = (row['Firstname'] + " " + row.get('Surname', '')).strip()
obj.edit(title=Fullname,
ClientPatientID = row.get('ClientPatientID', ''),
Salutation = row.get('Salutation', ''),
Firstname = row.get('Firstname', ''),
Surname = row.get('Surname', ''),
PrimaryReferrer = client.UID(),
Gender = row.get('Gender', 'dk'),
Age = row.get('Age', ''),
BirthDate = row.get('BirthDate', ''),
BirthDateEstimated =self.to_bool(row.get('BirthDateEstimated','False')),
BirthPlace = row.get('BirthPlace', ''),
Ethnicity = row.get('Ethnicity', ''),
Citizenship =row.get('Citizenship', ''),
MothersName = row.get('MothersName', ''),
CivilStatus =row.get('CivilStatus', ''),
Anonymous = self.to_bool(row.get('Anonymous','False'))
)
self.fill_contactfields(row, obj)
self.fill_addressfields(row, obj)
if 'Photo' in row and row['Photo']:
try:
path = resource_filename("bika.lims",
"setupdata/%s/%s" \
% (self.dataset_name, row['Photo']))
file_data = open(path, "rb").read()
obj.setPhoto(file_data)
except:
logger.error("Unable to load Photo %s"%row['Photo'])
if 'Feature' in row and row['Feature']:
try:
path = resource_filename("bika.lims",
"setupdata/%s/%s" \
% (self.dataset_name, row['Feature']))
file_data = open(path, "rb").read()
obj.setFeature(file_data)
except:
logger.error("Unable to load Feature %s"%row['Feature'])
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def _rise_error(self):
"""
Give the error missage
"""
tbex = traceback.format_exc()
logger.error(
'An error occurred while rendering the view: %s' % tbex)
self.destination_url = self.request.get_header(
"referer", self.context.absolute_url())
def get(self, instance, **kw):
"""Get the value of the field
"""
# Gracefully avoid programming errors in Computed fields
try:
return self._get(instance, **kw)
except AttributeError:
logger.error("Could not get the value of the computed field '{}'"
.format(self.get_field_name()))
return None
def changeWorkflowState(content, wf_id, state_id, acquire_permissions=False,
portal_workflow=None, **kw):
"""Change the workflow state of an object
@param content: Content obj which state will be changed
@param state_id: name of the state to put on content
@param acquire_permissions: True->All permissions unchecked and on riles and
acquired
False->Applies new state security map
@param portal_workflow: Provide workflow tool (optimisation) if known
@param kw: change the values of same name of the state mapping
@return: None
"""
if portal_workflow is None:
portal_workflow = getToolByName(content, 'portal_workflow')
# Might raise IndexError if no workflow is associated to this type
found_wf = 0
for wf_def in portal_workflow.getWorkflowsFor(content):
if wf_id == wf_def.getId():
found_wf = 1
break
if not found_wf:
logger.error("%s: Cannot find workflow id %s" % (content, wf_id))
wf_state = {
'action': None,
'actor': None,
'comments': "Setting state to %s" % state_id,
'review_state': state_id,
'time': DateTime(),
}
# Updating wf_state from keyword args
for k in kw.keys():
# Remove unknown items
if not wf_state.has_key(k):
del kw[k]
if kw.has_key('review_state'):
del kw['review_state']
wf_state.update(kw)
portal_workflow.setStatusOf(wf_id, content, wf_state)
if acquire_permissions:
# Acquire all permissions
for permission in content.possible_permissions():
content.manage_permission(permission, acquire=1)
else:
# Setting new state permissions
wf_def.updateRoleMappingsFor(content)
# Map changes to the catalogs
content.reindexObject(idxs=['allowedRolesAndUsers', 'review_state'])
return
def getWorksheet(self):
"""Returns the Worksheet to which this analysis belongs to, or None
"""
worksheet = self.getBackReferences('WorksheetAnalysis')
if not worksheet:
return None
if len(worksheet) > 1:
logger.error(
"Analysis %s is assigned to more than one worksheet."
% self.getId())
return worksheet[0]
def get(self, instance, **kwargs):
""" get() returns the list of contained analyses
By default, return a list of catalog brains.
If you want objects, pass full_objects = True
If you want to override "ViewRetractedAnalyses",
pass retracted=True
other kwargs are passed to bika_analysis_catalog
"""
full_objects = False
if 'full_objects' in kwargs:
full_objects = kwargs['full_objects']
del kwargs['full_objects']
if 'retracted' in kwargs:
retracted = kwargs['retracted']
del kwargs['retracted']
else:
mtool = getToolByName(instance, 'portal_membership')
retracted = mtool.checkPermission(ViewRetractedAnalyses,
instance)
bac = getToolByName(instance, 'bika_analysis_catalog')
contentFilter = dict([(k, v) for k, v in kwargs.items()
if k in bac.indexes()])
contentFilter['portal_type'] = "Analysis"
contentFilter['sort_on'] = "sortable_title"
contentFilter['path'] = {'query': "/".join(instance.getPhysicalPath()),
'level': 0}
analyses = bac(contentFilter)
if not retracted:
analyses = [a for a in analyses if a.review_state != 'retracted']
if full_objects:
# Unresolved error
# LIMS-1861 Recurrent error after managing analysis from an AR
# https://jira.bikalabs.com/browse/LIMS-1861
# Was:
# analyses = [a.getObject() for a in analyses]
ans = []
for a in analyses:
try:
obj = a.getObject()
except AttributeError, e:
logger.error("Unresolved error LIMS-1861: %s" % str(e))
continue
ans.append(obj)
analyses = ans
def migrate_instrument_locations(portal):
bsc = portal.bika_setup_catalog
bika_instrumentlocations = portal.bika_setup.get("bika_instrumentlocations")
if bika_instrumentlocations is None:
logger.error("bika_instrumentlocations not found in bika_setup!")
return # This should not happen
# move bika_instrumentlocations below bika_instrumenttypes
panel_ids = portal.bika_setup.objectIds()
target_idx = panel_ids.index("bika_instrumenttypes")
current_idx = panel_ids.index("bika_instrumentlocations")
delta = current_idx - target_idx
if delta > 1:
portal.bika_setup.moveObjectsUp("bika_instrumentlocations", delta=delta-1)
instrument_brains = bsc(portal_type="Instrument")
for instrument_brain in instrument_brains:
instrument = instrument_brain.getObject()
# get the string value of the `location` field
location = instrument.getLocation()
if not location:
continue # Skip if no location was set
# make a dictionary with the Titles as keys and the objects as values
instrument_locations = bika_instrumentlocations.objectValues()
instrument_location_titles = map(lambda o: o.Title(), instrument_locations)
locations = dict(zip(instrument_location_titles, instrument_locations))
instrument_location = None
if location in locations:
logger.info("Instrument Location {} exists in bika_instrumentlocations".format(location))
instrument_location = locations[location]
else:
# Create a new location and link it to the instruments InstrumentLocation field
instrument_location = _createObjectByType("InstrumentLocation", bika_instrumentlocations, tmpID())
instrument_location.setTitle(location)
instrument_location._renameAfterCreation()
instrument_location.reindexObject()
logger.info("Created Instrument Location {} in bika_instrumentlocations".format(location))
instrument.setLocation(None) # flush the old instrument location
instrument.setInstrumentLocation(instrument_location)
instrument.reindexObject()
logger.info("Linked Instrument Location {} to Instrument {}".format(location, instrument.id))
def getTransitionActor(obj, action_id):
"""Returns the identifier of the user who last performed the action
on the object.
"""
workflow = api.portal.get_tool("portal_workflow")
try:
review_history = list(workflow.getInfoFor(obj, "review_history"))
review_history.reverse()
for event in review_history:
if event.get("action") == action_id:
return event.get("actor")
return ''
except WorkflowException as e:
message = str(e)
logger.error("Cannot retrieve review_history on {}: {}".format(
obj, message))
return ''
def __call__(self):
"""
Returns the number of tasks in the sanitation-tasks queue
"""
try:
PostOnly(self.context.REQUEST)
except:
logger.error(traceback.format_exc())
return json.dumps({'count': 0})
try:
CheckAuthenticator(self.request.form)
except:
logger.error(traceback.format_exc())
return json.dumps({'count': 0})
task_queue = queryUtility(ITaskQueue, name='sanitation-tasks')
count = len(task_queue) if task_queue is not None else 0
return json.dumps({'count': count})
def getReviewHistory(instance):
"""Returns the review history for the instance in reverse order
:returns: the list of historic events as dicts
"""
review_history = []
workflow = getToolByName(instance, 'portal_workflow')
try:
# https://jira.bikalabs.com/browse/LIMS-2242:
# Sometimes the workflow history is inexplicably missing!
review_history = list(workflow.getInfoFor(instance, 'review_history'))
except WorkflowException:
logger.error(
"workflow history is inexplicably missing."
