def _sampler_data(self, sample=None):
data = {}
if not sample or not sample.getSampler():
return data
sampler = sample.getSampler()
mtool = getToolByName(self, 'portal_membership')
member = mtool.getMemberById(sampler)
if member:
mfullname = member.getProperty('fullname')
memail = member.getProperty('email')
mhomepage = member.getProperty('home_page')
pc = getToolByName(self, 'portal_catalog')
c = pc(portal_type='Contact', getUsername=member.id)
c = c[0].getObject() if c else None
cfullname = c.getFullname() if c else None
cemail = c.getEmailAddress() if c else None
data = {'id': member.id,
'fullname': to_utf8(cfullname) if cfullname else to_utf8(mfullname),
'email': cemail if cemail else memail,
'business_phone': c.getBusinessPhone() if c else '',
'business_fax': c.getBusinessFax() if c else '',
'home_phone': c.getHomePhone() if c else '',
'mobile_phone': c.getMobilePhone() if c else '',
'job_title': to_utf8(c.getJobTitle()) if c else '',
'department': to_utf8(c.getDepartment()) if c else '',
'physical_address': to_utf8(c.getPhysicalAddress()) if c else '',
'postal_address': to_utf8(c.getPostalAddress()) if c else '',
'home_page': to_utf8(mhomepage)}
return data
def __init__(self, parser, context,
idsearchcriteria=None,
override=[False, False],
allowed_ar_states=None,
allowed_analysis_states=None,
instrument_uid=None):
Logger.__init__(self)
self._parser = parser
self.context = context
self._allowed_ar_states = allowed_ar_states
self._allowed_analysis_states = allowed_analysis_states
self._override = override
self._idsearch = idsearchcriteria
self._priorizedsearchcriteria = ''
self.bsc = getToolByName(self.context, 'bika_setup_catalog')
self.bac = getToolByName(self.context, 'bika_analysis_catalog')
self.pc = getToolByName(self.context, 'portal_catalog')
self.bc = getToolByName(self.context, 'bika_catalog')
self.wf = getToolByName(self.context, 'portal_workflow')
if not self._allowed_ar_states:
self._allowed_ar_states=['sample_received',
'attachment_due',
'to_be_verified']
if not self._allowed_analysis_states:
self._allowed_analysis_states=['sampled',
'sample_received',
'attachment_due',
'to_be_verified']
if not self._idsearch:
self._idsearch=['getRequestID']
self.instrument_uid=instrument_uid
def __call__(self, value, *args, **kwargs):
instance = kwargs['instance']
# fieldname = kwargs['field'].getName()
# request = kwargs.get('REQUEST', {})
# form = request.get('form', {})
translate = getToolByName(instance, 'translation_service').translate
bsc = getToolByName(instance, 'bika_setup_catalog')
# uc = getToolByName(instance, 'uid_catalog')
failures = []
for category in value:
if not category:
continue
services = bsc(portal_type="AnalysisService",
getCategoryUID=category)
for service in services:
service = service.getObject()
calc = service.getCalculation()
deps = calc and calc.getDependentServices() or []
for dep in deps:
if dep.getCategoryUID() not in value:
title = dep.getCategoryTitle()
if title not in failures:
failures.append(title)
if failures:
msg = _("Validation failed: The selection requires the following "
"categories to be selected: ${categories}",
mapping={'categories': safe_unicode(','.join(failures))})
return to_utf8(translate(msg))
return True
def next_id(prefix):
# normalize before anything
prefix = fn_normalize(prefix)
plone = context.portal_url.getPortalObject()
# grab the first catalog we are indexed in.
at = getToolByName(plone, 'archetype_tool')
if context.portal_type in at.catalog_map:
catalog_name = at.catalog_map[context.portal_type][0]
else:
catalog_name = 'portal_catalog'
catalog = getToolByName(plone, catalog_name)
# get all IDS that start with prefix
# this must specifically exclude AR IDs (two -'s)
rr = re.compile("^"+prefix+separator+"[\d+]+$")
ids = [int(i.split(prefix+separator)[1]) \
for i in catalog.Indexes['id'].uniqueValues() \
if rr.match(i)]
#plone_tool = getToolByName(context, 'plone_utils')
#if not plone_tool.isIDAutoGenerated(l.id):
ids.sort()
_id = ids and ids[-1] or 0
new_id = _id + 1
return str(new_id)
def get_analysisrequest_verifier(self, analysisrequest):
"""Get the name of the member who last verified this AR
"""
wtool = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
verifier = None
try:
review_history = wtool.getInfoFor(analysisrequest, 'review_history')
except:
return 'access denied'
review_history = [review for review in review_history if review.get('action', '')]
if not review_history:
return 'no history'
for items in review_history:
action = items.get('action')
if action != 'verify':
continue
actor = items.get('actor')
member = mtool.getMemberById(actor)
if not member:
verifier = actor
continue
verifier = member.getProperty('fullname')
if verifier is None or verifier == '':
verifier = actor
return verifier
def workflow_script_unassign(self):
if skip(self, "unassign"):
return
workflow = getToolByName(self, 'portal_workflow')
self.reindexObject(idxs=["review_state", ])
rc = getToolByName(self, REFERENCE_CATALOG)
wsUID = self.REQUEST['context_uid']
ws = rc.lookupObject(wsUID)
# May need to promote the Worksheet's review_state
# if all other analyses are at a higher state than this one was.
# (or maybe retract it if there are no analyses left)
# Note: duplicates, controls and blanks have 'assigned' as a review_state.
can_submit = True
can_attach = True
can_verify = True
ws_empty = False
analyses = ws.getAnalyses()
# We flag this worksheet as empty if there is ONE UNASSIGNED
# analysis left: worksheet.removeAnalysis() hasn't removed it from
# the layout yet at this stage.
if len(analyses) == 1 \
and workflow.getInfoFor(analyses[0], 'review_state') == 'unassigned':
ws_empty = True
for a in analyses:
a_state = workflow.getInfoFor(a, 'review_state')
if a_state in \
('assigned', 'sample_due', 'sample_received',):
can_submit = False
else:
if not ws.getAnalyst():
can_submit = False
if a_state in \
('assigned', 'sample_due', 'sample_received', 'attachment_due',):
can_attach = False
if a_state in \
('assigned', 'sample_due', 'sample_received', 'attachment_due', 'to_be_verified',):
can_verify = False
if not ws_empty:
# Note: WS adds itself to the skiplist so we have to take it off again
# to allow multiple promotions (maybe by more than one self).
if can_submit and workflow.getInfoFor(ws, 'review_state') == 'open':
workflow.doActionFor(ws, 'submit')
skip(ws, 'submit', unskip=True)
if can_attach and workflow.getInfoFor(ws, 'review_state') == 'attachment_due':
workflow.doActionFor(ws, 'attach')
skip(ws, 'attach', unskip=True)
if can_verify and workflow.getInfoFor(ws, 'review_state') == 'to_be_verified':
self.REQUEST["workflow_skiplist"].append('verify all analyses')
workflow.doActionFor(ws, 'verify')
skip(ws, 'verify', unskip=True)
else:
if workflow.getInfoFor(ws, 'review_state') != 'open':
workflow.doActionFor(ws, 'retract')
skip(ws, 'retract', unskip=True)
def get(self, instance, aslist=False, **kwargs):
"""get() returns the list of objects referenced under the relationship.
"""
uc = getToolByName(instance, "uid_catalog")
try:
res = instance.getRefs(relationship=self.relationship)
except:
pass
pr = getToolByName(instance, 'portal_repository')
rd = {}
for r in res:
if r is None:
continue
uid = r.UID()
r = uc(UID=uid)[0].getObject()
if hasattr(instance, 'reference_versions') and \
hasattr(r, 'version_id') and \
uid in instance.reference_versions and \
instance.reference_versions[uid] != r.version_id and \
r.version_id is not None:
version_id = instance.reference_versions[uid]
try:
o = pr._retrieve(r,
selector=version_id,
preserve=(),
countPurged=True).object
except ArchivistRetrieveError:
o = r
else:
o = r
rd[uid] = o
# singlevalued ref fields return only the object, not a list,
# unless explicitely specified by the aslist option
if not self.multiValued:
if len(rd) > 1:
log("%s references for non multivalued field %s of %s" %
(len(rd), self.getName(), instance))
if not aslist:
if rd:
rd = [rd[uid] for uid in rd.keys()][0]
else:
rd = None
if not self.referencesSortable or not hasattr(aq_base(instance),
'at_ordered_refs'):
if isinstance(rd, dict):
return [rd[uid] for uid in rd.keys()]
else:
return rd
refs = instance.at_ordered_refs
order = refs[self.relationship]
return [rd[uid] for uid in order if uid in rd.keys()]
def addReferences(self, reference, service_uids):
""" Add reference analyses to reference
"""
addedanalyses = []
wf = getToolByName(self, 'portal_workflow')
bsc = getToolByName(self, 'bika_setup_catalog')
bac = getToolByName(self, 'bika_analysis_catalog')
ref_type = reference.getBlank() and 'b' or 'c'
ref_uid = reference.UID()
postfix = 1
for refa in reference.getReferenceAnalyses():
grid = refa.getReferenceAnalysesGroupID()
try:
cand = int(grid.split('-')[2])
if cand >= postfix:
postfix = cand + 1
except:
pass
postfix = str(postfix).zfill(int(3))
refgid = 'I%s-%s' % (reference.id, postfix)
for service_uid in service_uids:
# services with dependents don't belong in references
service = bsc(portal_type='AnalysisService', UID=service_uid)[0].getObject()
calc = service.getCalculation()
if calc and calc.getDependentServices():
continue
ref_uid = reference.addReferenceAnalysis(service_uid, ref_type)
ref_analysis = bac(portal_type='ReferenceAnalysis', UID=ref_uid)[0].getObject()
# Set ReferenceAnalysesGroupID (same id for the analyses from
# the same Reference Sample and same Worksheet)
# https://github.com/bikalabs/Bika-LIMS/issues/931
ref_analysis.setReferenceAnalysesGroupID(refgid)
ref_analysis.reindexObject()
# copy the interimfields
calculation = service.getCalculation()
if calc:
ref_analysis.setInterimFields(calc.getInterimFields())
# Comes from a worksheet or has been attached directly?
ws = ref_analysis.getBackReferences('WorksheetAnalysis')
if not ws or len(ws) == 0:
# This is a reference analysis attached directly to the
# Instrument, we apply the assign state
wf.doActionFor(ref_analysis, 'assign')
addedanalyses.append(ref_analysis)
self.setAnalyses(self.getAnalyses() + addedanalyses)
# Initialize LatestReferenceAnalyses cache
self.cleanReferenceAnalysesCache()
# Set DisposeUntilNextCalibrationTest to False
if (len(addedanalyses) > 0):
self.getField('DisposeUntilNextCalibrationTest').set(self, False)
return addedanalyses
def addReferences(self, position, reference, service_uids):
""" Add reference analyses to reference, and add to worksheet layout
"""
workflow = getToolByName(self, 'portal_workflow')
rc = getToolByName(self, REFERENCE_CATALOG)
layout = self.getLayout()
wst = self.getWorksheetTemplate()
wstlayout = wst and wst.getLayout() or []
ref_type = reference.getBlank() and 'b' or 'c'
ref_uid = reference.UID()
if position == 'new':
highest_existing_position = len(wstlayout)
for pos in [int(slot['position']) for slot in layout]:
if pos > highest_existing_position:
highest_existing_position = pos
position = highest_existing_position + 1
postfix = 1
for refa in reference.getReferenceAnalyses():
grid = refa.getReferenceAnalysesGroupID()
try:
cand = int(grid.split('-')[2])
if cand >= postfix:
postfix = cand + 1
except:
pass
postfix = str(postfix).zfill(int(3))
refgid = '%s-%s' % (reference.id, postfix)
for service_uid in service_uids:
# services with dependents don't belong in references
service = rc.lookupObject(service_uid)
calc = service.getCalculation()
if calc and calc.getDependentServices():
continue
ref_uid = reference.addReferenceAnalysis(service_uid, ref_type)
ref_analysis = rc.lookupObject(ref_uid)
# Set ReferenceAnalysesGroupID (same id for the analyses from
# the same Reference Sample and same Worksheet)
# https://github.com/bikalabs/Bika-LIMS/issues/931
ref_analysis.setReferenceAnalysesGroupID(refgid)
ref_analysis.reindexObject(idxs=["getReferenceAnalysesGroupID"])
# copy the interimfields
if calc:
ref_analysis.setInterimFields(calc.getInterimFields())
self.setLayout(
self.getLayout() + [{'position': position,
'type': ref_type,
'container_uid': reference.UID(),
'analysis_uid': ref_analysis.UID()}])
self.setAnalyses(
self.getAnalyses() + [ref_analysis, ])
workflow.doActionFor(ref_analysis, 'assign')
def getContacts(self):
pc = getToolByName(self, 'portal_catalog')
bc = getToolByName(self, 'bika_catalog')
bsc = getToolByName(self, 'bika_setup_catalog')
# fallback - all Lab Contacts
pairs = []
for contact in bsc(portal_type = 'LabContact',
inactive_state = 'active',
sort_on = 'sortable_title'):
pairs.append((contact.UID, contact.Title))
return DisplayList(pairs)
def getDefaultSpec(self):
""" Returns 'lab' or 'client' to set the initial value of the
specification radios
"""
mt = getToolByName(self.context, 'portal_membership')
pg = getToolByName(self.context, 'portal_groups')
member = mt.getAuthenticatedMember()
member_groups = [pg.getGroupById(group.id).getGroupName()
for group in pg.getGroupsByUserId(member.id)]
default_spec = ('Clients' in member_groups) and 'client' or 'lab'
return default_spec
def workflow_script_deactivat(self):
# A instance cannot be deactivated if it contains services
pu = getToolByName(self, 'plone_utils')
bsc = getToolByName(self, 'bika_setup_catalog')
ars = bsc(portal_type='AnalysisService', getCategoryUID=self.UID())
if ars:
message = _("Category cannot be deactivated because "
"it contains Analysis Services")
pu.addPortalMessage(message, 'error')
transaction.get().abort()
raise WorkflowException
def render(self):
portal_factory = getToolByName(self.context, 'portal_factory')
if portal_factory.isTemporary(self.context):
return self.index()
self.actions = []
portal_actions = getToolByName(self.context, 'portal_actions')
actions = portal_actions.listFilteredActionsFor(self.context)
if 'document_actions' in actions:
for action in actions['document_actions']:
self.actions.append(action)
return self.index()
def __call__(self):
CheckAuthenticator(self.request)
uid = self.request.get('UID', '')
title = self.request.get('Title', '')
ret = {
'UID': '',
'Title': '',
'Prefix': '',
'Hazardous': '',
'SampleMatrixUID': '',
'SampleMatrixTitle': '',
'MinimumVolume': '',
'ContainerTypeUID': '',
'ContainerTypeTitle': '',
'SamplePoints': ('',),
'StorageLocations': ('',),
}
proxies = None
if uid:
try:
bsc = getToolByName(self.context, 'bika_setup_catalog')
proxies = bsc(UID=uid)
except ParseError:
pass
elif title:
try:
bsc = getToolByName(self.context, 'bika_setup_catalog')
proxies = bsc(portal_type='SampleType', title=to_unicode(title))
except ParseError:
pass
if proxies and len(proxies) == 1:
st = proxies[0].getObject();
ret = {
'UID': st.UID(),
'Title': st.Title(),
'Prefix': st.getPrefix(),
'Hazardous': st.getHazardous(),
'SampleMatrixUID': st.getSampleMatrix() and \
st.getSampleMatrix().UID() or '',
'SampleMatrixTitle': st.getSampleMatrix() and \
st.getSampleMatrix().Title() or '',
'MinimumVolume': st.getMinimumVolume(),
'ContainerTypeUID': st.getContainerType() and \
st.getContainerType().UID() or '',
'ContainerTypeTitle': st.getContainerType() and \
st.getContainerType().Title() or '',
'SamplePoints': dict((sp.UID(),sp.Title()) for sp in st.getSamplePoints()),
'StorageLocations': dict((sp.UID(),sp.Title()) for sp in st.getStorageLocations()),
}
return json.dumps(ret)
def upgrade(tool):
"""Added bika.lims.analysisservice.edit.js
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
# apply new method/calculation data to old Analysis Services
portal = aq_parent(aq_inner(tool))
pc = getToolByName(portal, 'portal_catalog')
bsc = getToolByName(portal, 'bika_setup_catalog')
rc=getToolByName(portal, REFERENCE_CATALOG)
proxies = pc(portal_type="AnalysisService")
for proxy in proxies:
an = proxy.getObject()
rels = an.at_references.objectValues()
oldmethod = None
oldinstrument = None
oldcalc = None
for rel in rels:
if rel.relationship == 'AnalysisServiceCalculation':
oldcalc=rc.lookupObject(rel.targetUID)
elif rel.relationship == 'AnalysisServiceInstrument':
oldinstrument=rc.lookupObject(rel.targetUID)
elif rel.relationship == 'AnalysisServiceMethod':
oldmethod=rc.lookupObject(rel.targetUID)
if oldmethod and oldcalc and oldinstrument:
break
# Reset the method, instrument and calculations
if oldmethod:
an.Schema().getField('Methods').set(an, [oldmethod.UID(),])
an.Schema().getField('_Method').set(an, oldmethod.UID())
if oldinstrument:
an.Schema().getField('Instruments').set(an, [oldinstrument.UID(),])
an.Schema().getField('Instrument').set(an, oldinstrument.UID())
if oldcalc:
an.setUseDefaultCalculation(False);
an.Schema().getField('DeferredCalculation').set(an, oldcalc.UID())
return True
def isBasicTransitionAllowed(context, permission=None):
"""Most transition guards need to check the same conditions:
- Is the object active (cancelled or inactive objects can't transition)
- Has the user a certain permission, required for transition. This should
normally be set in the guard_permission in workflow definition.