" https://jira.bikalabs.com/browse/LIMS-2242")
# invert the list, so we always see the most recent matching event
review_history.reverse()
return review_history
def _addColumn(cat, col):
"""
This function adds a metadata column to the acatalog.
:cat: a catalog object
:col: a column id as string
:returns: a boolean as True if the element has been added and
False otherwise
"""
# First check if the metadata column already exists
if col not in cat.schema():
try:
cat.addColumn(col)
logger.info('Column %s added to %s.' % (col, cat.id))
return True
except:
logger.error(
'Catalog column %s error while adding to %s.' % (col, cat.id))
return False
def getTransitionDate(obj, action_id):
workflow = api.portal.get_tool("portal_workflow")
try:
# https://jira.bikalabs.com/browse/LIMS-2242:
# Sometimes the workflow history is inexplicably missing!
review_history = list(workflow.getInfoFor(obj, 'review_history'))
except WorkflowException as e:
message = str(e)
logger.error("Cannot retrieve review_history on {}: {}".format(
obj, message))
return None
# invert the list, so we always see the most recent matching event
review_history.reverse()
for event in review_history:
if event['action'] == action_id:
value = ulocalized_time(event['time'], long_format=True,
time_only=False, context=obj)
return value
return None
def _delIndex(catalog, index):
"""
This function desindexes the index element from the catalog.
:catalog: a catalog object
:index: an index id as string
:returns: a boolean as True if the element has been desindexed and it
returns False otherwise.
"""
if index in catalog.indexes():
try:
catalog.delIndex(index)
logger.info(
'Catalog index %s deleted from %s.' % (index, catalog.id))
return True
except:
logger.error(
'Catalog index %s error while deleting from %s.'
% (index, catalog.id))
return False
def _delColumn(cat, col):
"""
This function deletes a metadata column of the acatalog.
:cat: a catalog object
:col: a column id as string
:returns: a boolean as True if the element has been removed and
False otherwise
"""
# First check if the metadata column already exists
if col in cat.schema():
try:
cat.delColumn(col)
logger.info('Column %s deleted from %s.' % (col, cat.id))
return True
except:
logger.error(
'Catalog column %s error while deleting from %s.'
% (col, cat.id))
return False
def getTransitionDate(obj, action_id):
workflow = getToolByName(obj, 'portal_workflow')
try:
# https://jira.bikalabs.com/browse/LIMS-2242:
# Sometimes the workflow history is inexplicably missing!
review_history = list(workflow.getInfoFor(obj, 'review_history'))
except WorkflowException:
logger.error(
"workflow history is inexplicably missing."
" https://jira.bikalabs.com/browse/LIMS-2242")
return None
# invert the list, so we always see the most recent matching event
review_history.reverse()
for event in review_history:
if event['action'] == action_id:
value = ulocalized_time(event['time'], long_format=True,
time_only=False, context=obj)
return value
return None
def getContactByUsername(cls, username):
"""Convenience Classmethod which returns a Contact by a Username
"""
# Check if the User is linked already
pc = api.portal.get_tool("portal_catalog")
contacts = pc(portal_type=cls.portal_type,
getUsername=username)
# No Contact assigned to this username
if len(contacts) == 0:
return None
# Multiple Users assigned, this should never happen
if len(contacts) > 1:
logger.error("User '{}' is bound to multiple Contacts '{}'".format(
username, ",".join(map(lambda c: c.Title, contacts))))
return map(lambda x: x.getObject(), contacts)
# Return the found Contact object
return contacts[0].getObject()
def review_state(self):
"""Get workflow state of object in wf_id.
First try request: <form_id>_review_state
Then try 'default': self.default_review_state
:return: item from self.review_states
"""
if not self.review_states:
logger.error("%s.review_states is undefined." % self)
return None
# get state_id from (request or default_review_states)
key = "%s_review_state" % self.form_id
state_id = self.request.form.get(key, self.default_review_state)
states = [r for r in self.review_states if r['id'] == state_id]
if not states:
logger.error("%s.review_states does not contains id='%s'." %
(self, state_id))
return None
review_state = states[0] if states else self.review_states[0]
# set selected state into the request
self.request['%s_review_state' % self.form_id] = review_state['id']
return review_state
def generateUniqueId(context, **kw):
""" Generate pretty content IDs.
"""
# get the config for this portal type from the system setup
config = get_config(context, **kw)
# get the variables map for later string interpolation
variables = get_variables(context, **kw)
# The new generate sequence number
number = 0
# get the sequence type from the global config
sequence_type = config.get("sequence_type", "generated")
# Sequence Type is "Counter", so we use the length of the backreferences or
# contained objects of the evaluated "context" defined in the config
if sequence_type == 'counter':
number = get_counted_number(context, config, variables, **kw)
# Sequence Type is "Generated", so the ID is constructed according to the
# configured split length
if sequence_type == 'generated':
number = get_generated_number(context, config, variables, **kw)
# store the new sequence number to the variables map for str interpolation
variables["seq"] = number
# The ID formatting template from user config, e.g. {sampleId}-R{seq:02d}
id_template = config.get("form", "")
# Interpolate the ID template
try:
new_id = id_template.format(**variables)
except KeyError, e:
logger.error('KeyError: {} not in id_template {}'.format(
e, id_template))
raise
def _addIndex(catalog, index, indextype):
"""
This function indexes the index element into the catalog if it isn't yet.
:catalog: a catalog object
:index: an index id as string
:indextype: the type of the index as string
:returns: a boolean as True if the element has been indexed and it returns
False otherwise.
"""
if index not in catalog.indexes():
try:
if indextype == 'ZCTextIndex':
addZCTextIndex(catalog, index)
else:
catalog.addIndex(index, indextype)
logger.info('Catalog index %s added to %s.' % (index, catalog.id))
return True
except:
logger.error(
'Catalog index %s error while adding to %s.'
% (index, catalog.id))
return False
def get_review_history(brain_or_object, rev=True):
"""Get the review history for the given brain or context.
:param brain_or_object: A single catalog brain or content object
:type brain_or_object: ATContentType/DexterityContentType/CatalogBrain
:returns: Workflow history
:rtype: [{}, ...]
"""
obj = get_object(brain_or_object)
review_history = []
try:
workflow = get_tool("portal_workflow")
review_history = workflow.getInfoFor(obj, 'review_history')
except WorkflowException as e:
message = str(e)
logger.error("Cannot retrieve review_history on {}: {}".format(
obj, message))
if not isinstance(review_history, (list, tuple)):
logger.error("get_review_history: expected list, recieved {}".format(
review_history))
review_history = []
if rev is True:
review_history.reverse()
return review_history
def __call__(self):
# Do generic bika.lims stuff
BaseClass.__call__(self)
# Do bika-health specific actions when submit
action = BaseClass._get_form_workflow_action(self)
addPortalMessage = self.context.plone_utils.addPortalMessage
if action[0] == 'submit' and isActive(self.context):
inpanicanalyses = []
workflow = getToolByName(self.context, 'portal_workflow')
translate = self.context.translate
rc = getToolByName(self.context, REFERENCE_CATALOG)
uc = getToolByName(self.context, 'uid_catalog')
# retrieve the results from database and check if
# the values are exceeding panic levels
alerts = {}
for uid in self.request.form['Result'][0].keys():
analysis = rc.lookupObject(uid)
analysis = analysis.getObject() if hasattr(
analysis, 'getObject') else analysis
if not analysis:
continue
astate = workflow.getInfoFor(analysis, 'review_state')
if astate == 'retracted':
continue
alerts.update(ResultOutOfRange(analysis)())
if alerts:
message = translate(
_('Some results exceeded the '
'panic levels that may '
'indicate an imminent '
'life-threatening condition'))
addPortalMessage(message, 'warning')
self.request.response.redirect(self.context.absolute_url())
# If panic levels alert email enabled, send an email to
# labmanagers
bs = self.context.bika_setup
if hasattr(bs, 'getEnablePanicAlert') \
and bs.getEnablePanicAlert():
laboratory = self.context.bika_setup.laboratory
lab_address = "<br/>".join(laboratory.getPrintAddress())
managers = self.context.portal_groups.getGroupMembers(
'LabManagers')
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = _("Panic alert")
mime_msg['From'] = formataddr(
(encode_header(laboratory.getName()),
laboratory.getEmailAddress()))
to = []
for manager in managers:
user = self.portal.acl_users.getUser(manager)
uemail = user.getProperty('email')
ufull = user.getProperty('fullname')
to.append(formataddr((encode_header(ufull), uemail)))
mime_msg['To'] = ','.join(to)
strans = []
for analysis_uid, alertlist in alerts:
analysis = uc(analysis_uid).getObject()
for alert in alertlist:
strans.append("- {0}, {1}: {2}".format(
analysis.getService().Title(),
translate(_("Result")), analysis.getResult()))
stran = "<br/>".join(strans)
text = translate(
_(
"Some results from ${items} exceeded the panic levels "
"that may indicate an imminent life-threatening "
"condition: <br/><br/>{analysisresults}<br/><br/>"
"<b>Please, check the Analysis Request if you "
"want to re-test the analysis or immediately "
"alert the client.</b><br/><br/>{lab_address}",
mapping={
'items': self.context.getId(),
'analysisresults': stran,
'lab_address': lab_address
}))
msg_txt = MIMEText(safe_unicode(text).encode('utf-8'),
_subtype='html')
mime_msg.preamble = 'This is a multi-part MIME message.'
mime_msg.attach(msg_txt)
try:
host = getToolByName(self.context, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except Exception as msg:
ar = inpanicanalyses[0].getRequestID()
logger.error("Panic level email %s: %s" %
(ar, str(msg)))
message = self.context.translate(
_('Unable to send an email to alert lab '
'managers that some analyses exceeded the '
'panic levels') + (": %s" % str(msg)))
self.context.plone_utils.addPortalMessage(
message, 'warning')
def doActionFor(instance, action_id, idxs=None):
"""Tries to perform the transition to the instance.
Object is reindexed after the transition takes place, but only if succeeds.
If idxs is set, only these indexes will be reindexed. Otherwise, will try
to use the indexes defined in ACTIONS_TO_INDEX mapping if any.
:param instance: Object to be transitioned
:param action_id: transition id
:param idxs: indexes to be reindexed after the transition
:returns: True if the transition has been performed, together with message
:rtype: tuple (bool,str)
"""
if not instance:
return False, ""
if isinstance(instance, list):
# TODO Workflow . Check if this is strictly necessary
# This check is here because sometimes Plone creates a list
# from submitted form elements.
logger.warn("Got a list of obj in doActionFor!")
if len(instance) > 1:
logger.warn(
"doActionFor is getting an instance parameter which is a list "
"with more than one item. Instance: '{}', action_id: '{}'"
.format(instance, action_id)
)
return doActionFor(instance=instance[0], action_id=action_id, idxs=idxs)
# Since a given transition can cascade or promote to other objects, we want
# to reindex all objects for which the transition succeed at once, at the
# end of process. Otherwise, same object will be reindexed multiple times
# unnecessarily. Also, ActionsHandlerPool ensures the same transition is not
# applied twice to the same object due to cascade/promote recursions.
pool = ActionHandlerPool.get_instance()
if pool.succeed(instance, action_id):
return False, "Transition {} for {} already done"\
.format(action_id, instance.getId())
# Return False if transition is not permitted
if not isTransitionAllowed(instance, action_id):
return False, "Transition {} for {} is not allowed"\
.format(action_id, instance.getId())
# Add this batch process to the queue
pool.queue_pool()
succeed = False
message = ""
workflow = getToolByName(instance, "portal_workflow")
try:
workflow.doActionFor(instance, action_id)
succeed = True
except WorkflowException as e:
message = str(e)
curr_state = getCurrentState(instance)
clazz_name = instance.__class__.__name__
logger.warning(
"Transition '{0}' not allowed: {1} '{2}' ({3})"\
.format(action_id, clazz_name, instance.getId(), curr_state))
logger.error(message)
# If no indexes to reindex have been defined, try to use those defined in
# the ACTIONS_TO_INDEXES mapping. Reindexing only those indexes that might
# be affected by the transition boosts the overall performance!.
if idxs is None:
portal_type = instance.portal_type
idxs = ACTIONS_TO_INDEXES.get(portal_type, {}).get(action_id, [])
# Add the current object to the pool and resume
pool.push(instance, action_id, succeed, idxs=idxs)
pool.resume()
return succeed, message
def doActionToAnalysis(base, 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 the analysis has been retracted yet, just duplicate it
workflow = getToolByName(base, "portal_workflow")
state = workflow.getInfoFor(base, 'review_state')
action_rule_name = ''
if action.get('action', '') == 'setvisibility':
action_rule_name = 'Visibility set'
target_analysis = action.get('setvisibilityof', '')
if target_analysis == "original":
analysis = base
else:
analysis = _fetch_analysis_for_local_id(base, target_analysis)
elif action.get('action', '') == '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(base, 'retract')
analysis = base.aq_parent.getAnalyses(
sort_on='created')[-1].getObject()
action_rule_name = 'Repeated'
analysis.setResult('')
elif action.get('action', '') == 'duplicate' or state == 'retracted':
analysis = duplicateAnalysis(base)
action_rule_name = 'Duplicated'
analysis.setResult('')
elif action.get('action', '') == 'setresult':
target_analysis = action.get('setresulton', '')
action_rule_name = 'Result set'
result_value = action['setresultdiscrete'] if \
action.get('setresultdiscrete', '') else action['setresultvalue']
if target_analysis == 'original':
original = base.getOriginalReflexedAnalysis()
analysis = original
original.setResult(result_value)
elif target_analysis == 'new':
# Create a new analysis
analysis = duplicateAnalysis(base)
analysis.setResult(result_value)
doActionFor(analysis, 'submit')
else:
logger.error(
"Not known Reflex Rule action %s." % (action.get('action', '')))
return 0
analysis.setReflexRuleAction(action.get('action', ''))
analysis.setIsReflexAnalysis(True)
analysis.setReflexAnalysisOf(base)
analysis.setReflexRuleActionsTriggered(
base.getReflexRuleActionsTriggered()
)
if action.get('showinreport', '') == "invisible":
analysis.setHidden(True)
elif action.get('showinreport', '') == "visible":
analysis.setHidden(False)
# Setting the original reflected analysis
if base.getOriginalReflexedAnalysis():
analysis.setOriginalReflexedAnalysis(
base.getOriginalReflexedAnalysis())
else:
analysis.setOriginalReflexedAnalysis(base)
analysis.setReflexRuleLocalID(action.get('an_result_id', ''))
# Setting the remarks to base analysis
time = datetime.now().strftime('%Y-%m-%d %H:%M')
rule_num = action.get('rulenumber', 0)
rule_name = action.get('rulename', '')
base_remark = "Reflex rule number %s of '%s' applied at %s." % \
(rule_num, rule_name, time)
base_remark = base.getRemarks() + base_remark + '||'
base.setRemarks(base_remark)
# Setting the remarks to new analysis
analysis_remark = "%s due to reflex rule number %s of '%s' at %s" % \
(action_rule_name, rule_num, rule_name, time)
analysis_remark = analysis.getRemarks() + analysis_remark + '||'
analysis.setRemarks(analysis_remark)
return analysis
def get_variables(context, **kw):
"""Prepares a dictionary of key->value pairs usable for ID formatting
"""
# allow portal_type override
portal_type = kw.get("portal_type") or api.get_portal_type(context)
# The variables map hold the values that might get into the constructed id
variables = {
'context': context,
'id': api.get_id(context),
'portal_type': portal_type,
'year': get_current_year(),
'parent': api.get_parent(context),
'seq': 0,
}
# Augment the variables map depending on the portal type
if portal_type == "AnalysisRequest":
variables.update({
'sampleId': context.getSample().getId(),
'sample': context.getSample(),
})
elif portal_type == "SamplePartition":
variables.update({
'sampleId': context.aq_parent.getId(),
'sample': context.aq_parent,
})
elif portal_type == "Sample":
# get the prefix of the assigned sample type
sample_id = context.getId()
sample_type = context.getSampleType()
sampletype_prefix = sample_type.getPrefix()
date_now = DateTime()
sampling_date = context.getSamplingDate()
date_sampled = context.getDateSampled()
# Try to get the date sampled and sampling date
if sampling_date:
samplingDate = DT2dt(sampling_date)
else:
# No Sample Date?
logger.error("Sample {} has no sample date set".format(sample_id))
# fall back to current date
samplingDate = DT2dt(date_now)
if date_sampled:
dateSampled = DT2dt(date_sampled)
else:
# No Sample Date?
logger.error("Sample {} has no sample date set".format(sample_id))
dateSampled = DT2dt(date_now)
variables.update({
'clientId': context.aq_parent.getClientID(),
'dateSampled': dateSampled,
'samplingDate': samplingDate,
'sampleType': sampletype_prefix,
})
return variables
def _process_request(self):
"""Scan request for parameters and configure class attributes
accordingly. Setup AdvancedQuery or catalog contentFilter.