"""
workflow = getToolByName(context, "portal_workflow")
mtool = getToolByName(context, "portal_membership")
if workflow.getInfoFor(context, "cancellation_state", "") == "cancelled" \
or workflow.getInfoFor(context, "inactive_state", "") == "inactive" \
or (permission and mtool.checkPermission(permission, context)):
return False
return True
def lookupMime(self, name):
mimetool = getToolByName(self, 'mimetypes_registry')
mimetypes = mimetool.lookup(name)
if len(mimetypes):
return mimetypes[0].name()
else:
return name
def __call__(self, value, *args, **kwargs):
instance = kwargs['instance']
translate = getToolByName(instance, 'translation_service').translate
# remove spaces from formatted
IBAN = ''.join(c for c in value if c.isalnum())
IBAN = IBAN[4:] + IBAN[:4]
country = IBAN[-4:-2]
if country not in country_dic:
msg = _('Unknown IBAN country %s' % country)
return to_utf8(translate(msg))
length_c, name_c = country_dic[country]
if len(IBAN) != length_c:
diff = len(IBAN) - length_c
msg = _('Wrong IBAN length by %s: %s' % (('short by %i' % -diff) if diff < 0 else
('too long by %i' % diff), value))
return to_utf8(translate(msg))
# Validating procedure
elif int("".join(str(letter_dic[x]) for x in IBAN)) % 97 != 1:
msg = _('Incorrect IBAN number: %s' % value)
return to_utf8(translate(msg))
else:
# Accepted:
return True
def submitTransition(self, action, came_from, items):
""" Performs the action's transition for the specified items
Returns (numtransitions, destination), where:
- numtransitions: the number of objects successfully transitioned.
If no objects have been successfully transitioned, gets 0 value
- destination: the destination url to be loaded immediately
"""
dest = None
transitioned = []
workflow = getToolByName(self.context, 'portal_workflow')
# transition selected items from the bika_listing/Table.
for item in items:
# the only actions allowed on inactive/cancelled
# items are "reinstate" and "activate"
if not isActive(item) and action not in ('reinstate', 'activate'):
continue
if not skip(item, action, peek=True):
allowed_transitions = [it['id'] for it in \
workflow.getTransitionsFor(item)]
if action in allowed_transitions:
success, message = doActionFor(item, action)
if success:
transitioned.append(item.id)
else:
self.context.plone_utils.addPortalMessage(message, 'error')
# automatic label printing
if transitioned and action == 'receive' \
and 'receive' in self.portal.bika_setup.getAutoPrintStickers():
q = "/sticker?autoprint=1&template=%s&items=" % (self.portal.bika_setup.getAutoStickerTemplate())
# selected_items is a list of UIDs (stickers for AR_add use IDs)
q += ",".join(transitioned)
dest = self.context.absolute_url() + q
return len(transitioned), dest
def setSamplePoints(self, value, **kw):
""" For the moment, we're manually trimming the sampletype<>samplepoint
relation to be equal on both sides, here.
It's done strangely, because it may be required to behave strangely.
"""
bsc = getToolByName(self, 'bika_setup_catalog')
## convert value to objects
if value and type(value) == str:
value = [bsc(UID=value)[0].getObject(),]
elif value and type(value) in (list, tuple) and type(value[0]) == str:
value = [bsc(UID=uid)[0].getObject() for uid in value if uid]
## Find all SamplePoints that were removed
existing = self.Schema()['SamplePoints'].get(self)
removed = existing and [s for s in existing if s not in value] or []
added = value and [s for s in value if s not in existing] or []
ret = self.Schema()['SamplePoints'].set(self, value)
for sp in removed:
sampletypes = sp.getSampleTypes()
if self in sampletypes:
sampletypes.remove(self)
sp.setSampleTypes(sampletypes)
for sp in added:
sp.setSampleTypes(list(sp.getSampleTypes()) + [self,])
return ret
def __call__(self, value, *args, **kwargs):
instance = kwargs['instance']
fieldname = kwargs['field'].getName()
# request = kwargs.get('REQUEST', {})
# form = request.get('form', {})
translate = getToolByName(instance, 'translation_service').translate
if value == instance.get(fieldname):
return True
for item in aq_parent(instance).objectValues():
if hasattr(item, 'UID') and item.UID() != instance.UID() and \
fieldname in item.Schema() and \
str(item.Schema()[fieldname].get(item)) == str(value): # We have to compare them as strings because
# even if a number (as an id) is saved inside
# a string widget and string field, it will be
# returned as an int. I don't know if it is
# caused because is called with
# <item.Schema()[fieldname].get(item)>,
# but it happens...
msg = _("Validation failed: '${value}' is not unique",
mapping={'value': safe_unicode(value)})
return to_utf8(translate(msg))
return True
def getInstrumentTypes(self):
bsc = getToolByName(self, 'bika_setup_catalog')
items = [(c.UID, c.Title) \
for c in bsc(portal_type='InstrumentType',
inactive_state = 'active')]
items.sort(lambda x,y:cmp(x[1], y[1]))
return DisplayList(items)
def __init__(self, context, request, **kwargs):
self.field_icons = {}
super(BikaListingView, self).__init__(context, request)
path = hasattr(context, 'getPath') and context.getPath() \
or "/".join(context.getPhysicalPath())
if hasattr(self, 'contentFilter'):
if not 'path' in self.contentFilter:
self.contentFilter['path'] = {"query": path, "level" : 0 }
else:
if not 'path' in self.contentFilter:
self.contentFilter = {'path': {"query": path, "level" : 0 }}
if 'show_categories' in kwargs:
self.show_categories = kwargs['show_categories']
if 'expand_all_categories' in kwargs:
self.expand_all_categories = kwargs['expand_all_categories']
self.portal = getToolByName(context, 'portal_url').getPortalObject()
self.portal_url = self.portal.absolute_url()
self.base_url = context.absolute_url()
self.view_url = self.base_url
self.translate = self.context.translate
self.show_all = False
def folderitems(self):
mtool = getToolByName(self.context, 'portal_membership')
if mtool.checkPermission(ManageBika, self.context):
del self.review_states[0]['transitions']
self.show_select_column = True
self.review_states.append(
{'id':'active',
'title': _('Active'),
'contentFilter': {'inactive_state': 'active'},
'transitions': [{'id':'deactivate'}, ],
'columns': ['Title', 'Description']})
self.review_states.append(
{'id':'inactive',
'title': _('Dormant'),
'contentFilter': {'inactive_state': 'inactive'},
'transitions': [{'id':'activate'}, ],
'columns': ['Title', 'Description']})
items = BikaListingView.folderitems(self)
for x in range(len(items)):
if not items[x].has_key('obj'): continue
items[x]['replace']['Title'] = "<a href='%s'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
return items
def __call__(self):
uid = self.request.get('Sample_uid', False)
if not uid:
return []
uc = getToolByName(self.context, "uid_catalog")
proxies = uc(UID=uid)
if not proxies:
return []
sample = proxies[0].getObject()
sample_schema = sample.Schema()
sample_fields = dict([(f.getName(), f) for f in sample_schema.fields()])
ar_schema = self.context.Schema()
ar_fields = [f.getName() for f in ar_schema.fields()
if f.widget.isVisible(self.context, 'secondary') == 'disabled']
ret = []
for fieldname in ar_fields:
if fieldname in sample_fields:
fieldvalue = sample_fields[fieldname].getAccessor(sample)()
if fieldvalue is None:
fieldvalue = ''
if hasattr(fieldvalue, 'Title'):
fieldvalue = fieldvalue.Title()
if hasattr(fieldvalue, 'year'):
fieldvalue = fieldvalue.strftime(self.date_format_short)
else:
fieldvalue = ''
ret.append([fieldname, fieldvalue])
return json.dumps(ret)
def upgrade(tool):
""" Sort by Type in instruments
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
bsc = getToolByName(portal, 'bika_setup_catalog', None)
if 'getInstrumentType' not in bsc.indexes():
bsc.addIndex('getInstrumentType', 'FieldIndex')
bsc.addColumn('getInstrumentType')
bsc.addIndex('getInstrumentTypeName','FieldIndex')
bsc.addColumn('getInstrumentTypeName')
#Del old "getType" Index, it's not used now.
if 'getType' in bsc.indexes():
bsc.delIndex('getType')
if 'getType' in bsc.indexes():
bsc.delColumn('getType')
setup = portal.portal_setup
logger.info("Reindex added indexes in bika_setup_catalog")
bsc.manage_reindexIndex(
ids=['getInstrumentType', 'getInstrumentTypeName', ])
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow-csv')
# /supplyorders folder permissions
mp = portal.supplyorders.manage_permission
mp(CancelAndReinstate, ['Manager', 'LabManager', 'LabClerk'], 0)
mp(ManagePricelists, ['Manager', 'LabManager', 'Owner'], 1)
mp(permissions.ListFolderContents, ['Member'], 1)
mp(permissions.AddPortalContent, ['Manager', 'LabManager', 'Owner'], 0)
mp(permissions.DeleteObjects, ['Manager', 'LabManager', 'Owner'], 0)
mp(permissions.View, ['Manager', 'LabManager'], 0)
portal.supplyorders.reindexObject()
wf = getToolByName(portal, 'portal_workflow')
wf.updateRoleMappings()
return True
def copy_to_new_allowed(self):
mtool = getToolByName(self.context, 'portal_membership')
if mtool.checkPermission(ManageAnalysisRequests, self.context) \
or mtool.checkPermission(ModifyPortalContent, self.context) \
or mtool.checkPermission(AddAnalysisRequest, self.portal):
return True
return False
def addReferenceAnalysis(self, service_uid, reference_type):
""" add an analysis to the sample """
rc = getToolByName(self, REFERENCE_CATALOG)
service = rc.lookupObject(service_uid)
analysis = _createObjectByType("ReferenceAnalysis", self, tmpID())
analysis.unmarkCreationFlag()
calculation = service.getCalculation()
interim_fields = calculation and calculation.getInterimFields() or []
renameAfterCreation(analysis)
# maxtime = service.getMaxTimeAllowed() and service.getMaxTimeAllowed() \
# or {'days':0, 'hours':0, 'minutes':0}
# starttime = DateTime()
# max_days = float(maxtime.get('days', 0)) + \
# (
# (float(maxtime.get('hours', 0)) * 3600 + \
# float(maxtime.get('minutes', 0)) * 60)
# / 86400
# )
# duetime = starttime + max_days
analysis.setReferenceType(reference_type)
analysis.setService(service_uid)
analysis.setInterimFields(interim_fields)
return analysis.UID()
def getSuppliers(self):
bsc = getToolByName(self, 'bika_setup_catalog')
items = [(c.UID, c.getName) \
for c in bsc(portal_type='Supplier',
inactive_state = 'active')]
items.sort(lambda x,y:cmp(x[1], y[1]))
return DisplayList(items)
def __init__(self, context, request):
super(WorksheetFolderListingView, self).__init__(context, request)
self.catalog = 'bika_catalog'
self.contentFilter = {
'portal_type': 'Worksheet',
'review_state': ['open', 'to_be_verified', 'verified', 'rejected'],
'sort_on': 'id',
'sort_order': 'reverse'
}
self.context_actions = {
_('Add'): {
'url': 'worksheet_add',
'icon': '++resource++bika.lims.images/add.png',
'class': 'worksheet_add'
}
}
self.show_table_only = False
self.show_sort_column = False
self.show_select_row = False
self.show_select_all_checkbox = True
self.show_select_column = True
self.pagesize = 25
self.restrict_results = False
request.set('disable_border', 1)
self.icon = self.portal_url + "/++resource++bika.lims.images/worksheet_big.png"
self.title = self.context.translate(_("Worksheets"))
self.description = ""
pm = getToolByName(context, "portal_membership")
# this is a property of self, because self.getAnalysts returns it
self.analysts = getUsers(self, ['Manager', 'LabManager', 'Analyst'])
self.analysts = self.analysts.sortedByKey()
bsc = getToolByName(context, 'bika_setup_catalog')
templates = [
t for t in bsc(portal_type='WorksheetTemplate',
inactive_state='active')
]
self.templates = [(t.UID, t.Title) for t in templates]
self.templates.sort(lambda x, y: cmp(x[1], y[1]))
self.instruments = [
(i.UID, i.Title)
for i in bsc(portal_type='Instrument', inactive_state='active')
]
self.instruments.sort(lambda x, y: cmp(x[1], y[1]))
self.templateinstruments = {}
for t in templates:
i = t.getObject().getInstrument()
if i:
self.templateinstruments[t.UID] = i.UID()
else:
self.templateinstruments[t.UID] = ''
self.columns = {
'Title': {
'title': _('Worksheet'),
'index': 'sortable_title'
},
'Priority': {
'title': _('Priority'),
'index': 'Priority',
'toggle': True
},
'Analyst': {
'title': _('Analyst'),
'index': 'getAnalyst',
'toggle': True
},
'Template': {
'title': _('Template'),
'toggle': True
},
'Services': {
'title': _('Services'),
'sortable': False,
'toggle': False
},
'SampleTypes': {
'title': _('Sample Types'),
'sortable': False,
'toggle': False
},
'Instrument': {
'title': _('Instrument'),
'sortable': False,
'toggle': False
},
'QC': {
'title': _('QC'),
'sortable': False,
'toggle': False
},
'QCTotals': {
'title': _('QC Samples(Analyses)'),
'sortable': False,
'toggle': False
},
'RoutineTotals': {
'title': _('Routine Samples(Analyses)'),
'sortable': False,
'toggle': False
},
'CreationDate': {
'title': PMF('Date Created'),
'toggle': True,
'index': 'created'
},
'state_title': {
'title': _('State'),
'index': 'review_state'
},
}
self.review_states = [
{
'id':
'default',
'title':
_('All'),
'contentFilter': {
'portal_type':
'Worksheet',
'review_state':
['open', 'to_be_verified', 'verified', 'rejected'],
'sort_on':
'id',
'sort_order':
'reverse'
},
'transitions': [{
'id': 'retract'
}, {
'id': 'verify'
}, {
'id': 'reject'
}],
'columns': [
'Title', 'Priority', 'Analyst', 'Template', 'Services',
'SampleTypes', 'Instrument', 'QC', 'QCTotals',
'RoutineTotals', 'CreationDate', 'state_title'
]