Request parameters:
<form_id>_limit_from: index of the first item to display
<form_id>_rows_only: returns only the rows
<form_id>_sort_on: list items are sorted on this key
<form_id>_manual_sort_on: no index - sort with python
<form_id>_pagesize: number of items
<form_id>_filter: A string, will be regex matched against
indexes in <form_id>_filter_indexes
<form_id>_filter_indexes: list of index names which will be searched
for the value of <form_id>_filter
<form_id>_<index_name>: Any index name can be used after <form_id>_.
any request variable named ${form_id}_{index_name} will pass it's
value to that index in self.contentFilter.
All conditions using ${form_id}_{index_name} are searched with AND.
The parameter value will be matched with regexp if a FieldIndex or
TextIndex. Else, AdvancedQuery.Generic is used.
"""
form_id = self.form_id
form = self.request.form
workflow = getToolByName(self.context, 'portal_workflow')
catalog = getToolByName(self.context, self.catalog)
# Some ajax calls duplicate form values? I have not figured out why!
if self.request.form:
for key, value in self.request.form.items():
if isinstance(value, list):
self.request.form[key] = self.request.form[key][0]
# If table_only specifies another form_id, then we abort.
# this way, a single table among many can request a redraw,
# and only it's content will be rendered.
if form_id not in self.request.get('table_only', form_id) \
or form_id not in self.request.get('rows_only', form_id):
return ''
self.rows_only = self.request.get('rows_only','') == form_id
self.limit_from = int(self.request.get(form_id + '_limit_from',0))
# contentFilter is allowed in every self.review_state.
for k, v in self.review_state.get('contentFilter', {}).items():
self.contentFilter[k] = v
# sort on
self.sort_on = self.sort_on \
if hasattr(self, 'sort_on') and self.sort_on \
else None
self.sort_on = self.request.get(form_id + '_sort_on', self.sort_on)
self.sort_order = self.request.get(form_id + '_sort_order', 'ascending')
self.manual_sort_on = self.request.get(form_id + '_manual_sort_on', None)
if self.sort_on:
if self.sort_on in self.columns.keys():
if self.columns[self.sort_on].get('index', None):
self.request.set(form_id+'_sort_on', self.sort_on)
# The column can be sorted directly using an index
idx = self.columns[self.sort_on]['index']
self.sort_on = idx
# Don't sort manually!
self.manual_sort_on = None
else:
# The column must be manually sorted using python
self.manual_sort_on = self.sort_on
else:
# We cannot sort for a column that doesn't exist!
msg = "{}: sort_on is '{}', not a valid column".format(
self, self.sort_on)
logger.error(msg)
self.sort_on = None
if self.manual_sort_on:
self.manual_sort_on = self.manual_sort_on[0] \
if type(self.manual_sort_on) in (list, tuple) \
else self.manual_sort_on
if self.manual_sort_on not in self.columns.keys():
# We cannot sort for a column that doesn't exist!
msg = "{}: manual_sort_on is '{}', not a valid column".format(
self, self.manual_sort_on)
logger.error(msg)
self.manual_sort_on = None
if self.sort_on or self.manual_sort_on:
# By default, if sort_on is set, sort the items ASC
# Trick to allow 'descending' keyword instead of 'reverse'
self.sort_order = 'reverse' if self.sort_order \
and self.sort_order[0] in ['d','r'] \
else 'ascending'
else:
# By default, sort on created
self.sort_order = 'reverse'
self.sort_on = 'created'
self.contentFilter['sort_order'] = self.sort_order
if self.sort_on:
self.contentFilter['sort_on'] = self.sort_on
# pagesize
pagesize = self.request.get(form_id + '_pagesize', self.pagesize)
if type(pagesize) in (list, tuple):
pagesize = pagesize[0]
try:
pagesize = int(pagesize)
except:
pagesize = self.pagesize = 10
self.pagesize = pagesize
# Plone's batching wants this variable:
self.request.set('pagesize', self.pagesize)
# and we want to make our choice remembered in bika_listing also
self.request.set(self.form_id + '_pagesize', self.pagesize)
# index filters.
self.And = []
self.Or = []
##logger.info("contentFilter: %s"%self.contentFilter)
for k, v in self.columns.items():
if not v.has_key('index') \
or v['index'] == 'review_state' \
or v['index'] in self.filter_indexes:
continue
self.filter_indexes.append(v['index'])
##logger.info("Filter indexes: %s"%self.filter_indexes)
# any request variable named ${form_id}_{index_name}
# will pass it's value to that index in self.contentFilter.
# all conditions using ${form_id}_{index_name} are searched with AND
for index in self.filter_indexes:
idx = catalog.Indexes.get(index, None)
if not idx:
logger.debug("index named '%s' not found in %s. "
"(Perhaps the index is still empty)." %
(index, self.catalog))
continue
request_key = "%s_%s" % (form_id, index)
value = self.request.get(request_key, '')
if len(value) > 1:
##logger.info("And: %s=%s"%(index, value))
if idx.meta_type in('ZCTextIndex', 'FieldIndex'):
self.And.append(MatchRegexp(index, value))
elif idx.meta_type == 'DateIndex':
logger.info("Unhandled DateIndex search on '%s'"%index)
continue
else:
self.Or.append(Generic(index, value))
# if there's a ${form_id}_filter in request, then all indexes
# are are searched for it's value.
# ${form_id}_filter is searched with OR agains all indexes
request_key = "%s_filter" % form_id
value = self.request.get(request_key, '')
if type(value) in (list, tuple):
value = value[0]
if len(value) > 1:
for index in self.filter_indexes:
idx = catalog.Indexes.get(index, None)
if not idx:
logger.debug("index named '%s' not found in %s. "
"(Perhaps the index is still empty)." %
(index, self.catalog))
continue
##logger.info("Or: %s=%s"%(index, value))
if idx.meta_type in('ZCTextIndex', 'FieldIndex'):
self.Or.append(MatchRegexp(index, value))
self.expand_all_categories = True
# https://github.com/bikalabs/Bika-LIMS/issues/1069
vals = value.split('-')
if len(vals) > 2:
valroot = vals[0]
for i in range(1, len(vals)):
valroot = '%s-%s' % (valroot, vals[i])
self.Or.append(MatchRegexp(index, valroot+'-*'))
self.expand_all_categories = True
elif idx.meta_type == 'DateIndex':
if type(value) in (list, tuple):
value = value[0]
if value.find(":") > -1:
try:
lohi = [DateTime(x) for x in value.split(":")]
except:
logger.info("Error (And, DateIndex='%s', term='%s')"%(index,value))
self.Or.append(Between(index, lohi[0], lohi[1]))
self.expand_all_categories = True
else:
try:
self.Or.append(Eq(index, DateTime(value)))
self.expand_all_categories = True
except:
logger.info("Error (Or, DateIndex='%s', term='%s')"%(index,value))
else:
self.Or.append(Generic(index, value))
self.expand_all_categories = True
self.Or.append(MatchRegexp('review_state', value))
# get toggle_cols cookie value
# and modify self.columns[]['toggle'] to match.
toggle_cols = self.get_toggle_cols()
for col in self.columns.keys():
if col in toggle_cols:
self.columns[col]['toggle'] = True
else:
self.columns[col]['toggle'] = False
def get_variables(context, **kw):
"""Prepares a dictionary of key->value pairs usable for ID formatting
"""
# allow portal_type override
portal_type = kw.get("portal_type") or api.get_portal_type(context)
# The variables map hold the values that might get into the construced id
variables = {
'context': context,
'id': api.get_id(context),
'portal_type': portal_type,
'year': get_current_year(),
'parent': api.get_parent(context),
'seq': 0,
}
# Augment the variables map depending on the portal type
if portal_type == "AnalysisRequest":
variables.update({
'sampleId': context.getSample().getId(),
'sample': context.getSample(),
})
elif portal_type == "SamplePartition":
variables.update({
'sampleId': context.aq_parent.getId(),
'sample': context.aq_parent,
})
elif portal_type == "Sample":
# get the prefix of the assigned sample type
sample_id = context.getId()
sample_type = context.getSampleType()
sampletype_prefix = sample_type.getPrefix()
date_now = DateTime()
sampling_date = context.getSamplingDate()
date_sampled = context.getDateSampled()
# Try to get the date sampled and sampling date
if sampling_date:
samplingDate = DT2dt(sampling_date)
else:
# No Sample Date?
logger.error("Sample {} has no sample date set".format(sample_id))
# fall back to current date
samplingDate = DT2dt(date_now)
if date_sampled:
dateSampled = DT2dt(date_sampled)
else:
# No Sample Date?
logger.error("Sample {} has no sample date set".format(sample_id))
dateSampled = DT2dt(date_now)
variables.update({
'clientId': context.aq_parent.getClientID(),
'dateSampled': dateSampled,
'samplingDate': samplingDate,
'sampleType': sampletype_prefix,
})
return variables
def doActionToAnalysis(base, 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 the analysis has been retracted yet, just duplicate it
workflow = getToolByName(base, "portal_workflow")
state = workflow.getInfoFor(base, 'review_state')
action_rule_name = ''
if action.get('action', '') == 'setvisibility':
action_rule_name = 'Visibility set'
target_analysis = action.get('setvisibilityof', '')
if target_analysis == "original":
analysis = base
else:
analysis = _fetch_analysis_for_local_id(base, target_analysis)
elif action.get('action', '') == '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(base, 'retract')
analysis = base.aq_parent.getAnalyses(
sort_on='created')[-1].getObject()
action_rule_name = 'Repeated'
analysis.setResult('')
elif action.get('action', '') == 'duplicate' or state == 'retracted':
analysis = duplicateAnalysis(base)
action_rule_name = 'Duplicated'
analysis.setResult('')
elif action.get('action', '') == 'setresult':
target_analysis = action.get('setresulton', '')
action_rule_name = 'Result set'
result_value = action['setresultdiscrete'] if \
action.get('setresultdiscrete', '') else action['setresultvalue']
if target_analysis == 'original':
original = base.getOriginalReflexedAnalysis()
analysis = original
original.setResult(result_value)
elif target_analysis == 'new':
# Create a new analysis
analysis = duplicateAnalysis(base)
analysis.setResult(result_value)
doActionFor(analysis, 'submit')
else:
logger.error("Not known Reflex Rule action %s." %
(action.get('action', '')))
return 0
analysis.setReflexRuleAction(action.get('action', ''))
analysis.setIsReflexAnalysis(True)
analysis.setReflexAnalysisOf(base)
analysis.setReflexRuleActionsTriggered(
base.getReflexRuleActionsTriggered())
if action.get('showinreport', '') == "invisible":
analysis.setHidden(True)
elif action.get('showinreport', '') == "visible":
analysis.setHidden(False)
# Setting the original reflected analysis
if base.getOriginalReflexedAnalysis():
analysis.setOriginalReflexedAnalysis(
base.getOriginalReflexedAnalysis())
else:
analysis.setOriginalReflexedAnalysis(base)
analysis.setReflexRuleLocalID(action.get('an_result_id', ''))
# Setting the remarks to base analysis
time = datetime.now().strftime('%Y-%m-%d %H:%M')
rule_num = action.get('rulenumber', 0)
rule_name = action.get('rulename', '')
base_remark = "Reflex rule number %s of '%s' applied at %s." % \
(rule_num, rule_name, time)
base_remark = base.getRemarks() + base_remark + '||'
base.setRemarks(base_remark)
# Setting the remarks to new analysis
analysis_remark = "%s due to reflex rule number %s of '%s' at %s" % \
(action_rule_name, rule_num, rule_name, time)
analysis_remark = analysis.getRemarks() + analysis_remark + '||'
analysis.setRemarks(analysis_remark)
return analysis
def _process_request(self):
"""Scan request for parameters and configure class attributes
accordingly. Setup AdvancedQuery or catalog contentFilter.
Request parameters:
<form_id>_limit_from: index of the first item to display
<form_id>_rows_only: returns only the rows
<form_id>_sort_on: list items are sorted on this key
<form_id>_manual_sort_on: no index - sort with python
<form_id>_pagesize: number of items
<form_id>_filter: A string, will be regex matched against
indexes in <form_id>_filter_indexes
<form_id>_filter_indexes: list of index names which will be searched
for the value of <form_id>_filter
<form_id>_<index_name>: Any index name can be used after <form_id>_.
any request variable named ${form_id}_{index_name} will pass it's
value to that index in self.contentFilter.
All conditions using ${form_id}_{index_name} are searched with AND.
The parameter value will be matched with regexp if a FieldIndex or
TextIndex. Else, AdvancedQuery.Generic is used.
"""
form_id = self.form_id
form = self.request.form
workflow = getToolByName(self.context, 'portal_workflow')
catalog = getToolByName(self.context, self.catalog)
# Some ajax calls duplicate form values? I have not figured out why!
if self.request.form:
for key, value in self.request.form.items():
if isinstance(value, list):
self.request.form[key] = self.request.form[key][0]
# If table_only specifies another form_id, then we abort.
# this way, a single table among many can request a redraw,
# and only it's content will be rendered.
if form_id not in self.request.get('table_only', form_id) \
or form_id not in self.request.get('rows_only', form_id):
return ''
self.rows_only = self.request.get('rows_only', '') == form_id
self.limit_from = int(self.request.get(form_id + '_limit_from', 0))
# contentFilter is allowed in every self.review_state.
for k, v in self.review_state.get('contentFilter', {}).items():
self.contentFilter[k] = v
# sort on
self.sort_on = self.sort_on \
if hasattr(self, 'sort_on') and self.sort_on \
else None
self.sort_on = self.request.get(form_id + '_sort_on', self.sort_on)
self.sort_order = self.request.get(form_id + '_sort_order',
'ascending')
self.manual_sort_on = self.request.get(form_id + '_manual_sort_on',
None)
if self.sort_on:
if self.sort_on in self.columns.keys():
if self.columns[self.sort_on].get('index', None):
self.request.set(form_id + '_sort_on', self.sort_on)
# The column can be sorted directly using an index
idx = self.columns[self.sort_on]['index']
self.sort_on = idx
# Don't sort manually!
self.manual_sort_on = None
else:
# The column must be manually sorted using python
self.manual_sort_on = self.sort_on
else:
# We cannot sort for a column that doesn't exist!
msg = "{}: sort_on is '{}', not a valid column".format(
self, self.sort_on)
logger.error(msg)
self.sort_on = None
if self.manual_sort_on:
self.manual_sort_on = self.manual_sort_on[0] \
if type(self.manual_sort_on) in (list, tuple) \
else self.manual_sort_on
if self.manual_sort_on not in self.columns.keys():
# We cannot sort for a column that doesn't exist!
msg = "{}: manual_sort_on is '{}', not a valid column".format(
self, self.manual_sort_on)
logger.error(msg)
self.manual_sort_on = None
if self.sort_on or self.manual_sort_on:
# By default, if sort_on is set, sort the items ASC
# Trick to allow 'descending' keyword instead of 'reverse'
self.sort_order = 'reverse' if self.sort_order \
and self.sort_order[0] in ['d','r'] \
else 'ascending'
else:
# By default, sort on created
self.sort_order = 'reverse'
self.sort_on = 'created'
self.contentFilter['sort_order'] = self.sort_order
if self.sort_on:
self.contentFilter['sort_on'] = self.sort_on
# pagesize
pagesize = self.request.get(form_id + '_pagesize', self.pagesize)
if type(pagesize) in (list, tuple):
pagesize = pagesize[0]
try:
pagesize = int(pagesize)
except:
pagesize = self.pagesize = 10
self.pagesize = pagesize
# Plone's batching wants this variable:
self.request.set('pagesize', self.pagesize)
# and we want to make our choice remembered in bika_listing also
self.request.set(self.form_id + '_pagesize', self.pagesize)
# index filters.
self.And = []
self.Or = []
##logger.info("contentFilter: %s"%self.contentFilter)
for k, v in self.columns.items():
if not v.has_key('index') \
or v['index'] == 'review_state' \
or v['index'] in self.filter_indexes:
continue
self.filter_indexes.append(v['index'])
##logger.info("Filter indexes: %s"%self.filter_indexes)
# any request variable named ${form_id}_{index_name}
# will pass it's value to that index in self.contentFilter.
# all conditions using ${form_id}_{index_name} are searched with AND
for index in self.filter_indexes:
idx = catalog.Indexes.get(index, None)
if not idx:
logger.debug("index named '%s' not found in %s. "
"(Perhaps the index is still empty)." %
(index, self.catalog))
continue
request_key = "%s_%s" % (form_id, index)
value = self.request.get(request_key, '')
if len(value) > 1:
##logger.info("And: %s=%s"%(index, value))
if idx.meta_type in ('ZCTextIndex', 'FieldIndex'):
self.And.append(MatchRegexp(index, value))
elif idx.meta_type == 'DateIndex':
logger.info("Unhandled DateIndex search on '%s'" % index)
continue
else:
self.Or.append(Generic(index, value))
# if there's a ${form_id}_filter in request, then all indexes
# are are searched for it's value.
# ${form_id}_filter is searched with OR agains all indexes
request_key = "%s_filter" % form_id
value = self.request.get(request_key, '')
if type(value) in (list, tuple):
value = value[0]
if len(value) > 1:
for index in self.filter_indexes:
idx = catalog.Indexes.get(index, None)
if not idx:
logger.debug("index named '%s' not found in %s. "
"(Perhaps the index is still empty)." %
(index, self.catalog))
continue
##logger.info("Or: %s=%s"%(index, value))
if idx.meta_type in ('ZCTextIndex', 'FieldIndex'):
self.Or.append(MatchRegexp(index, value))
self.expand_all_categories = True
# https://github.com/bikalabs/Bika-LIMS/issues/1069
vals = value.split('-')
if len(vals) > 2:
valroot = vals[0]
for i in range(1, len(vals)):
valroot = '%s-%s' % (valroot, vals[i])
self.Or.append(MatchRegexp(index, valroot + '-*'))
self.expand_all_categories = True
elif idx.meta_type == 'DateIndex':
if type(value) in (list, tuple):
value = value[0]
if value.find(":") > -1:
try:
lohi = [DateTime(x) for x in value.split(":")]
except:
logger.info(
"Error (And, DateIndex='%s', term='%s')" %
(index, value))
self.Or.append(Between(index, lohi[0], lohi[1]))
self.expand_all_categories = True
else:
try:
self.Or.append(Eq(index, DateTime(value)))
self.expand_all_categories = True
except:
logger.info(
"Error (Or, DateIndex='%s', term='%s')" %
(index, value))
else:
self.Or.append(Generic(index, value))
self.expand_all_categories = True
self.Or.append(MatchRegexp('review_state', value))
# get toggle_cols cookie value
# and modify self.columns[]['toggle'] to match.
toggle_cols = self.get_toggle_cols()
for col in self.columns.keys():
if col in toggle_cols:
self.columns[col]['toggle'] = True
else:
self.columns[col]['toggle'] = False
def Import(self):
folder = self.context.patients
rows = self.get_rows(3)
for row in rows:
if not row['Firstname'] or not row['PrimaryReferrer']:
continue
pc = getToolByName(self.context, 'portal_catalog')
client = pc(portal_type='Client', Title=row['PrimaryReferrer'])
if len(client) == 0:
error = "Primary referrer invalid: '%s'. Patient '%s %s' will not be uploaded"
logger.error(error, row['PrimaryReferrer'], row['Firstname'],
row.get('Surname', ''))
continue
client = client[0].getObject()
# Getting an existing ethnicity
bsc = getToolByName(self.context, 'bika_setup_catalog')
ethnicity = bsc(portal_type='Ethnicity',
Title=row.get('Ethnicity', ''))
if len(ethnicity) == 0:
raise IndexError("Invalid ethnicity: '%s'" % row['Ethnicity'])
ethnicity = ethnicity[0].getObject()
_id = folder.invokeFactory('Patient', id=tmpID())
obj = folder[_id]
obj.unmarkCreationFlag()
renameAfterCreation(obj)
Fullname = (row['Firstname'] + " " +
row.get('Surname', '')).strip()
obj.edit(
PatientID=row.get('PatientID'),
title=Fullname,
ClientPatientID=row.get('ClientPatientID', ''),
Salutation=row.get('Salutation', ''),
Firstname=row.get('Firstname', ''),
Surname=row.get('Surname', ''),
PrimaryReferrer=client.UID(),
Gender=row.get('Gender', 'dk'),
Age=row.get('Age', ''),
BirthDate=row.get('BirthDate', ''),
BirthDateEstimated=self.to_bool(
row.get('BirthDateEstimated', 'False')),
BirthPlace=row.get('BirthPlace', ''),
# TODO Ethnicity_Obj -> Ethnicity on health v319
Ethnicity_Obj=ethnicity.UID(),
Citizenship=row.get('Citizenship', ''),
MothersName=row.get('MothersName', ''),
CivilStatus=row.get('CivilStatus', ''),
Anonymous=self.to_bool(row.get('Anonymous', 'False')))
self.fill_contactfields(row, obj)
self.fill_addressfields(row, obj)
if 'Photo' in row and row['Photo']:
try:
path = resource_filename(self.dataset_project,
"setupdata/%s/%s" \
% (self.dataset_name, row['Photo']))
file_data = open(path, "rb").read() if os.path.isfile(path) \
else open(path+'.jpg', "rb").read()
obj.setPhoto(file_data)
except:
logger.error("Unable to load Photo %s" % row['Photo'])
if 'Feature' in row and row['Feature']:
try:
path = resource_filename(self.dataset_project,
"setupdata/%s/%s" \
% (self.dataset_name, row['Feature']))
file_data = open(path, "rb").read() if os.path.isfile(path) \
else open(path+'.pdf', "rb").read()
obj.setFeature(file_data)
except:
logger.error("Unable to load Feature %s" % row['Feature'])
obj.unmarkCreationFlag()
transaction.savepoint(optimistic=True)
if row.get('PatientID'):
# To maintain the patient spreadsheet's IDs, we cannot do a 'renameaftercreation()'
if obj.getPatientID() != row.get('PatientID'):
transaction.savepoint(optimistic=True)
obj.aq_inner.aq_parent.manage_renameObject(
obj.id, row.get('PatientID'))
else:
renameAfterCreation(obj)
def doActionFor(instance, action_id, active_only=True, allowed_transition=True):
"""Performs the transition (action_id) to the instance.
The transition will only be triggered if the current state of the object
allows the action_id passed in (delegate to isTransitionAllowed) and the
instance hasn't been flagged as to be skipped previously.
If active_only is set to True, the instance will only be transitioned if
it's current state is active (not cancelled nor inactive)
:param instance: Object to be transitioned
:param action_id: transition id
:param active_only: True if transition must apply to active objects
:param allowed_transition: True for a allowed transition check
:returns: true if the transition has been performed and message
:rtype: list
"""
actionperformed = False
message = ''
if isinstance(instance, list):
# This check is here because sometimes Plone creates a list
# from submitted form elements.
if len(instance) > 1:
logger.error(
"doActionFor is getting an instance paramater which is alist "
"with more than one item. Instance: '{}', action_id: '{}'"
.format(instance, action_id)
)
instance = instance[0]
if not instance:
return actionperformed, message
workflow = getToolByName(instance, "portal_workflow")
skipaction = skip(instance, action_id, peek=True)
if skipaction:
#clazzname = instance.__class__.__name__
#msg = "Skipping transition '{0}': {1} '{2}'".format(action_id,
# clazzname,
# instance.getId())
#logger.info(msg)
return actionperformed, message
if allowed_transition:
allowed = isTransitionAllowed(instance, action_id, active_only)
if not allowed:
transitions = workflow.getTransitionsFor(instance)
transitions = [trans['id'] for trans in transitions]
transitions = ', '.join(transitions)
currstate = getCurrentState(instance)
clazzname = instance.__class__.__name__
msg = "Transition '{0}' not allowed: {1} '{2}' ({3}). " \
"Available transitions: {4}".format(action_id, clazzname,
instance.getId(),
currstate, transitions)
logger.warning(msg)
_logTransitionFailure(instance, action_id)
return actionperformed, message
else:
logger.warning(
"doActionFor should never (ever) be called with allowed_transition"
"set to True as it avoids permission checks.")
try:
workflow.doActionFor(instance, action_id)
actionperformed = True
except WorkflowException as e:
message = str(e)
logger.error(message)
return actionperformed, message
def remove_cascaded_analyses_of_root_samples(portal):
"""Removes Analyses from Root Samples that belong to Partitions
https://github.com/senaite/senaite.core/issues/1504
"""
logger.info("Removing cascaded analyses from Root Samples...")