},
# getAuthenticatedMember does not work in __init__
# so 'mine' is configured further in 'folderitems' below.
{
'id':
'mine',
'title':
_('Mine'),
'contentFilter': {
'portal_type':
'Worksheet',
'review_state':
['open', 'to_be_verified', 'verified', 'rejected'],
'sort_on':
'id',
'sort_order':
'reverse'
},
'transitions': [{
'id': 'retract'
}, {
'id': 'verify'
}, {
'id': 'reject'
}],
'columns': [
'Title', 'Priority', 'Analyst', 'Template', 'Services',
'SampleTypes', 'Instrument', 'QC', 'QCTotals',
'RoutineTotals', 'CreationDate', 'state_title'
]
},
{
'id':
'open',
'title':
_('Open'),
'contentFilter': {
'portal_type': 'Worksheet',
'review_state': 'open',
'sort_on': 'id',
'sort_order': 'reverse'
},
'transitions': [],
'columns': [
'Title', 'Priority', 'Analyst', 'Template', 'Services',
'SampleTypes', 'Instrument', 'QC', 'QCTotals',
'RoutineTotals', 'CreationDate', 'state_title'
]
},
{
'id':
'to_be_verified',
'title':
_('To be verified'),
'contentFilter': {
'portal_type': 'Worksheet',
'review_state': 'to_be_verified',
'sort_on': 'id',
'sort_order': 'reverse'
},
'transitions': [{
'id': 'retract'
}, {
'id': 'verify'
}, {
'id': 'reject'
}],
'columns': [
'Title', 'Priority', 'Analyst', 'Template', 'Services',
'SampleTypes', 'Instrument', 'QC', 'QCTotals',
'RoutineTotals', 'CreationDate', 'state_title'
]
},
{
'id':
'verified',
'title':
_('Verified'),
'contentFilter': {
'portal_type': 'Worksheet',
'review_state': 'verified',
'sort_on': 'id',
'sort_order': 'reverse'
},
'transitions': [],
'columns': [
'Title', 'Priority', 'Analyst', 'Template', 'Services',
'SampleTypes', 'Instrument', 'QC', 'QCTotals',
'RoutineTotals', 'CreationDate', 'state_title'
]
},
]
def isSubmitted(self):
wftool = getToolByName(self, 'portal_workflow')
return wftool.getInfoFor(
self.context.aq_parent, 'review_state') == 'submitted'
def __call__(self):
parms = []
titles = []
rt = getToolByName(self.context, 'portal_repository')
mt = getToolByName(self.context, 'portal_membership')
# Apply filters
self.contentFilter = {
'portal_type':
('Analysis', 'AnalysisCategory', 'AnalysisProfile',
'AnalysisRequest', 'AnalysisService', 'AnalysisSpec',
'ARTemplate', 'Attachment', 'Batch', 'Calculation', 'Client',
'Contact', 'Container', 'ContainerType', 'Department',
'DuplicateAnalysis', 'Instrument', 'InstrumentCalibration',
'InstrumentCertification', 'InstrumentMaintenanceTask',
'InstrumentScheduledTask', 'InstrumentType',
'InstrumentValidation', 'Manufacturer'
'Method', 'Preservation', 'Pricelist', 'ReferenceAnalysis',
'ReferenceDefinition', 'ReferenceSample', 'Sample',
'SampleMatrix', 'SamplePoint', 'SampleType', 'Supplier',
'SupplierContact', 'Worksheet', 'WorksheetTemplate')
}
val = self.selection_macros.parse_daterange(self.request,
'getModificationDate',
_('Modification date'))
if val:
self.contentFilter['modified'] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
user = ''
userfullname = ''
titles.append(user)
if self.request.form.get('User', '') != '':
user = self.request.form['User']
userobj = mt.getMemberById(user)
userfullname = userobj.getProperty('fullname') \
if userobj else ''
parms.append({
'title': _('User'),
'value': ("%s (%s)" % (userfullname, user))
})
# Query the catalog and store results in a dictionary
entities = self.bika_setup_catalog(self.contentFilter)
if not entities:
message = _("No historical actions matched your query")
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
datalines = []
tmpdatalines = {}
footlines = {}
for entity in entities:
entity = entity.getObject()
entitytype = _(entity.__class__.__name__)
# Workflow states retrieval
for workflowid, workflow in entity.workflow_history.iteritems():
for action in workflow:
actiontitle = _('Created')
if not action['action'] or (action['action'] and
action['action'] == 'create'):
if workflowid == 'bika_inactive_workflow':
continue
actiontitle = _('Created')
else:
actiontitle = _(action['action'])
if (user == '' or action['actor'] == user):
actorfullname = userfullname == '' and mt.getMemberById(
user) or userfullname
dataline = {
'EntityNameOrId':
entity.title_or_id(),
'EntityAbsoluteUrl':
entity.absolute_url(),
'EntityCreationDate':
entity.CreationDate(),
'EntityModificationDate':
entity.ModificationDate(),
'EntityType':
entitytype,
'Workflow':
_(workflowid),
'Action':
actiontitle,
'ActionDate':
action['time'],
'ActionDateStr':
self.ulocalized_time(action['time'], 1),
'ActionActor':
action['actor'],
'ActionActorFullName':
actorfullname,
'ActionComments':
action['comments']
}
tmpdatalines[action['time']] = dataline
# History versioning retrieval
history = rt.getHistoryMetadata(entity)
if history:
hislen = history.getLength(countPurged=False)
for index in range(hislen):
meta = history.retrieve(index)['metadata']['sys_metadata']
metatitle = _(meta['comment'])
if (user == '' or meta['principal'] == user):
actorfullname = userfullname == '' and \
mt.getMemberById(user) or userfullname
dataline = {
'EntityNameOrId': entity.title_or_id(),
'EntityAbsoluteUrl': entity.absolute_url(),
'EntityCreationDate': entity.CreationDate(),
'EntityModificationDate':
entity.ModificationDate(),
'EntityType': entitytype,
'Workflow': '',
'Action': metatitle,
'ActionDate': meta['timestamp'],
'ActionDateStr': meta['timestamp'],
'ActionActor': meta['principal'],
'ActionActorFullName': actorfullname,
'ActionComments': ''
}
tmpdatalines[meta['timestamp']] = dataline
if len(tmpdatalines) == 0:
message = _("No actions found for user ${user}",
mapping={"user": userfullname})
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
else:
# Sort datalines
tmpkeys = tmpdatalines.keys()
tmpkeys.sort(reverse=True)
for index in range(len(tmpkeys)):
datalines.append(tmpdatalines[tmpkeys[index]])
self.report_data = {
'parameters': parms,
'datalines': datalines,
'footlines': footlines
}
return {
'report_title': _('Users history'),
'report_data': self.template()
}
def folderitems(self):
rc = getToolByName(self.context, REFERENCE_CATALOG)
bsc = getToolByName(self.context, 'bika_setup_catalog')
workflow = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
checkPermission = mtool.checkPermission
if not self.allow_edit:
can_edit_analyses = False
else:
if self.contentFilter.get('getPointOfCapture', '') == 'field':
can_edit_analyses = checkPermission(EditFieldResults,
self.context)
else:
can_edit_analyses = checkPermission(EditResults, self.context)
self.allow_edit = can_edit_analyses
self.show_select_column = self.allow_edit
context_active = isActive(self.context)
self.categories = []
items = super(AnalysesView, self).folderitems(full_objects=True)
# manually skim retracted analyses from the list
new_items = []
for i, item in enumerate(items):
# self.contentsMethod may return brains or objects.
if not ('obj' in items[i]):
continue
obj = hasattr(items[i]['obj'], 'getObject') and \
items[i]['obj'].getObject() or \
items[i]['obj']
if workflow.getInfoFor(obj, 'review_state') == 'retracted' \
and not checkPermission(ViewRetractedAnalyses, self.context):
continue
new_items.append(item)
items = new_items
methods = self.get_methods_vocabulary()
self.interim_fields = {}
self.interim_columns = {}
self.specs = {}
show_methodinstr_columns = False
for i, item in enumerate(items):
# self.contentsMethod may return brains or objects.
obj = hasattr(items[i]['obj'], 'getObject') and \
items[i]['obj'].getObject() or \
items[i]['obj']
if workflow.getInfoFor(obj, 'review_state') == 'retracted' \
and not checkPermission(ViewRetractedAnalyses, self.context):
continue
result = obj.getResult()
service = obj.getService()
calculation = service.getCalculation()
unit = service.getUnit()
keyword = service.getKeyword()
if self.show_categories:
cat = obj.getService().getCategoryTitle()
items[i]['category'] = cat
if cat not in self.categories:
self.categories.append(cat)
# Check for InterimFields attribute on our object,
interim_fields = hasattr(obj, 'getInterimFields') \
and obj.getInterimFields() or []
# kick some pretty display values in.
for x in range(len(interim_fields)):
interim_fields[x]['formatted_value'] = \
format_numeric_result(obj, interim_fields[x]['value'])
self.interim_fields[obj.UID()] = interim_fields
items[i]['service_uid'] = service.UID()
items[i]['Service'] = service.Title()
items[i]['Keyword'] = keyword
items[i]['Unit'] = format_supsub(unit) if unit else ''
items[i]['Result'] = ''
items[i]['formatted_result'] = ''
items[i]['interim_fields'] = interim_fields
items[i]['Remarks'] = obj.getRemarks()
items[i]['Uncertainty'] = ''
items[i]['DetectionLimit'] = ''
items[i]['retested'] = obj.getRetested()
items[i]['class']['retested'] = 'center'
items[i]['result_captured'] = self.ulocalized_time(
obj.getResultCaptureDate(), long_format=0)
items[i]['calculation'] = calculation and True or False
try:
items[i]['Partition'] = obj.getSamplePartition().getId()
except AttributeError:
items[i]['Partition'] = ''
if obj.portal_type == "ReferenceAnalysis":
items[i]['DueDate'] = self.ulocalized_time(
obj.aq_parent.getExpiryDate(), long_format=0)
else:
items[i]['DueDate'] = self.ulocalized_time(obj.getDueDate(),
long_format=1)
cd = obj.getResultCaptureDate()
items[i]['CaptureDate'] = cd and self.ulocalized_time(
cd, long_format=1) or ''
items[i]['Attachments'] = ''
item['allow_edit'] = []
client_or_lab = ""
tblrowclass = items[i].get('table_row_class')
if obj.portal_type == 'ReferenceAnalysis':
items[i]['st_uid'] = obj.aq_parent.UID()
items[i]['table_row_class'] = ' '.join(
[tblrowclass, 'qc-analysis'])
elif obj.portal_type == 'DuplicateAnalysis' and \
obj.getAnalysis().portal_type == 'ReferenceAnalysis':
items[i]['st_uid'] = obj.aq_parent.UID()
items[i]['table_row_class'] = ' '.join(
[tblrowclass, 'qc-analysis'])
else:
sample = None
if self.context.portal_type == 'AnalysisRequest':
sample = self.context.getSample()
elif self.context.portal_type == 'Worksheet':
if obj.portal_type in ('DuplicateAnalysis',
'RejectAnalysis'):
sample = obj.getAnalysis().getSample()
else:
sample = obj.aq_parent.getSample()
elif self.context.portal_type == 'Sample':
sample = self.context
st_uid = sample.getSampleType().UID() if sample else ''
items[i]['st_uid'] = st_uid
if checkPermission(ManageBika, self.context):
service_uid = service.UID()
latest = rc.lookupObject(service_uid).version_id
items[i]['Service'] = service.Title()
items[i]['class']['Service'] = "service_title"
# Show version number of out-of-date objects
# No: This should be done in another column, if at all.
# The (vX) value confuses some more fragile forms.
# if hasattr(obj, 'reference_versions') and \
# service_uid in obj.reference_versions and \
# latest != obj.reference_versions[service_uid]:
# items[i]['after']['Service'] = "(v%s)" % \
# (obj.reference_versions[service_uid])
# choices defined on Service apply to result fields.
choices = service.getResultOptions()
if choices:
item['choices']['Result'] = choices
# permission to view this item's results
can_view_result = \
getSecurityManager().checkPermission(ViewResults, obj)
# permission to edit this item's results
# Editing Field Results is possible while in Sample Due.
poc = self.contentFilter.get("getPointOfCapture", 'lab')
can_edit_analysis = self.allow_edit and context_active and \
( (poc == 'field' and getSecurityManager().checkPermission(EditFieldResults, obj))
or
(poc != 'field' and getSecurityManager().checkPermission(EditResults, obj)) )
allowed_method_states = [
'to_be_sampled', 'to_be_preserved', 'sample_received',
'sample_registered', 'sampled', 'assigned'
]
# Prevent from being edited if the instrument assigned
# is not valid (out-of-date or uncalibrated), except if
# the analysis is a QC with assigned status
can_edit_analysis = can_edit_analysis \
and (obj.isInstrumentValid() \
or (obj.portal_type == 'ReferenceAnalysis' \
and item['review_state'] in allowed_method_states))
if can_edit_analysis:
items[i]['allow_edit'].extend(['Analyst', 'Result', 'Remarks'])
# if the Result field is editable, our interim fields are too
for f in self.interim_fields[obj.UID()]:
items[i]['allow_edit'].append(f['keyword'])
# if there isn't a calculation then result must be re-testable,
# and if there are interim fields, they too must be re-testable.
if not items[i]['calculation'] or \
(items[i]['calculation'] and self.interim_fields[obj.UID()]):
items[i]['allow_edit'].append('retested')
# TODO: Only the labmanager must be able to change the method
# can_set_method = getSecurityManager().checkPermission(SetAnalysisMethod, obj)
can_set_method = can_edit_analysis \
and item['review_state'] in allowed_method_states
method = obj.getMethod() \
if hasattr(obj, 'getMethod') and obj.getMethod() \
else service.getMethod()
# Display the methods selector if the AS has at least one
# method assigned
item['Method'] = ''
item['replace']['Method'] = ''
if can_set_method:
voc = self.get_methods_vocabulary(obj)
if voc:
# The service has at least one method available
item['Method'] = method.UID() if method else ''
item['choices']['Method'] = voc
item['allow_edit'].append('Method')
show_methodinstr_columns = True
elif method:
# This should never happen
# The analysis has set a method, but its parent
# service hasn't any method available O_o
item['Method'] = method.Title()
item['replace']['Method'] = "<a href='%s'>%s</a>" % \
(method.absolute_url(), method.Title())
show_methodinstr_columns = True
elif method:
# Edition not allowed, but method set
item['Method'] = method.Title()
item['replace']['Method'] = "<a href='%s'>%s</a>" % \
(method.absolute_url(), method.Title())
show_methodinstr_columns = True
# TODO: Instrument selector dynamic behavior in worksheet Results
# Only the labmanager must be able to change the instrument to be used. Also,
# the instrument selection should be done in accordance with the method selected
# can_set_instrument = service.getInstrumentEntryOfResults() and getSecurityManager().checkPermission(SetAnalysisInstrument, obj)
can_set_instrument = service.getInstrumentEntryOfResults() \
and can_edit_analysis \
and item['review_state'] in allowed_method_states
item['Instrument'] = ''
item['replace']['Instrument'] = ''
if service.getInstrumentEntryOfResults():
instrument = None
# If the analysis has an instrument already assigned, use it
if service.getInstrumentEntryOfResults() \
and hasattr(obj, 'getInstrument') \
and obj.getInstrument():
instrument = obj.getInstrument()
# Otherwise, use the Service's default instrument
elif service.getInstrumentEntryOfResults():
instrument = service.getInstrument()
if can_set_instrument:
# Edition allowed
voc = self.get_instruments_vocabulary(obj)
if voc:
# The service has at least one instrument available
item['Instrument'] = instrument.UID(
) if instrument else ''
item['choices']['Instrument'] = voc
item['allow_edit'].append('Instrument')
show_methodinstr_columns = True
elif instrument:
# This should never happen
# The analysis has an instrument set, but the
# service hasn't any available instrument
item['Instrument'] = instrument.Title()
item['replace']['Instrument'] = "<a href='%s'>%s</a>" % \
(instrument.absolute_url(), instrument.Title())
show_methodinstr_columns = True
elif instrument:
# Edition not allowed, but instrument set
item['Instrument'] = instrument.Title()
item['replace']['Instrument'] = "<a href='%s'>%s</a>" % \
(instrument.absolute_url(), instrument.Title())
show_methodinstr_columns = True
else:
# Manual entry of results, instrument not allowed
item['Instrument'] = _('Manual')
msgtitle = t(
_(
"Instrument entry of results not allowed for ${service}",
mapping={"service": safe_unicode(service.Title())},
))
item['replace']['Instrument'] = \
'<a href="#" title="%s">%s</a>' % (msgtitle, t(_('Manual')))
# Sets the analyst assigned to this analysis
if can_edit_analysis:
analyst = obj.getAnalyst()
# widget default: current user
if not analyst:
analyst = mtool.getAuthenticatedMember().getUserName()
items[i]['Analyst'] = analyst
item['choices']['Analyst'] = self.getAnalysts()
else:
items[i]['Analyst'] = obj.getAnalystName()
# If the user can attach files to analyses, show the attachment col
can_add_attachment = \
getSecurityManager().checkPermission(AddAttachment, obj)
if can_add_attachment or can_view_result:
attachments = ""
if hasattr(obj, 'getAttachment'):
for attachment in obj.getAttachment():
af = attachment.getAttachmentFile()
icon = af.getBestIcon()
attachments += "<span class='attachment' attachment_uid='%s'>" % (
attachment.UID())
if icon:
attachments += "<img src='%s/%s'/>" % (
self.portal_url, icon)
attachments += '<a href="%s/at_download/AttachmentFile"/>%s</a>' % (
attachment.absolute_url(), af.filename)
if can_edit_analysis:
attachments += "<img class='deleteAttachmentButton' attachment_uid='%s' src='%s'/>" % (
attachment.UID(),
"++resource++bika.lims.images/delete.png")
attachments += "</br></span>"
items[i]['replace'][
'Attachments'] = attachments[:-12] + "</span>"
# Only display data bearing fields if we have ViewResults
# permission, otherwise just put an icon in Result column.
if can_view_result:
items[i]['Result'] = result
scinot = self.context.bika_setup.getScientificNotationResults()
dmk = self.context.bika_setup.getResultsDecimalMark()
items[i]['formatted_result'] = obj.getFormattedResult(
sciformat=int(scinot), decimalmark=dmk)
# LIMS-1379 Allow manual uncertainty value input
# https://jira.bikalabs.com/browse/LIMS-1379
fu = format_uncertainty(obj,
result,
decimalmark=dmk,
sciformat=int(scinot))
fu = fu if fu else ''
if can_edit_analysis and service.getAllowManualUncertainty(
) == True:
unc = obj.getUncertainty(result)
item['allow_edit'].append('Uncertainty')
items[i]['Uncertainty'] = unc if unc else ''
items[i]['before']['Uncertainty'] = '± '
items[i]['after'][
'Uncertainty'] = '<em class="discreet" style="white-space:nowrap;"> %s</em>' % items[
i]['Unit']
elif fu:
items[i]['Uncertainty'] = fu
items[i]['before']['Uncertainty'] = '± '
items[i]['after'][
'Uncertainty'] = '<em class="discreet" style="white-space:nowrap;"> %s</em>' % items[
i]['Unit']
# LIMS-1700. Allow manual input of Detection Limits
# LIMS-1775. Allow to select LDL or UDL defaults in results with readonly mode
# https://jira.bikalabs.com/browse/LIMS-1700
# https://jira.bikalabs.com/browse/LIMS-1775
if can_edit_analysis and \
hasattr(obj, 'getDetectionLimitOperand') and \
hasattr(service, 'getDetectionLimitSelector') and \
service.getDetectionLimitSelector() == True:
isldl = obj.isBelowLowerDetectionLimit()
isudl = obj.isAboveUpperDetectionLimit()
dlval = ''
if isldl or isudl:
dlval = '<' if isldl else '>'
item['allow_edit'].append('DetectionLimit')
item['DetectionLimit'] = dlval
choices = [{
'ResultValue': '<',
'ResultText': '<'
}, {
'ResultValue': '>',
'ResultText': '>'
}]
item['choices']['DetectionLimit'] = choices
self.columns['DetectionLimit']['toggle'] = True
srv = obj.getService()
defdls = {
'min': srv.getLowerDetectionLimit(),
'max': srv.getUpperDetectionLimit(),
'manual': srv.getAllowManualDetectionLimit()
}
defin = '<input type="hidden" id="DefaultDLS.%s" value=\'%s\'/>'
defin = defin % (obj.UID(), json.dumps(defdls))
item['after']['DetectionLimit'] = defin
# LIMS-1769. Allow to use LDL and UDL in calculations.
# https://jira.bikalabs.com/browse/LIMS-1769
# Since LDL, UDL, etc. are wildcards that can be used
# in calculations, these fields must be loaded always
# for 'live' calculations.
if can_edit_analysis:
dls = {
'default_ldl': 'none',
'default_udl': 'none',
'below_ldl': False,
'above_udl': False,
'is_ldl': False,
'is_udl': False,
'manual_allowed': False,
'dlselect_allowed': False
}
if hasattr(obj, 'getDetectionLimits'):
dls['below_ldl'] = obj.isBelowLowerDetectionLimit()
dls['above_udl'] = obj.isBelowLowerDetectionLimit()
dls['is_ldl'] = obj.isLowerDetectionLimit()
dls['is_udl'] = obj.isUpperDetectionLimit()
dls['default_ldl'] = service.getLowerDetectionLimit()
dls['default_udl'] = service.getUpperDetectionLimit()
dls['manual_allowed'] = service.getAllowManualDetectionLimit(
)
dls['dlselect_allowed'] = service.getDetectionLimitSelector(
)
dlsin = '<input type="hidden" id="AnalysisDLS.%s" value=\'%s\'/>'
dlsin = dlsin % (obj.UID(), json.dumps(dls))
item['after']['Result'] = dlsin
else:
items[i]['Specification'] = ""
if 'Result' in items[i]['allow_edit']:
items[i]['allow_edit'].remove('Result')
items[i]['before']['Result'] = \
'<img width="16" height="16" ' + \
'src="%s/++resource++bika.lims.images/to_follow.png"/>' % \
(self.portal_url)
# Everyone can see valid-ranges
spec = self.get_analysis_spec(obj)
if spec:
min_val = spec.get('min', '')
min_str = ">{0}".format(min_val) if min_val else ''
max_val = spec.get('max', '')
max_str = "<{0}".format(max_val) if max_val else ''
error_val = spec.get('error', '')
error_str = "{0}%".format(error_val) if error_val else ''
rngstr = ",".join(
[x for x in [min_str, max_str, error_str] if x])
else:
rngstr = ""
items[i]['Specification'] = rngstr
# Add this analysis' interim fields to the interim_columns list
for f in self.interim_fields[obj.UID()]:
if f['keyword'] not in self.interim_columns and not f.get(
'hidden', False):
self.interim_columns[f['keyword']] = f['title']
# and to the item itself
items[i][f['keyword']] = f
items[i]['class'][f['keyword']] = 'interim'
# check if this analysis is late/overdue
resultdate = obj.aq_parent.getDateSampled() \
if obj.portal_type == 'ReferenceAnalysis' \
else obj.getResultCaptureDate()
duedate = obj.aq_parent.getExpiryDate() \
if obj.portal_type == 'ReferenceAnalysis' \
else obj.getDueDate()
items[i]['replace']['DueDate'] = \
self.ulocalized_time(duedate, long_format=1)
if items[i]['review_state'] not in [
'to_be_sampled', 'to_be_preserved', 'sample_due',
'published'
]:
if (resultdate and resultdate > duedate) \
or (not resultdate and DateTime() > duedate):
items[i]['replace']['DueDate'] = '%s <img width="16" height="16" src="%s/++resource++bika.lims.images/late.png" title="%s"/>' % \
(self.ulocalized_time(duedate, long_format=1),
self.portal_url,
t(_("Late Analysis")))
# Submitting user may not verify results (admin can though)
if items[i]['review_state'] == 'to_be_verified' and \
not checkPermission(VerifyOwnResults, obj):
user_id = getSecurityManager().getUser().getId()
self_submitted = False
try:
review_history = list(
workflow.getInfoFor(obj, 'review_history'))
review_history.reverse()
for event in review_history:
if event.get('action') == 'submit':
if event.get('actor') == user_id:
self_submitted = True
break
if self_submitted:
items[i]['after']['state_title'] = \
"<img src='++resource++bika.lims.images/submitted-by-current-user.png' title='%s'/>" % \
(t(_("Cannot verify: Submitted by current user")))
except WorkflowException:
pass
# add icon for assigned analyses in AR views
if self.context.portal_type == 'AnalysisRequest':
obj = items[i]['obj']
if obj.portal_type in ['ReferenceAnalysis',
'DuplicateAnalysis'] or \
workflow.getInfoFor(obj, 'worksheetanalysis_review_state') == 'assigned':
br = obj.getBackReferences('WorksheetAnalysis')
if len(br) > 0:
ws = br[0]
items[i]['after']['state_title'] = \
"<a href='%s'><img src='++resource++bika.lims.images/worksheet.png' title='%s'/></a>" % \
(ws.absolute_url(),
t(_("Assigned to: ${worksheet_id}",
mapping={'worksheet_id': safe_unicode(ws.id)})))
# the TAL requires values for all interim fields on all
# items, so we set blank values in unused cells
for item in items:
for field in self.interim_columns:
if field not in item:
item[field] = ''
# XXX order the list of interim columns
interim_keys = self.interim_columns.keys()
interim_keys.reverse()
# add InterimFields keys to columns
for col_id in interim_keys:
if col_id not in self.columns:
self.columns[col_id] = {
'title': self.interim_columns[col_id],
'input_width': '6',
'input_class': 'ajax_calculate numeric',
'sortable': False
}
if can_edit_analyses:
new_states = []
for state in self.review_states:
# InterimFields are displayed in review_state
# They are anyway available through View.columns though.
# In case of hidden fields, the calcs.py should check calcs/services
# for additional InterimFields!!
pos = 'Result' in state['columns'] and \
state['columns'].index('Result') or len(state['columns'])
for col_id in interim_keys:
if col_id not in state['columns']:
state['columns'].insert(pos, col_id)
# retested column is added after Result.
pos = 'Result' in state['columns'] and \
state['columns'].index('Uncertainty') + 1 or len(state['columns'])
state['columns'].insert(pos, 'retested')
new_states.append(state)
self.review_states = new_states
# Allow selecting individual analyses
self.show_select_column = True
# Dry Matter.
# The Dry Matter column is never enabled for reference sample contexts
# and refers to getReportDryMatter in ARs.
if items and \
(hasattr(self.context, 'getReportDryMatter') and \
self.context.getReportDryMatter()):
# look through all items
# if the item's Service supports ReportDryMatter, add getResultDM().
for item in items:
if item['obj'].getService().getReportDryMatter():
item['ResultDM'] = item['obj'].getResultDM()
else:
item['ResultDM'] = ''
if item['ResultDM']:
item['after']['ResultDM'] = "<em class='discreet'>%</em>"
# modify the review_states list to include the ResultDM column
new_states = []
for state in self.review_states:
pos = 'Result' in state['columns'] and \
state['columns'].index('Uncertainty') + 1 or len(state['columns'])
state['columns'].insert(pos, 'ResultDM')
new_states.append(state)
self.review_states = new_states
self.categories.sort()
# self.json_specs = json.dumps(self.specs)
self.json_interim_fields = json.dumps(self.interim_fields)
self.items = items
# Method and Instrument columns must be shown or hidden at the
# same time, because the value assigned to one causes
# a value reassignment to the other (one method can be performed
# by different instruments)
self.columns['Method']['toggle'] = show_methodinstr_columns
self.columns['Instrument']['toggle'] = show_methodinstr_columns
return items
def _create_ar(self, context, request):
"""Creates AnalysisRequest object, with supporting Sample, Partition
and Analysis objects. The client is retrieved from the obj_path
key in the request.