# Query all root Samples
query = {
"isRootAncestor": True,
"sort_on": "created",
"sort_order": "ascending",
}
root_samples = api.search(query, "bika_catalog_analysisrequest_listing")
total = len(root_samples)
logger.info("{} Samples to check... ".format(total))
to_clean = []
for num, brain in enumerate(root_samples):
logger.debug("Checking Root Sample {}/{}".format(num+1, total))
# No Partitions, continue...
if not brain.getDescendantsUIDs:
continue
# get the root sample
root_sample = api.get_object(brain)
# get the contained analyses of the root sample
root_analyses = root_sample.objectIds(spec=["Analysis"])
# Mapping of cascaded Analysis -> Partition
analysis_mapping = {}
# check if a root analysis is located as well in one of the partitions
for partition in root_sample.getDescendants():
# get the contained analyses of the partition
part_analyses = partition.objectIds(spec=["Analysis"])
# filter analyses that cascade root analyses
cascaded = filter(lambda an: an in root_analyses, part_analyses)
# keep a mapping of analysis -> partition
for analysis in cascaded:
analysis_mapping[analysis] = partition
if analysis_mapping:
to_clean.append((root_sample, analysis_mapping))
# count the cases for each condition
case_counter = defaultdict(int)
# cleanup cascaded analyses
# mapping maps the analysis id -> partition
for sample, mapping in to_clean:
# go through the cascaded analyses and decide if the cascaded analysis
# should be removed from (a) the root sample or (b) the partition.
for analysis_id, partition in mapping.items():
# analysis from the root sample
root_an = sample[analysis_id]
# WF state from the root sample analysis
root_an_state = api.get_workflow_status_of(root_an)
# analysis from the partition sample
part_an = partition[analysis_id]
# WF state from the partition sample analysis
part_an_state = api.get_workflow_status_of(part_an)
case_counter["{}_{}".format(root_an_state, part_an_state)] += 1
# both analyses have the same WF state
if root_an_state == part_an_state:
# -> remove the analysis from the root sample
sample._delObject(analysis_id)
logger.info(
"Remove analysis '{}' in state '{}' from sample {}: {}"
.format(analysis_id, root_an_state,
api.get_id(sample), api.get_url(sample)))
# both are in verified/published state
elif IVerified.providedBy(root_an) and IVerified.providedBy(part_an):
root_an_result = root_an.getResult()
part_an_result = root_an.getResult()
if root_an_result == part_an_result:
# remove the root analysis
sample._delObject(analysis_id)
logger.info(
"Remove analysis '{}' in state '{}' from sample {}: {}"
.format(analysis_id, root_an_state,
api.get_id(sample), api.get_url(sample)))
else:
# -> unsolvable edge case
# display an error message
logger.error(
"Analysis '{}' of root sample in state '{}' "
"and Analysis of partition in state {}. "
"Please fix manually: {}"
.format(analysis_id, root_an_state, part_an_state,
api.get_url(sample)))
# root analysis is in invalid state
elif root_an_state in ["rejected", "retracted"]:
# -> probably the retest was automatically created in the
# parent instead of the partition
pass
# partition analysis is in invalid state
elif part_an_state in ["rejected", "retracted"]:
# -> probably the retest was automatically created in the
# parent instead of the partition
pass
# root analysis was submitted, but not the partition analysis
elif ISubmitted.providedBy(root_an) and not ISubmitted.providedBy(part_an):
# -> remove the analysis from the partition
partition._delObject(analysis_id)
logger.info(
"Remove analysis '{}' in state '{}' from partition {}: {}"
.format(analysis_id, part_an_state,
api.get_id(partition), api.get_url(partition)))
# partition analysis was submitted, but not the root analysis
elif ISubmitted.providedBy(part_an) and not ISubmitted.providedBy(root_an):
# -> remove the analysis from the root sample
sample._delObject(analysis_id)
logger.info(
"Remove analysis '{}' in state '{}' from sample {}: {}"
.format(analysis_id, root_an_state,
api.get_id(sample), api.get_url(sample)))
# inconsistent state
else:
logger.warning(
"Can not handle analysis '{}' located in '{}' (state {}) and '{}' (state {})"
.format(analysis_id,
repr(sample), root_an_state,
repr(partition), part_an_state))
logger.info("Removing cascaded analyses from Root Samples... [DONE]")
logger.info("State Combinations (root_an_state, part_an_state): {}"
.format(sorted(case_counter.items(), key=itemgetter(1), reverse=True)))
def handle_http_request(self):
request = self.request
form = request.form
submitted = form.get("submitted", False)
send = form.get("send", False)
cancel = form.get("cancel", False)
if submitted and send:
logger.info("*** SENDING EMAIL ***")
# Parse used defined values from the request form
recipients = form.get("recipients", [])
responsibles = form.get("responsibles", [])
subject = form.get("subject")
body = form.get("body")
reports = self.get_reports()
# Merge recipiens and responsibles
recipients = set(recipients + responsibles)
# sanity checks
if not recipients:
message = _("No email recipients selected")
self.add_status_message(message, "error")
if not subject:
message = _("Please add an email subject")
self.add_status_message(message, "error")
if not body:
message = _("Please add an email text")
self.add_status_message(message, "error")
if not reports:
message = _("No attachments")
self.add_status_message(message, "error")
success = False
if all([recipients, subject, body, reports]):
attachments = []
# report pdfs
for report in reports:
pdf = self.get_pdf(report)
if pdf is None:
logger.error("Skipping empty PDF for report {}"
.format(report.getId()))
continue
ar = report.getAnalysisRequest()
filename = "{}.pdf".format(ar.getId())
filedata = pdf.data
attachments.append(
self.to_email_attachment(filename, filedata))
# additional attachments
for attachment in self.get_attachments():
af = attachment.getAttachmentFile()
filedata = af.data
filename = af.filename
attachments.append(
self.to_email_attachment(filename, filedata))
success = self.send_email(
recipients, subject, body, attachments=attachments)
if success:
# selected name, email pairs which received the email
pairs = map(self.parse_email, recipients)
send_to_names = map(lambda p: p[0], pairs)
# set recipients to the reports
for report in reports:
ar = report.getAnalysisRequest()
# publish the AR
self.publish(ar)
# Publish all linked ARs of this report
# N.B. `ContainedAnalysisRequests` is an extended field
field = report.getField("ContainedAnalysisRequests")
contained_ars = field.get(report) or []
for obj in contained_ars:
self.publish(obj)
# add new recipients to the AR Report
new_recipients = filter(
lambda r: r.get("Fullname") in send_to_names,
self.get_recipients(ar))
self.set_report_recipients(report, new_recipients)
message = _(u"Message sent to {}"
.format(", ".join(send_to_names)))
self.add_status_message(message, "info")
return request.response.redirect(self.exit_url)
else:
message = _("Failed to send Email(s)")
self.add_status_message(message, "error")
if submitted and cancel:
logger.info("*** EMAIL CANCELLED ***")
message = _("Email cancelled")
self.add_status_message(message, "info")
return request.response.redirect(self.exit_url)
# get the selected ARReport objects
reports = self.get_reports()
attachments = self.get_attachments()
# calculate the total size of all PDFs
self.total_size = self.get_total_size(reports, attachments)
if self.total_size > self.max_email_size:
# don't allow to send oversized emails
self.allow_send = False
message = _("Total size of email exceeded {:.1f} MB ({:.2f} MB)"
.format(self.max_email_size / 1024,
self.total_size / 1024))
self.add_status_message(message, "error")
# prepare the data for the template
self.reports = map(self.get_report_data, reports)
self.recipients = self.get_recipients_data(reports)
self.responsibles = self.get_responsibles_data(reports)
# inform the user about invalid recipients
if not all(map(lambda r: r.get("valid"), self.recipients)):
message = _(
"Not all contacts are equal for the selected Reports. "
"Please manually select recipients for this email.")