Required request parameters:
- Contact: One client contact Fullname. The contact must exist
in the specified client. The first Contact with the specified
value in it's Fullname field will be used.
- SampleType_<index> - Must be an existing sample type.
Optional request parameters:
- CCContacts: A list of contact Fullnames, which will be copied on
all messages related to this AR and it's sample or results.
- CCEmails: A list of email addresses to include as above.
- Sample_id: Create a secondary AR with an existing sample. If
unspecified, a new sample is created.
- Specification: a lookup to set Analysis specs default values
for all analyses
- Analysis_Specification: specs (or overrides) per analysis, using
a special lookup format.
&Analysis_Specification:list=<Keyword>:min:max:error&...
"""
wftool = getToolByName(context, 'portal_workflow')
bc = getToolByName(context, 'bika_catalog')
bsc = getToolByName(context, 'bika_setup_catalog')
pc = getToolByName(context, 'portal_catalog')
ret = {
"url": router.url_for("create", force_external=True),
"success": True,
"error": False,
}
SamplingWorkflowEnabled = context.bika_setup.getSamplingWorkflowEnabled()
for field in [
'Client',
'SampleType',
'Contact',
'SamplingDate',
'Services']:
self.require(field)
self.used(field)
try:
client = resolve_request_lookup(context, request, 'Client')[0].getObject()
except IndexError:
raise Exception("Client not found")
# Sample_id
if 'Sample' in request:
try:
sample = resolve_request_lookup(context, request, 'Sample')[0].getObject()
except IndexError:
raise Exception("Sample not found")
else:
# Primary AR
sample = _createObjectByType("Sample", client, tmpID())
sample.unmarkCreationFlag()
fields = set_fields_from_request(sample, request)
for field in fields:
self.used(field)
sample._renameAfterCreation()
sample.setSampleID(sample.getId())
event.notify(ObjectInitializedEvent(sample))
sample.at_post_create_script()
if SamplingWorkflowEnabled:
wftool.doActionFor(sample, 'sampling_workflow')
else:
wftool.doActionFor(sample, 'no_sampling_workflow')
ret['sample_id'] = sample.getId()
parts = [{'services': [],
'container': [],
'preservation': '',
'separate': False}]
specs = self.get_specs_from_request()
ar = _createObjectByType("AnalysisRequest", client, tmpID())
ar.unmarkCreationFlag()
fields = set_fields_from_request(ar, request)
for field in fields:
self.used(field)
ar.setSample(sample.UID())
ar._renameAfterCreation()
ret['ar_id'] = ar.getId()
brains = resolve_request_lookup(context, request, 'Services')
service_uids = [p.UID for p in brains]
new_analyses = ar.setAnalyses(service_uids, specs=specs)
ar.setRequestID(ar.getId())
ar.reindexObject()
event.notify(ObjectInitializedEvent(ar))
ar.at_post_create_script()
# Create sample partitions
parts_and_services = {}
for _i in range(len(parts)):
p = parts[_i]
part_prefix = sample.getId() + "-P"
if '%s%s' % (part_prefix, _i + 1) in sample.objectIds():
parts[_i]['object'] = sample['%s%s' % (part_prefix, _i + 1)]
parts_and_services['%s%s' % (part_prefix, _i + 1)] = p['services']
part = parts[_i]['object']
else:
part = _createObjectByType("SamplePartition", sample, tmpID())
parts[_i]['object'] = part
container = None
preservation = p['preservation']
parts[_i]['prepreserved'] = False
part.edit(
Container=container,
Preservation=preservation,
)
part.processForm()
if SamplingWorkflowEnabled:
wftool.doActionFor(part, 'sampling_workflow')
else:
wftool.doActionFor(part, 'no_sampling_workflow')
parts_and_services[part.id] = p['services']
if SamplingWorkflowEnabled:
wftool.doActionFor(ar, 'sampling_workflow')
else:
wftool.doActionFor(ar, 'no_sampling_workflow')
# Add analyses to sample partitions
# XXX jsonapi create AR: right now, all new analyses are linked to the first samplepartition
if new_analyses:
analyses = list(part.getAnalyses())
analyses.extend(new_analyses)
part.edit(
Analyses=analyses,
)
for analysis in new_analyses:
analysis.setSamplePartition(part)
# If Preservation is required for some partitions,
# and the SamplingWorkflow is disabled, we need
# to transition to to_be_preserved manually.
if not SamplingWorkflowEnabled:
to_be_preserved = []
sample_due = []
lowest_state = 'sample_due'
for p in sample.objectValues('SamplePartition'):
if p.getPreservation():
lowest_state = 'to_be_preserved'
to_be_preserved.append(p)
else:
sample_due.append(p)
for p in to_be_preserved:
doActionFor(p, 'to_be_preserved')
for p in sample_due:
doActionFor(p, 'sample_due')
doActionFor(sample, lowest_state)
for analysis in ar.objectValues('Analysis'):
doActionFor(analysis, lowest_state)
doActionFor(ar, lowest_state)
# receive secondary AR
if request.get('Sample_id', ''):
doActionFor(ar, 'sampled')
doActionFor(ar, 'sample_due')
not_receive = ['to_be_sampled', 'sample_due', 'sampled',
'to_be_preserved']
sample_state = wftool.getInfoFor(sample, 'review_state')
if sample_state not in not_receive:
doActionFor(ar, 'receive')
for analysis in ar.getAnalyses(full_objects=1):
doActionFor(analysis, 'sampled')
doActionFor(analysis, 'sample_due')
if sample_state not in not_receive:
doActionFor(analysis, 'receive')
if self.unused:
raise BadRequest("The following request fields were not used: %s. Request aborted." % self.unused)
return ret
def workflow_action_retract_ar(self):
workflow = getToolByName(self.context, 'portal_workflow')
# AR should be retracted
# Can't transition inactive ARs
if not isActive(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
# 1. Copies the AR linking the original one and viceversa
ar = self.context
newar = self.cloneAR(ar)
# 2. The old AR gets a status of 'invalid'
workflow.doActionFor(ar, 'retract_ar')
# 3. The new AR copy opens in status 'to be verified'
changeWorkflowState(newar, 'bika_ar_workflow', 'to_be_verified')
# 4. The system immediately alerts the client contacts who ordered
# the results, per email and SMS, that a possible mistake has been
# picked up and is under investigation.
# A much possible information is provided in the email, linking
# to the AR online.
laboratory = self.context.bika_setup.laboratory
lab_address = "<br/>".join(laboratory.getPrintAddress())
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = t(
_("Erroneus result publication from ${request_id}",
mapping={"request_id": ar.getRequestID()}))
mime_msg['From'] = formataddr((encode_header(laboratory.getName()),
laboratory.getEmailAddress()))
to = []
contact = ar.getContact()
if contact:
to.append(
formataddr((encode_header(contact.Title()),
contact.getEmailAddress())))
for cc in ar.getCCContact():
formatted = formataddr(
(encode_header(cc.Title()), cc.getEmailAddress()))
if formatted not in to:
to.append(formatted)
managers = self.context.portal_groups.getGroupMembers('LabManagers')
for bcc in managers:
user = self.portal.acl_users.getUser(bcc)
if user:
uemail = user.getProperty('email')
ufull = user.getProperty('fullname')
formatted = formataddr((encode_header(ufull), uemail))
if formatted not in to:
to.append(formatted)
mime_msg['To'] = ','.join(to)
aranchor = "<a href='%s'>%s</a>" % (ar.absolute_url(),
ar.getRequestID())
naranchor = "<a href='%s'>%s</a>" % (newar.absolute_url(),
newar.getRequestID())
addremarks = ('addremarks' in self.request
and ar.getRemarks()) \
and ("<br/><br/>"
+ _("Additional remarks:")
+ "<br/>"
+ ar.getRemarks().split("===")[1].strip()
+ "<br/><br/>") \
or ''
sub_d = dict(request_link=aranchor,
new_request_link=naranchor,
remarks=addremarks,
lab_address=lab_address)
body = Template(
"Some errors have been detected in the results report "
"published from the Analysis Request $request_link. The Analysis "
"Request $new_request_link has been created automatically and the "
"previous has been invalidated.<br/>The possible mistake "
"has been picked up and is under investigation.<br/><br/>"
"$remarks $lab_address").safe_substitute(sub_d)
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)
try:
host = getToolByName(self.context, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except Exception as msg:
message = _(
'Unable to send an email to alert lab '
'client contacts that the Analysis Request has been '
'retracted: ${error}',
mapping={'error': safe_unicode(msg)})
self.context.plone_utils.addPortalMessage(message, 'warning')
message = _('${items} invalidated.',
mapping={'items': ar.getRequestID()})
self.context.plone_utils.addPortalMessage(message, 'warning')
self.request.response.redirect(newar.absolute_url())
def __call__(self):
context = self.context
workflow = getToolByName(context, 'portal_workflow')
# Collect related data and objects
invoice = context.getInvoice()
sample = context.getSample()
samplePoint = sample.getSamplePoint()
reviewState = workflow.getInfoFor(context, 'review_state')
# Collection invoice information
if invoice:
self.invoiceId = invoice.getId()
else:
self.invoiceId = _('Proforma (Not yet invoiced)')
# Collect verified invoice information
verified = reviewState in VERIFIED_STATES
if verified:
self.verifiedBy = context.getVerifier()
self.verified = verified
self.request['verified'] = verified
# Collect published date
datePublished = context.getDatePublished()
if datePublished is not None:
datePublished = self.ulocalized_time(datePublished, long_format=1)
self.datePublished = datePublished
# Collect received date
dateReceived = context.getDateReceived()
if dateReceived is not None:
dateReceived = self.ulocalized_time(dateReceived, long_format=1)
self.dateReceived = dateReceived
# Collect general information
self.reviewState = reviewState
contact = context.getContact()
self.contact = contact.Title() if contact else ""
self.clientOrderNumber = context.getClientOrderNumber()
self.clientReference = context.getClientReference()
self.clientSampleId = sample.getClientSampleID()
self.sampleType = sample.getSampleType().Title()
self.samplePoint = samplePoint and samplePoint.Title()
self.requestId = context.getRequestID()
self.headers = [
{
'title': 'Invoice ID',
'value': self.invoiceId
},
{
'title': 'Client Reference',
'value': self.clientReference
},
{
'title': 'Sample Type',
'value': self.sampleType
},
{
'title': 'Request ID',
'value': self.requestId
},
{
'title': 'Date Received',
'value': self.dateReceived
},
]
if not isAttributeHidden('AnalysisRequest', 'ClientOrderNumber'):
self.headers.append({
'title': 'Client Sample Id',
'value': self.clientOrderNumber
})
if not isAttributeHidden('AnalysisRequest', 'SamplePoint'):
self.headers.append({
'title': 'Sample Point',
'value': self.samplePoint
})
if self.verified:
self.headers.append({
'title': 'Verified By',
'value': self.verifiedBy
})
if self.datePublished:
self.headers.append({
'title': 'datePublished',
'value': self.datePublished
})
# <tal:published tal:condition="view/datePublished">
# <th i18n:translate="">Date Published</th>
# <td tal:content="view/datePublished"></td>
# </tal:published>
#</tr>
analyses = []
profiles = []
# Retrieve required data from analyses collection
all_analyses, all_profiles, analyses_from_profiles = context.getServicesAndProfiles(
)
# Relating category with solo analysis
for analysis in all_analyses:
service = analysis.getService()
categoryName = service.getCategory().Title()
# Find the category
try:
category = (o for o in analyses
if o['name'] == categoryName).next()
except:
category = {'name': categoryName, 'analyses': []}
analyses.append(category)
# Append the analysis to the category
category['analyses'].append({
'title':
analysis.Title(),
'price':
analysis.getPrice(),
'priceVat':
"%.2f" % analysis.getVATAmount(),
'priceTotal':
"%.2f" % analysis.getTotalPrice(),
})
# Relating analysis services with their profiles
# We'll take the analysis contained on each profile
for profile in all_profiles:
# If profile's checkbox "Use Analysis Profile Price" is enabled, only the profile price will be displayed.
# Otherwise each analysis will display its own price.
pservices = []
if profile.getUseAnalysisProfilePrice():
# We have to use the profiles price only
for pservice in profile.getService():
pservices.append({
'title': pservice.Title(),
'price': None,
'priceVat': None,
'priceTotal': None,
})
profiles.append({
'name': profile.title,
'price': profile.getAnalysisProfilePrice(),
'priceVat': profile.getVATAmount(),
'priceTotal': profile.getTotalPrice(),
'analyses': pservices
})
else:
# We need the analyses prices instead of profile price
for pservice in profile.getService():
# We want the analysis instead of the service, because we want the price for the client
# (for instance the bulk price)
panalysis = self._getAnalysisForProfileService(
pservice.getKeyword(), analyses_from_profiles)
pservices.append({
'title':
pservice.Title(),
'price':
panalysis.getPrice()
if panalysis else pservice.getPrice(),
'priceVat':
"%.2f" % panalysis.getVATAmount()
if panalysis else pservice.getVATAmount(),
'priceTotal':
"%.2f" % panalysis.getTotalPrice()
if panalysis else pservice.getTotalPrice(),
})
profiles.append({
'name': profile.title,
'price': None,
'priceVat': None,
'priceTotal': None,
'analyses': pservices
})
self.analyses = analyses
self.profiles = profiles
# Get subtotals
self.subtotal = context.getSubtotal()
self.subtotalVATAmount = "%.2f" % context.getSubtotalVATAmount()
self.subtotalTotalPrice = "%.2f" % context.getSubtotalTotalPrice()
# Get totals
self.memberDiscount = Decimal(context.getDefaultMemberDiscount())
self.discountAmount = context.getDiscountAmount()
self.VATAmount = "%.2f" % context.getVATAmount()
self.totalPrice = "%.2f" % context.getTotalPrice()
# Render the template
return self.template()
def __call__(self):
bsc = getToolByName(self.context, 'bika_setup_catalog')
bac = getToolByName(self.context, 'bika_analysis_catalog')
self.report_content = {}
parms = []
headings = {}
headings['header'] = _("Analyses out of range")
headings['subheader'] = _("Analyses results out of specified range")
count_all = 0
query = {"portal_type": "Analysis", "sort_order": "reverse"}
spec_uid = self.request.form.get("spec", False)
spec_obj = None
spec_title = ""
if spec_uid:
brains = bsc(UID=spec_uid)
if brains:
spec_obj = brains[0].getObject()
spec_title = spec_obj.Title()
parms.append({
"title": _("Range spec"),
"value": spec_title,
"type": "text"
})
date_query = formatDateQuery(self.context, 'Received')
if date_query:
query['getDateReceived'] = date_query
received = formatDateParms(self.context, 'Received')
else:
received = 'Undefined'
parms.append({
'title': _('Received'),
'value': received,
'type': 'text'
})
wf_tool = getToolByName(self.context, 'portal_workflow')
if self.request.form.has_key('bika_analysis_workflow'):
query['review_state'] = self.request.form['bika_analysis_workflow']
review_state = wf_tool.getTitleForStateOnType(
self.request.form['bika_analysis_workflow'], 'Analysis')
else:
review_state = 'Undefined'
parms.append({
'title': _('Status'),
'value': review_state,
'type': 'text'
})
if self.request.form.has_key('bika_cancellation_workflow'):
query['cancellation_state'] = self.request.form[
'bika_cancellation_workflow']
cancellation_state = wf_tool.getTitleForStateOnType(
self.request.form['bika_cancellation_workflow'], 'Analysis')
else:
cancellation_state = 'Undefined'
parms.append({
'title': _('Active'),
'value': cancellation_state,
'type': 'text'
})
if self.request.form.has_key('bika_worksheetanalysis_workflow'):
query['worksheetanalysis_review_state'] = self.request.form[
'bika_worksheetanalysis_workflow']
ws_review_state = wf_tool.getTitleForStateOnType(
self.request.form['bika_worksheetanalysis_workflow'],
'Analysis')
else:
ws_review_state = 'Undefined'
parms.append({
'title': _('Assigned to worksheet'),
'value': ws_review_state,
'type': 'text'
})
# and now lets do the actual report lines
col_heads = [
_('Client'),
_('Request'),
_('Sample type'),
_('Sample point'),
_('Category'),
_('Analysis'),
_('Result'),
_('Min'),
_('Max'),
_('Status'),
]
if isAttributeHidden('Sample', 'SamplePoint'):
col_heads.remove(_('Sample point'))
formats = {
'columns': 10,
'col_heads': col_heads,
'class': '',
}
datalines = []
for a_proxy in bac(query):
analysis = a_proxy.getObject()
if analysis.getResult():
try:
result = float(analysis.getResult())
except:
continue
else:
continue
keyword = analysis.getKeyword()
# determine which specs to use for this particular analysis
# 1) if a spec is given in the query form, use it.
# 2) if a spec is entered directly on the analysis, use it.
# otherwise just continue to the next object.
spec_dict = False
if spec_obj:
rr = spec_obj.getResultsRangeDict()
if keyword in rr:
spec_dict = rr[keyword]
else:
ar = analysis.aq_parent
rr = dicts_to_dict(ar.getResultsRange(), 'keyword')
if keyword in rr:
spec_dict = rr[keyword]
else:
continue
if not spec_dict:
continue
try:
spec_min = float(spec_dict['min'])
spec_max = float(spec_dict['max'])
except ValueError:
continue
if spec_min <= result <= spec_max:
continue
# check if in shoulder: out of range, but in acceptable
# error percentage
shoulder = False
error = 0
try:
error = float(spec_dict.get('error', '0'))
except:
error = 0
pass
error_amount = (result / 100) * error
error_min = result - error_amount
error_max = result + error_amount
if ((result < spec_min) and (error_max >= spec_min)) or \
((result > spec_max) and (error_min <= spec_max)):
shoulder = True
dataline = []
dataitem = {'value': analysis.getClientTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getRequestID()}
dataline.append(dataitem)
dataitem = {'value': analysis.aq_parent.getSampleTypeTitle()}
dataline.append(dataitem)
if isAttributeHidden('Sample', 'SamplePoint'):
dataitem = {'value': analysis.aq_parent.getSamplePointTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getCategoryTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getServiceTitle()}
dataline.append(dataitem)
if shoulder:
dataitem = {
'value': analysis.getResult(),
'img_after': '++resource++bika.lims.images/exclamation.png'
}
else:
dataitem = {'value': analysis.getResult()}
dataline.append(dataitem)
dataitem = {'value': spec_dict['min']}
dataline.append(dataitem)
dataitem = {'value': spec_dict['max']}
dataline.append(dataitem)
state = wf_tool.getInfoFor(analysis, 'review_state', '')
review_state = wf_tool.getTitleForStateOnType(state, 'Analysis')
dataitem = {'value': review_state}
dataline.append(dataitem)
datalines.append(dataline)
count_all += 1
# table footer data
footlines = []
footline = []
footitem = {
'value': _('Number of analyses out of range for period'),
'colspan': 9,
'class': 'total_label'
}
footline.append(footitem)
footitem = {'value': count_all}
footline.append(footitem)
footlines.append(footline)
# report footer data
footnotes = []
footline = []
footitem = {
'value': _('Analysis result within error range'),
'img_before': '++resource++bika.lims.images/exclamation.png'
}
footline.append(footitem)
footnotes.append(footline)
self.report_content = {
'headings': headings,
'parms': parms,
'formats': formats,
'datalines': datalines,
'footings': footlines,
'footnotes': footnotes
}
title = t(headings['header'])
return {'report_title': title, 'report_data': self.template()}
def set(self, instance, value, **kwargs):
""" Mutator. """
rc = getToolByName(instance, REFERENCE_CATALOG)
targetUIDs = [
ref.targetUID
for ref in rc.getReferences(instance, self.relationship)
]
# empty value
if not value:
value = ()
# list with one empty item
if type(value) in (list, tuple) and len(value) == 1 and not value[0]:
value = ()
if not value and not targetUIDs:
return
if not isinstance(value, (list, tuple)):
value = value,
elif not self.multiValued and len(value) > 1:
raise ValueError(
"Multiple values given for single valued field %r" % self)
ts = getToolByName(instance, "translation_service").translate
#convert objects to uids
#convert uids to objects
uids = []
targets = {}
for v in value:
if isinstance(v, basestring):
uids.append(v)
targets[v] = rc.lookupObject(v)
elif hasattr(v, 'UID'):
target_uid = callable(v.UID) and v.UID() or v.UID
uids.append(target_uid)
targets[target_uid] = v
else:
logger.info("Target has no UID: %s/%s" % (v, value))
sub = [t for t in targetUIDs if t not in uids]
add = [v for v in uids if v and v not in targetUIDs]
newuids = [t for t in list(targetUIDs) + list(uids) if t not in sub]
for uid in newuids:
# update version_id of all existing references that aren't
# about to be removed anyway (contents of sub)
version_id = hasattr(targets[uid], 'version_id') and \
targets[uid].version_id or None
if version_id is None:
# attempt initial save of unversioned targets
pr = getToolByName(instance, 'portal_repository')
if pr.isVersionable(targets[uid]):
pr.save(obj=targets[uid],
comment=to_utf8(ts(_("Initial revision"))))
if not hasattr(instance, 'reference_versions'):
instance.reference_versions = {}
if not hasattr(targets[uid], 'version_id'):
targets[uid].version_id = None
instance.reference_versions[uid] = targets[uid].version_id
# tweak keyword arguments for addReference
addRef_kw = kwargs.copy()
addRef_kw.setdefault('referenceClass', self.referenceClass)
if 'schema' in addRef_kw:
del addRef_kw['schema']
for uid in add:
__traceback_info__ = (instance, uid, value, targetUIDs)
# throws IndexError if uid is invalid
rc.addReference(instance, uid, self.relationship, **addRef_kw)
for uid in sub:
rc.deleteReference(instance, uid, self.relationship)
if self.referencesSortable:
if not hasattr(aq_base(instance), 'at_ordered_refs'):
instance.at_ordered_refs = {}
instance.at_ordered_refs[self.relationship] = \
tuple(filter(None, uids))
if self.callStorageOnSet:
#if this option is set the reference fields's values get written
#to the storage even if the reference field never use the storage
#e.g. if i want to store the reference UIDs into an SQL field
ObjectField.set(self, instance, self.getRaw(instance), **kwargs)
def __call__(self):
# get all the data into datalines
pc = getToolByName(self.context, 'portal_catalog')
rc = getToolByName(self.context, 'reference_catalog')
self.report_content = {}
parms = []
headings = {}
headings['header'] = _("Attachments")
headings['subheader'] = _(
"The attachments linked to analysis requests and analyses")
count_all = 0
query = {'portal_type': 'Attachment'}
if 'ClientUID' in self.request.form:
client_uid = self.request.form['ClientUID']
query['getClientUID'] = client_uid
client = rc.lookupObject(client_uid)
client_title = client.Title()
else:
client = logged_in_client(self.context)
if client:
client_title = client.Title()
query['getClientUID'] = client.UID()
else:
client_title = 'All'
parms.append(
{'title': _('Client'),
'value': client_title,
'type': 'text'})
date_query = formatDateQuery(self.context, 'Loaded')
if date_query:
query['getDateLoaded'] = date_query
loaded = formatDateParms(self.context, 'Loaded')
parms.append(
{'title': _('Loaded'),
'value': loaded,
'type': 'text'})
# and now lets do the actual report lines
formats = {'columns': 6,
'col_heads': [_('Request'),
_('File'),
_('Attachment type'),
_('Content type'),
_('Size'),
_('Loaded'),
],
'class': '',
}
datalines = []
attachments = pc(query)
for a_proxy in attachments:
attachment = a_proxy.getObject()
attachment_file = attachment.getAttachmentFile()
icon = attachment_file.getBestIcon()
filename = attachment_file.filename
filesize = attachment_file.get_size()
filesize = filesize / 1024
sizeunit = "Kb"
if filesize > 1024:
filesize = filesize / 1024
sizeunit = "Mb"
dateloaded = attachment.getDateLoaded()
dataline = []
dataitem = {'value': attachment.getTextTitle()}
dataline.append(dataitem)
dataitem = {'value': filename,
'img_before': icon}
dataline.append(dataitem)
dataitem = {
'value': attachment.getAttachmentType().Title() if attachment.getAttachmentType() else ''}
dataline.append(dataitem)
dataitem = {
'value': self.context.lookupMime(attachment_file.getContentType())}
dataline.append(dataitem)
dataitem = {'value': '%s%s' % (filesize, sizeunit)}
dataline.append(dataitem)
dataitem = {'value': self.ulocalized_time(dateloaded)}
dataline.append(dataitem)
datalines.append(dataline)
count_all += 1
# footer data
footlines = []
footline = []
footitem = {'value': _('Total'),
'colspan': 5,
'class': 'total_label'}
footline.append(footitem)
footitem = {'value': count_all}
footline.append(footitem)
footlines.append(footline)
self.report_content = {
'headings': headings,
'parms': parms,
'formats': formats,
'datalines': datalines,
'footings': footlines}
if self.request.get('output_format', '') == 'CSV':
import csv
import StringIO
import datetime
fieldnames = [
_('Request'),
_('File'),
_('Attachment type'),
_('Content type'),
_('Size'),
_('Loaded'),
]
output = StringIO.StringIO()
dw = csv.DictWriter(output, fieldnames=fieldnames)
dw.writerow(dict((fn, fn) for fn in fieldnames))
for row in datalines:
dw.writerow(row)
report_data = output.getvalue()
output.close()
date = datetime.datetime.now().strftime("%Y%m%d%H%M")
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader("Content-Disposition",
"attachment;filename=\"analysesattachments_%s.csv\"" % date)
self.request.RESPONSE.write(report_data)
else:
return {'report_title': t(headings['header']),
'report_data': self.template()}
def __call__(self):
# get all the data into datalines
pc = getToolByName(self.context, 'portal_catalog')
bac = getToolByName(self.context, 'bika_analysis_catalog')
bc = getToolByName(self.context, 'bika_catalog')
rc = getToolByName(self.context, 'reference_catalog')
self.report_content = {}
parm_lines = {}
parms = []
headings = {}
count_all_ars = 0
count_all_analyses = 0
query = {}
this_client = logged_in_client(self.context)
if not this_client and 'ClientUID' in self.request.form:
client_uid = self.request.form['ClientUID']
this_client = rc.lookupObject(client_uid)
parms.append({
'title': _('Client'),
'value': this_client.Title(),
'type': 'text'
})
if this_client:
headings['header'] = _("Analysis requests and analyses")
headings['subheader'] = _(
"Number of Analysis requests and analyses")
else:
headings['header'] = _("Analysis requests and analyses per client")
headings['subheader'] = _(
"Number of Analysis requests and analyses per client")
date_query = formatDateQuery(self.context, 'Requested')
if date_query:
query['created'] = date_query
requested = formatDateParms(self.context, 'Requested')
parms.append({
'title': _('Requested'),
'value': requested,
'type': 'text'
})
workflow = getToolByName(self.context, 'portal_workflow')
if 'bika_analysis_workflow' in self.request.form:
query['review_state'] = self.request.form['bika_analysis_workflow']
review_state = workflow.getTitleForStateOnType(
self.request.form['bika_analysis_workflow'], 'Analysis')
parms.append({
'title': _('Status'),
'value': review_state,
'type': 'text'
})
if 'bika_cancellation_workflow' in self.request.form:
query['cancellation_state'] = self.request.form[
'bika_cancellation_workflow']
cancellation_state = workflow.getTitleForStateOnType(
self.request.form['bika_cancellation_workflow'], 'Analysis')
parms.append({
'title': _('Active'),
'value': cancellation_state,
'type': 'text'
})
if 'bika_worksheetanalysis_workflow' in self.request.form:
query['worksheetanalysis_review_state'] = self.request.form[
'bika_worksheetanalysis_workflow']
ws_review_state = workflow.getTitleForStateOnType(
self.request.form['bika_worksheetanalysis_workflow'],
'Analysis')
parms.append({
'title': _('Assigned to worksheet'),
'value': ws_review_state,
'type': 'text'
})
if 'bika_worksheetanalysis_workflow' in self.request.form:
query['worksheetanalysis_review_state'] = self.request.form[
'bika_worksheetanalysis_workflow']
ws_review_state = workflow.getTitleForStateOnType(
self.request.form['bika_worksheetanalysis_workflow'],
'Analysis')
parms.append({
'title': _('Assigned to worksheet'),
'value': ws_review_state,
'type': 'text'
})
# and now lets do the actual report lines
formats = {
'columns':
3,
'col_heads':
[_('Client'),
_('Number of requests'),
_('Number of analyses')],
'class':
''
}
datalines = []
if this_client:
c_proxies = pc(portal_type="Client", UID=this_client.UID())
else:
c_proxies = pc(portal_type="Client", sort_on='sortable_title')
for client in c_proxies:
query['getClientUID'] = client.UID
dataline = [
{
'value': client.Title
},
]
query['portal_type'] = 'AnalysisRequest'
ars = bc(query)
count_ars = len(ars)
dataitem = {'value': count_ars}
dataline.append(dataitem)
query['portal_type'] = 'Analysis'
analyses = bac(query)
count_analyses = len(analyses)
dataitem = {'value': count_analyses}
dataline.append(dataitem)
datalines.append(dataline)
count_all_analyses += count_analyses
count_all_ars += count_ars
# footer data
footlines = []
if not this_client:
footline = []
footitem = {'value': _('Total'), 'class': 'total_label'}
footline.append(footitem)
footitem = {'value': count_all_ars}
footline.append(footitem)
footitem = {'value': count_all_analyses}
footline.append(footitem)
footlines.append(footline)
self.report_content = {
'headings': headings,
'parms': parms,
'formats': formats,
'datalines': datalines,
'footings': footlines
}
if self.request.get('output_format', '') == 'CSV':
import csv
import StringIO
import datetime
fieldnames = [
'Client',
'Analysis Requests',
'Analyses',
]
output = StringIO.StringIO()
dw = csv.DictWriter(output,
extrasaction='ignore',
fieldnames=fieldnames)
dw.writerow(dict((fn, fn) for fn in fieldnames))
for row in datalines:
dw.writerow({
'Client': row[0]['value'],
'Analysis Requests': row[1]['value'],
'Analyses': row[2]['value'],
})
report_data = output.getvalue()
output.close()
date = datetime.datetime.now().strftime("%Y%m%d%H%M")
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader(
"Content-Disposition",
"attachment;filename=\"analysesperclient_%s.csv\"" % date)
self.request.RESPONSE.write(report_data)
else:
return {
'report_title': t(headings['header']),
'report_data': self.template()
}
def ObjectModifiedEventHandler(obj, event):
""" Various types need automation on edit.