self.add_status_message(message, "warning")
return self.template()
def __call__(self):
# Do generic bika.lims stuff
BaseClass.__call__(self)
# Do bika-health specific actions when submit
action = BaseClass._get_form_workflow_action(self)
addPortalMessage = self.context.plone_utils.addPortalMessage
if action[0] == 'submit' and isActive(self.context):
inpanicanalyses = []
workflow = getToolByName(self.context, 'portal_workflow')
translate = self.context.translate
rc = getToolByName(self.context, REFERENCE_CATALOG)
uc = getToolByName(self.context, 'uid_catalog')
# retrieve the results from database and check if
# the values are exceeding panic levels
alerts = {}
for uid in self.request.form.get('Result', [{}])[0].keys():
analysis = rc.lookupObject(uid)
analysis = analysis.getObject() if hasattr(analysis, 'getObject') else analysis
if not analysis:
continue
astate = workflow.getInfoFor(analysis, 'review_state')
if astate == 'retracted':
continue
alerts.update(ResultOutOfRange(analysis)())
if alerts:
message = translate(_('Some results exceeded the '
'panic levels that may '
'indicate an imminent '
'life-threatening condition'
))
addPortalMessage(message, 'warning')
self.request.response.redirect(self.context.absolute_url())
# If panic levels alert email enabled, send an email to
# labmanagers
bs = self.context.bika_setup
if hasattr(bs, 'getEnablePanicAlert') \
and bs.getEnablePanicAlert():
laboratory = self.context.bika_setup.laboratory
lab_address = "<br/>".join(laboratory.getPrintAddress())
managers = self.context.portal_groups.getGroupMembers('LabManagers')
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = _("Panic alert")
mime_msg['From'] = formataddr(
(encode_header(laboratory.getName()),
laboratory.getEmailAddress()))
to = []
for manager in managers:
user = self.portal.acl_users.getUser(manager)
uemail = user.getProperty('email')
ufull = user.getProperty('fullname')
to.append(formataddr((encode_header(ufull), uemail)))
mime_msg['To'] = ','.join(to)
strans = []
ars = {}
for analysis_uid, alertlist in alerts:
analysis = uc(analysis_uid).getObject()
for alert in alertlist:
ars[analysis.aq_parent.Title()] = 1
strans.append("- {0}, {1}: {2}".format(
analysis.getService().Title(),
translate(_("Result")),
analysis.getResult()))
ars = ", ".join(ars.keys())
stran = "<br/>".join(strans)
text = translate(_(
"Some results from ${items} exceeded the panic levels "
"that may indicate an imminent life-threatening "
"condition: <br/><br/>{analysisresults}<br/><br/>"
"<b>Please, check the Analysis Request if you "
"want to re-test the analysis or immediately "
"alert the client.</b><br/><br/>{lab_address}",
mapping={'items': ars,
'analysisresults': stran,
'lab_address': lab_address}))
msg_txt = MIMEText(safe_unicode(text).encode('utf-8'),
_subtype='html')
mime_msg.preamble = 'This is a multi-part MIME message.'
mime_msg.attach(msg_txt)
try:
host = getToolByName(self.context, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except Exception as msg:
ar = inpanicanalyses[0].getRequestID()
logger.error("Panic level email %s: %s" %
(ar, str(msg)))
message = translate(
_('Unable to send an email to alert lab '
'managers that some analyses exceeded the '
'panic levels') + (": %s" % str(msg)))
addPortalMessage(message, 'warning')
def _process_request(self):
# Use this function from a template that is using bika_listing_table
# in such a way that the table_only request var will be used to
# in-place-update the table.
form_id = self.form_id
form = self.request.form
workflow = getToolByName(self.context, 'portal_workflow')
catalog = getToolByName(self.context, self.catalog)
# If table_only specifies another form_id, then we abort.
# this way, a single table among many can request a redraw,
# and only it's content will be rendered.
if form_id not in self.request.get('table_only', form_id):
return ''
## review_state_selector
cookie = json.loads(self.request.get("review_state", '{}'))
cookie_key = "%s%s" % (self.context.portal_type, form_id)
# first check POST
selected_state = self.request.get("%s_review_state" % form_id, '')
if not selected_state:
# then check cookie
selected_state = cookie.get(cookie_key, 'default')
# get review_state id=selected_state
states = [r for r in self.review_states if r['id'] == selected_state]
review_state = states and states[0] or self.review_states[0]
# set request and cookie to currently selected state id
if not selected_state:
selected_state = self.review_states[0]['id']
self.review_state = cookie[cookie_key] = selected_state
cookie = json.dumps(cookie)
self.request['review_state'] = cookie
self.request.response.setCookie('review_state', cookie, path="/")
# contentFilter is expected in every review_state.
for k, v in review_state['contentFilter'].items():
self.contentFilter[k] = v
# sort on
sort_on = self.request.get(form_id + '_sort_on', '')
# manual_sort_on: only sort the current batch of items
# this is a compromise for sorting without column indexes
self.manual_sort_on = None
if sort_on \
and sort_on in self.columns.keys() \
and self.columns[sort_on].get('index', None):
idx = self.columns[sort_on].get('index', sort_on)
self.contentFilter['sort_on'] = idx
else:
if sort_on:
self.manual_sort_on = sort_on
if 'sort_on' in self.contentFilter:
del self.contentFilter['sort_on']
# sort order
self.sort_order = self.request.get(form_id + '_sort_order', '')
if self.sort_order:
self.contentFilter['sort_order'] = self.sort_order
else:
if 'sort_order' not in self.contentFilter:
self.sort_order = 'ascending'
self.contentFilter['sort_order'] = 'ascending'
self.request.set(form_id + '_sort_order', 'ascending')
else:
self.sort_order = self.contentFilter['sort_order']
if self.manual_sort_on:
del self.contentFilter['sort_order']
# pagesize
pagesize = self.request.get(form_id + '_pagesize', self.pagesize)
if type(pagesize) in (list, tuple):
pagesize = pagesize[0]
try:
pagesize = int(pagesize)
except:
pagesize = self.pagesize
self.pagesize = pagesize
# Plone's batching wants this variable:
self.request.set('pagesize', self.pagesize)
# pagenumber
self.pagenumber = int(
self.request.get(form_id + '_pagenumber', self.pagenumber))
# Plone's batching wants this variable:
self.request.set('pagenumber', self.pagenumber)
# index filters.
self.And = []
self.Or = []
##logger.info("contentFilter: %s"%self.contentFilter)
for k, v in self.columns.items():
if not v.has_key('index') \
or v['index'] == 'review_state' \
or v['index'] in self.filter_indexes:
continue
self.filter_indexes.append(v['index'])
##logger.info("Filter indexes: %s"%self.filter_indexes)
# any request variable named ${form_id}_{index_name}
# will pass it's value to that index in self.contentFilter.
# all conditions using ${form_id}_{index_name} are searched with AND
for index in self.filter_indexes:
idx = catalog.Indexes.get(index, None)
if not idx:
logger.debug("index named '%s' not found in %s. "
"(Perhaps the index is still empty)." %
(index, self.catalog))
continue
request_key = "%s_%s" % (form_id, index)
value = self.request.get(request_key, '')
if len(value) > 1:
##logger.info("And: %s=%s"%(index, value))
if idx.meta_type in ('ZCTextIndex', 'FieldIndex'):
self.And.append(MatchRegexp(index, value))
elif idx.meta_type == 'DateIndex':
logger.error("Unhandled DateIndex search on '%s'" % index)
continue
else:
self.Or.append(Generic(index, value))
# if there's a ${form_id}_filter in request, then all indexes
# are are searched for it's value.
# ${form_id}_filter is searched with OR agains all indexes
request_key = "%s_filter" % form_id
value = self.request.get(request_key, '')
if len(value) > 1:
for index in self.filter_indexes:
idx = catalog.Indexes.get(index, None)
if not idx:
logger.debug("index named '%s' not found in %s. "
"(Perhaps the index is still empty)." %
(index, self.catalog))
continue
##logger.info("Or: %s=%s"%(index, value))
if idx.meta_type in ('ZCTextIndex', 'FieldIndex'):
self.Or.append(MatchRegexp(index, value))
elif idx.meta_type == 'DateIndex':
if value.find(":") > -1:
try:
lohi = [DateTime(x) for x in value.split(":")]
except:
logger.error(
"Error (And, DateIndex='%s', term='%s')" %
(index, value))
self.Or.append(Between(index, lohi[0], lohi[1]))
else:
try:
self.Or.append(Eq(index, DateTime(value)))
except:
logger.error(
"Error (Or, DateIndex='%s', term='%s')" %
(index, value))
else:
self.Or.append(Generic(index, value))
self.Or.append(MatchRegexp('review_state', value))
# get toggle_cols cookie value
# and modify self.columns[]['toggle'] to match.
toggle_cols = self.get_toggle_cols()
for col in self.columns.keys():
if col in toggle_cols:
self.columns[col]['toggle'] = True
else:
self.columns[col]['toggle'] = False