"""
if not hasattr(obj, 'portal_type'):
return
if obj.portal_type == 'Calculation':
pr = getToolByName(obj, 'portal_repository')
uc = getToolByName(obj, 'uid_catalog')
obj = uc(UID=obj.UID())[0].getObject()
backrefs = obj.getBackReferences('AnalysisServiceCalculation')
for i, target in enumerate(backrefs):
target = uc(UID=target.UID())[0].getObject()
pr.save(obj=target,
comment="Calculation updated to version %s" %
(obj.version_id + 1, ))
reference_versions = getattr(target, 'reference_versions', {})
reference_versions[obj.UID()] = obj.version_id + 1
target.reference_versions = reference_versions
backrefs = obj.getBackReferences('MethodCalculation')
for i, target in enumerate(backrefs):
target = uc(UID=target.UID())[0].getObject()
pr.save(obj=target,
comment="Calculation updated to version %s" %
(obj.version_id + 1, ))
reference_versions = getattr(target, 'reference_versions', {})
reference_versions[obj.UID()] = obj.version_id + 1
target.reference_versions = reference_versions
elif obj.portal_type == 'Client':
mp = obj.manage_permission
mp(permissions.ListFolderContents, [
'Manager', 'LabManager', 'LabClerk', 'Analyst', 'Sampler',
'Preserver', 'Owner'
], 0)
mp(permissions.View, [
'Manager', 'LabManager', 'LabClerk', 'Analyst', 'Sampler',
'Preserver', 'Owner'
], 0)
mp(permissions.ModifyPortalContent, ['Manager', 'LabManager', 'Owner'],
0)
mp(AddSupplyOrder, ['Manager', 'LabManager', 'Owner'], 0)
mp('Access contents information', [
'Manager', 'LabManager', 'Member', 'LabClerk', 'Analyst',
'Sampler', 'Preserver', 'Owner'
], 0)
elif obj.portal_type == 'Contact':
mp = obj.manage_permission
mp(permissions.View, [
'Manager', 'LabManager', 'LabClerk', 'Owner', 'Analyst', 'Sampler',
'Preserver'
], 0)
mp(permissions.ModifyPortalContent, ['Manager', 'LabManager', 'Owner'],
0)
elif obj.portal_type == 'AnalysisCategory':
for analysis in obj.getBackReferences(
'AnalysisServiceAnalysisCategory'):
analysis.reindexObject(idxs=[
"getCategoryTitle",
"getCategoryUID",
])
def getDepartments(self):
bsc = getToolByName(self, 'bika_setup_catalog')
deps = []
for d in bsc(portal_type='Department', inactive_state='active'):
deps.append((d.UID, d.Title))
return DisplayList(deps)
def folderitems(self):
rc = getToolByName(self.context, REFERENCE_CATALOG)
wf = getToolByName(self.context, 'portal_workflow')
pr = getToolByName(self.context, 'portal_repository')
isVersionable = pr.isVersionable(aq_inner(self.context))
try:
review_history = wf.getInfoFor(self.context, 'review_history')
review_history = list(review_history)
review_history.reverse()
except WorkflowException:
review_history = []
items = []
for entry in review_history:
# this folderitems doesn't subclass from the bika_listing.py
# so we create items from scratch
review_state = entry.get('review_state')
state_title = wf.getTitleForStateOnType(review_state,
self.context.portal_type)
item = {
'obj': self.context,
'id': self.context.id,
'uid': self.context.UID(),
'title': self.context.title_or_id(),
'type_class': '',
'url': self.context.absolute_url(),
'relative_url': self.context.absolute_url(),
'view_url': self.context.absolute_url(),
'path': "/".join(self.context.getPhysicalPath()),
'replace': {},
'before': {},
'after': {},
'choices': {},
'class': {},
'state_class': '',
'allow_edit': [],
'required': [],
'Version':
isVersionable and self.context.get('version_id', '') or '0',
'Date': self.ulocalized_time(entry.get('time')),
'sortable_date': entry.get('time'),
'User': entry.get('actor'),
'Action': entry.get('action') and entry.get('action')
or 'Create',
'Description': "review state: %s" % state_title,
}
items.append(item)
if isVersionable:
request = TestRequest()
chv = ContentHistoryViewlet(self.context, request, None, None)
chv.navigation_root_url = chv.site_url = 'http://localhost:8080/bikas'
version_history = chv.revisionHistory()
else:
version_history = []
for entry in version_history:
# this folderitems doesn't subclass from the bika_listing.py
# so we create items from scratch
# disregard the first entry of version history, as it is
# represented by the first entry in review_history
if not entry.get('version_id'):
continue
item = {
'obj': self.context,
'id': self.context.id,
'uid': self.context.UID(),
'title': self.context.title_or_id(),
'type_class': '',
'url': self.context.absolute_url(),
'relative_url': self.context.absolute_url(),
'view_url': self.context.absolute_url(),
'path': "/".join(self.context.getPhysicalPath()),
'replace': {},
'before': {},
'after': {},
'choices': {},
'class': {},
'state_class': '',
'allow_edit': [],
'required': [],
'Version': entry.get('version_id'),
'Date': self.ulocalized_time(DateTime(entry.get('time'))),
'sortable_date': entry.get('time'),
'User': entry.get('actor').get('fullname'),
'Action': entry.get('action') and entry.get('action')
or 'Create',
'Description': entry.get('comments'),
}
items.append(item)
items = sorted(items, key=itemgetter('sortable_date'))
items.reverse()
return items
def getDefaultLifetime(self):
""" get the default retention period """
settings = getToolByName(self, 'bika_setup')
return settings.getDefaultSampleLifetime()
def workflow_action_save_analyses_button(self):
form = self.request.form
workflow = getToolByName(self.context, 'portal_workflow')
bsc = self.context.bika_setup_catalog
action, came_from = WorkflowAction._get_form_workflow_action(self)
# AR Manage Analyses: save Analyses
ar = self.context
sample = ar.getSample()
objects = WorkflowAction._get_selected_items(self)
if not objects:
message = _("No analyses have been selected")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url() + "/analyses"
self.request.response.redirect(self.destination_url)
return
Analyses = objects.keys()
prices = form.get("Price", [None])[0]
# Hidden analyses?
# https://jira.bikalabs.com/browse/LIMS-1324
outs = []
hiddenans = form.get('Hidden', {})
for uid in Analyses:
hidden = hiddenans.get(uid, '')
hidden = True if hidden == 'on' else False
outs.append({'uid': uid, 'hidden': hidden})
ar.setAnalysisServicesSettings(outs)
specs = {}
if form.get("min", None):
for service_uid in Analyses:
service = bsc(UID=service_uid)[0].getObject()
keyword = service.getKeyword()
specs[service_uid] = {
"min": form["min"][0][service_uid],
"max": form["max"][0][service_uid],
"error": form["error"][0][service_uid],
"keyword": keyword,
"uid": service_uid,
}
else:
for service_uid in Analyses:
service = bsc(UID=service_uid)[0].getObject()
keyword = service.getKeyword()
specs[service_uid] = {
"min": "",
"max": "",
"error": "",
"keyword": keyword,
"uid": service_uid
}
new = ar.setAnalyses(Analyses, prices=prices, specs=specs.values())
# link analyses and partitions
# If Bika Setup > Analyses > 'Display individual sample
# partitions' is checked, no Partitions available.
# https://github.com/bikalabs/Bika-LIMS/issues/1030
if 'Partition' in form:
for service_uid, service in objects.items():
part_id = form['Partition'][0][service_uid]
part = sample[part_id]
analysis = ar[service.getKeyword()]
analysis.setSamplePartition(part)
analysis.reindexObject()
if new:
for analysis in new:
# if the AR has progressed past sample_received, we need to bring it back.
ar_state = workflow.getInfoFor(ar, 'review_state')
if ar_state in ('attachment_due', 'to_be_verified'):
# Apply to AR only; we don't want this transition to cascade.
ar.REQUEST['workflow_skiplist'].append(
"retract all analyses")
workflow.doActionFor(ar, 'retract')
ar.REQUEST['workflow_skiplist'].remove(
"retract all analyses")
ar_state = workflow.getInfoFor(ar, 'review_state')
# Then we need to forward new analyses state
analysis.updateDueDate()
changeWorkflowState(analysis, 'bika_analysis_workflow',
ar_state)
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
def folderitems(self):
wf = getToolByName(self, 'portal_workflow')
rc = getToolByName(self, REFERENCE_CATALOG)
pm = getToolByName(self.context, "portal_membership")
self.member = pm.getAuthenticatedMember()
roles = self.member.getRoles()
self.restrict_results = 'Manager' not in roles \
and 'LabManager' not in roles \
and 'LabClerk' not in roles \
and 'RegulatoryInspector' not in roles \
and self.context.bika_setup.getRestrictWorksheetUsersAccess()
if self.restrict_results == True:
# Remove 'Mine' button and hide 'Analyst' column
del self.review_states[1] # Mine
self.columns['Analyst']['toggle'] = False
can_manage = pm.checkPermission(ManageWorksheets, self.context)
self.selected_state = self.request.get(
"%s_review_state" % self.form_id, 'default')
items = BikaListingView.folderitems(self)
new_items = []
analyst_choices = []
for a in self.analysts:
analyst_choices.append({
'ResultValue': a,
'ResultText': self.analysts.getValue(a)
})
can_reassign = False
self.allow_edit = self.isEditionAllowed()
for x in range(len(items)):
if not items[x].has_key('obj'):
new_items.append(items[x])
continue
obj = items[x]['obj']
analyst = obj.getAnalyst().strip()
creator = obj.Creator().strip()
items[x]['Analyst'] = analyst
priority = obj.getPriority()
items[x]['Priority'] = ''
instrument = obj.getInstrument()
items[x]['Instrument'] = instrument and instrument.Title() or ''
items[x]['Title'] = obj.Title()
wst = obj.getWorksheetTemplate()
items[x]['Template'] = wst and wst.Title() or ''
if wst:
items[x]['replace']['Template'] = "<a href='%s'>%s</a>" % \
(wst.absolute_url(), wst.Title())
items[x]['getPriority'] = ''
items[x]['CreationDate'] = self.ulocalized_time(obj.creation_date)
nr_analyses = len(obj.getAnalyses())
if nr_analyses == '0':
# give empties pretty classes.
items[x]['table_row_class'] = 'state-empty-worksheet'
layout = obj.getLayout()
if len(layout) > 0:
items[x]['replace']['Title'] = "<a href='%s/manage_results'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
else:
items[x]['replace']['Title'] = "<a href='%s/add_analyses'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
# set Services
ws_services = {}
for slot in [s for s in layout if s['type'] == 'a']:
analysis = rc.lookupObject(slot['analysis_uid'])
service = analysis.getService()
title = service.Title()
if title not in ws_services:
ws_services[title] = "<a href='%s'>%s,</a>" % \
(service.absolute_url(), title)
keys = list(ws_services.keys())
keys.sort()
services = []
for key in keys:
services.append(ws_services[key])
if services:
services[-1] = services[-1].replace(",", "")
items[x]['Services'] = ""
items[x]['replace']['Services'] = " ".join(services)
# set Sample Types
pos_parent = {}
for slot in layout:
# compensate for bad data caused by a stupid bug.
if type(slot['position']) in (list, tuple):
slot['position'] = slot['position'][0]
if slot['position'] == 'new':
continue
if slot['position'] in pos_parent:
continue
pos_parent[slot['position']] = rc.lookupObject(
slot['container_uid'])
sampletypes = {}
blanks = {}
controls = {}
for container in pos_parent.values():
if container.portal_type == 'AnalysisRequest':
sampletypes["<a href='%s'>%s,</a>" % \
(container.getSample().getSampleType().absolute_url(),
container.getSample().getSampleType().Title())] = 1
if container.portal_type == 'ReferenceSample' and container.getBlank(
):
blanks["<a href='%s'>%s,</a>" % \
(container.absolute_url(),
container.Title())] = 1
if container.portal_type == 'ReferenceSample' and not container.getBlank(
):
controls["<a href='%s'>%s,</a>" % \
(container.absolute_url(),
container.Title())] = 1
sampletypes = list(sampletypes.keys())
sampletypes.sort()
blanks = list(blanks.keys())
blanks.sort()
controls = list(controls.keys())
controls.sort()
# remove trailing commas
if sampletypes:
sampletypes[-1] = sampletypes[-1].replace(",", "")
if controls:
controls[-1] = controls[-1].replace(",", "")
else:
if blanks:
blanks[-1] = blanks[-1].replace(",", "")
items[x]['SampleTypes'] = ""
items[x]['replace']['SampleTypes'] = " ".join(sampletypes)
items[x]['QC'] = ""
items[x]['replace']['QC'] = " ".join(blanks + controls)
items[x]['QCTotals'] = ''
# Get all Worksheet QC Analyses
totalQCAnalyses = [
a for a in obj.getAnalyses()
if a.portal_type == 'ReferenceAnalysis'
or a.portal_type == 'DuplicateAnalysis'
]
totalQCSamples = []
# Get all Worksheet QC samples
for analysis in totalQCAnalyses:
if analysis.getSample().UID() not in totalQCSamples:
totalQCSamples.append(analysis.getSample().UID())
# Total QC Samples (Total Routine Analyses)
items[x]['QCTotals'] = str(len(totalQCSamples)) + '(' + str(
len(totalQCAnalyses)) + ')'
totalRoutineAnalyses = [
a for a in obj.getAnalyses() if a not in totalQCAnalyses
]
totalRoutineSamples = []
for analysis in totalRoutineAnalyses:
if analysis.getSample().UID() not in totalRoutineSamples:
totalRoutineSamples.append(analysis.getSample().UID())
# Total Routine Samples (Total Routine Analyses)
items[x]['RoutineTotals'] = str(
len(totalRoutineSamples)) + '(' + str(
len(totalRoutineAnalyses)) + ')'
if items[x]['review_state'] == 'open' \
and self.allow_edit \
and self.restrict_results == False \
and can_manage == True:
items[x]['allow_edit'] = [
'Analyst',
]
items[x]['required'] = [
'Analyst',
]
can_reassign = True
items[x]['choices'] = {'Analyst': analyst_choices}
new_items.append(items[x])
if can_reassign:
for x in range(len(self.review_states)):
if self.review_states[x]['id'] in ['default', 'mine', 'open']:
self.review_states[x]['custom_actions'] = [
{
'id': 'reassign',
'title': _('Reassign')
},
]
self.show_select_column = can_reassign
self.show_workflow_action_buttons = can_reassign
return new_items
def workflow_action_preserve(self):
form = self.request.form
workflow = getToolByName(self.context, 'portal_workflow')
action, came_from = WorkflowAction._get_form_workflow_action(self)
checkPermission = self.context.portal_membership.checkPermission
# Partition Preservation
# the partition table shown in AR and Sample views sends it's
# action button submits here.
objects = WorkflowAction._get_selected_items(self)
transitioned = []
incomplete = []
for obj_uid, obj in objects.items():
part = obj
# can't transition inactive items
if workflow.getInfoFor(part, 'inactive_state', '') == 'inactive':
continue
if not checkPermission(PreserveSample, part):
continue
# grab this object's Preserver and DatePreserved from the form
Preserver = form['getPreserver'][0][obj_uid].strip()
Preserver = Preserver and Preserver or ''
DatePreserved = form['getDatePreserved'][0][obj_uid].strip()
DatePreserved = DatePreserved and DateTime(DatePreserved) or ''
# write them to the sample
part.setPreserver(Preserver)
part.setDatePreserved(DatePreserved)
# transition the object if both values are present
if Preserver and DatePreserved:
workflow.doActionFor(part, action)
transitioned.append(part.id)
else:
incomplete.append(part.id)
part.reindexObject()
part.aq_parent.reindexObject()
message = None
if len(transitioned) > 1:
message = _(
'${items} are waiting to be received.',
mapping={'items': safe_unicode(', '.join(transitioned))})
self.context.plone_utils.addPortalMessage(message, 'info')
elif len(transitioned) == 1:
message = _(
'${item} is waiting to be received.',
mapping={'item': safe_unicode(', '.join(transitioned))})
self.context.plone_utils.addPortalMessage(message, 'info')
if not message:
message = _('No changes made.')
self.context.plone_utils.addPortalMessage(message, 'info')
if len(incomplete) > 1:
message = _('${items} are missing Preserver or Date Preserved',
mapping={'items': safe_unicode(', '.join(incomplete))})
self.context.plone_utils.addPortalMessage(message, 'error')
elif len(incomplete) == 1:
message = _('${item} is missing Preserver or Preservation Date',
mapping={'item': safe_unicode(', '.join(incomplete))})
self.context.plone_utils.addPortalMessage(message, 'error')
self.destination_url = self.request.get_header(
"referer", self.context.absolute_url())
self.request.response.redirect(self.destination_url)
def isEditionAllowed(self):
pm = getToolByName(self.context, "portal_membership")
checkPermission = self.context.portal_membership.checkPermission
return checkPermission(EditWorksheet, self.context)
def workflow_action_submit(self):
form = self.request.form
rc = getToolByName(self.context, REFERENCE_CATALOG)
action, came_from = WorkflowAction._get_form_workflow_action(self)
checkPermission = self.context.portal_membership.checkPermission
if not isActive(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
# calcs.js has kept item_data and form input interim values synced,
# so the json strings from item_data will be the same as the form values
item_data = {}
if 'item_data' in form:
if isinstance(form['item_data'], list):
for i_d in form['item_data']:
for i, d in json.loads(i_d).items():
item_data[i] = d
else:
item_data = json.loads(form['item_data'])
selected_analyses = WorkflowAction._get_selected_items(self)
results = {}
hasInterims = {}
# check that the form values match the database
# save them if not.
for uid, result in self.request.form.get('Result', [{}])[0].items():
# if the AR has ReportDryMatter set, get dry_result from form.
dry_result = ''
if hasattr(self.context, 'getReportDryMatter') \
and self.context.getReportDryMatter():
for k, v in self.request.form['ResultDM'][0].items():
if uid == k:
dry_result = v
break
if uid in selected_analyses:
analysis = selected_analyses[uid]
else:
analysis = rc.lookupObject(uid)
if not analysis:
# ignore result if analysis object no longer exists
continue
results[uid] = result
interimFields = item_data[uid]
if len(interimFields) > 0:
hasInterims[uid] = True
else:
hasInterims[uid] = False
retested = 'retested' in form and uid in form['retested']
remarks = form.get('Remarks', [
{},
])[0].get(uid, '')
# Don't save uneccessary things
# https://github.com/bikalabs/Bika-LIMS/issues/766:
# Somehow, using analysis.edit() fails silently when
# logged in as Analyst.
if analysis.getInterimFields() != interimFields or \
analysis.getRetested() != retested or \
analysis.getRemarks() != remarks:
analysis.setInterimFields(interimFields)
analysis.setRetested(retested)
analysis.setRemarks(remarks)
# save results separately, otherwise capture date is rewritten
if analysis.getResult() != result or \
analysis.getResultDM() != dry_result:
analysis.setResultDM(dry_result)
analysis.setResult(result)
methods = self.request.form.get('Method', [{}])[0]
instruments = self.request.form.get('Instrument', [{}])[0]
analysts = self.request.form.get('Analyst', [{}])[0]
uncertainties = self.request.form.get('Uncertainty', [{}])[0]
dlimits = self.request.form.get('DetectionLimit', [{}])[0]
# discover which items may be submitted
submissable = []
for uid, analysis in selected_analyses.items():
analysis_active = isActive(analysis)
# Need to save the instrument?
if uid in instruments and analysis_active:
# TODO: Add SetAnalysisInstrument permission
# allow_setinstrument = sm.checkPermission(SetAnalysisInstrument)
allow_setinstrument = True
# ---8<-----
if allow_setinstrument == True:
# The current analysis allows the instrument regards
# to its analysis service and method?
if (instruments[uid] == ''):
previnstr = analysis.getInstrument()
if previnstr:
previnstr.removeAnalysis(analysis)
analysis.setInstrument(None)
elif analysis.isInstrumentAllowed(instruments[uid]):
previnstr = analysis.getInstrument()
if previnstr:
previnstr.removeAnalysis(analysis)
analysis.setInstrument(instruments[uid])
instrument = analysis.getInstrument()
instrument.addAnalysis(analysis)
# Need to save the method?
if uid in methods and analysis_active:
# TODO: Add SetAnalysisMethod permission
# allow_setmethod = sm.checkPermission(SetAnalysisMethod)
allow_setmethod = True
# ---8<-----
if allow_setmethod == True and analysis.isMethodAllowed(
methods[uid]):
analysis.setMethod(methods[uid])
# Need to save the analyst?
if uid in analysts and analysis_active:
analysis.setAnalyst(analysts[uid])
# Need to save the uncertainty?
if uid in uncertainties and analysis_active:
analysis.setUncertainty(uncertainties[uid])
# Need to save the detection limit?
if analysis_active:
analysis.setDetectionLimitOperand(dlimits.get(uid, None))
if uid not in results or not results[uid]:
continue
can_submit = True
# guard_submit does a lot of the same stuff, too.
# the code there has also been commented.
# we must find a better way to allow dependencies to control
# this process.
# for dependency in analysis.getDependencies():
# dep_state = workflow.getInfoFor(dependency, 'review_state')
# if hasInterims[uid]:
# if dep_state in ('to_be_sampled', 'to_be_preserved',
# 'sample_due', 'sample_received',
# 'attachment_due', 'to_be_verified',):
# can_submit = False
# break
# else:
# if dep_state in ('to_be_sampled', 'to_be_preserved',
# 'sample_due', 'sample_received',):
# can_submit = False
# break
if can_submit and analysis not in submissable:
submissable.append(analysis)
# and then submit them.
for analysis in submissable:
doActionFor(analysis, 'submit')
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
if checkPermission(EditResults, self.context):
self.destination_url = self.context.absolute_url(
) + "/manage_results"
else:
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
def __init__(self, context, request):
super(ReferenceSamplesView, self).__init__(context, request)
portal = getToolByName(context, 'portal_url').getPortalObject()
self.icon = self.portal_url + "/++resource++bika.lims.images/referencesample_big.png"
self.title = self.context.translate(_("Reference Samples"))
self.description = self.context.translate(
_("All reference samples in the system are displayed here."))
self.catalog = 'bika_catalog'
self.contentFilter = {
'portal_type': 'ReferenceSample',
'sort_on': 'id',
'sort_order': 'reverse',
'path': {
"query": ["/"],
"level": 0
},
}
self.context_actions = {}
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = True
self.pagesize = 50
request.set('disable_border', 1)
self.columns = {
'ID': {
'title': _('ID'),
'index': 'id'
},
'Title': {
'title': _('Title'),
'index': 'sortable_title',
'toggle': True
},
'Supplier': {
'title': _('Supplier'),
'toggle': True
},
'Definition': {
'title': _('Reference Definition'),
'toggle': True
},
'DateSampled': {
'title': _('Date Sampled'),
'index': 'getDateSampled',
'toggle': True
},
'DateReceived': {
'title': _('Date Received'),
'index': 'getDateReceived',
'toggle': True
},
'ExpiryDate': {
'title': _('Expiry Date'),
'index': 'getExpiryDate',
'toggle': True
},
'state_title': {
'title': _('State'),
'toggle': True
},
}
self.review_states = [
{
'id':
'default',
'title':
_('Current'),
'contentFilter': {
'review_state': 'current'
},
'columns': [
'ID', 'Title', 'Supplier', 'Definition', 'DateSampled',
'DateReceived', 'ExpiryDate'
]
},
{
'id':
'expired',
'title':
_('Expired'),
'contentFilter': {
'review_state': 'expired'
},
'columns': [
'ID', 'Title', 'Supplier', 'Definition', 'DateSampled',
'DateReceived', 'ExpiryDate'
]
},
{
'id':
'disposed',
'title':
_('Disposed'),
'contentFilter': {
'review_state': 'disposed'
},
'columns': [
'ID', 'Title', 'Supplier', 'Definition', 'DateSampled',
'DateReceived', 'ExpiryDate'
]
},
{
'id':
'all',
'title':
_('All'),
'contentFilter': {},
'columns': [
'ID', 'Title', 'Supplier', 'Definition', 'DateSampled',
'DateReceived', 'ExpiryDate', 'state_title'
]
},
]
def __call__(self):
wf = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
self.allow_edit = mtool.checkPermission('Modify portal content',
self.context)
return self.template()
def __call__(self):
ar = self.context
workflow = getToolByName(self.context, 'portal_workflow')
if 'transition' in self.request.form:
doActionFor(self.context, self.request.form['transition'])
# Contacts get expanded for view
contact = self.context.getContact()
contacts = []
for cc in self.context.getCCContact():
contacts.append(cc)
if contact in contacts:
contacts.remove(contact)
ccemails = []
for cc in contacts:
ccemails.append(
"%s <<a href='mailto:%s'>%s</a>>" %
(cc.Title(), cc.getEmailAddress(), cc.getEmailAddress()))
# CC Emails become mailto links
emails = self.context.getCCEmails()
if isinstance(emails, str):
emails = emails and [
emails,
] or []
cc_emails = []
cc_hrefs = []
for cc in emails:
cc_emails.append(cc)
cc_hrefs.append("<a href='mailto:%s'>%s</a>" % (cc, cc))
# render header table
self.header_table = HeaderTableView(self.context, self.request)()
# Create Partitions View for this ARs sample
p = SamplePartitionsView(self.context.getSample(), self.request)
p.show_column_toggles = False
self.parts = p.contents_table()
# Create Field and Lab Analyses tables
self.tables = {}
for poc in POINTS_OF_CAPTURE:
if self.context.getAnalyses(getPointOfCapture=poc):
t = self.createAnalysesView(
ar,
self.request,
getPointOfCapture=poc,
show_categories=self.context.bika_setup.
getCategoriseAnalysisServices())
t.allow_edit = True
t.form_id = "%s_analyses" % poc
t.review_states[0]['transitions'] = [{
'id': 'submit'
}, {
'id': 'retract'
}, {
'id': 'verify'
}]
t.show_workflow_action_buttons = True
t.show_select_column = True
if getSecurityManager().checkPermission(EditFieldResults, self.context) \
and poc == 'field':
t.review_states[0]['columns'].remove('DueDate')
self.tables[POINTS_OF_CAPTURE.getValue(
poc)] = t.contents_table()
# Un-captured field analyses may cause confusion
if ar.getAnalyses(getPointOfCapture='field',
review_state=['sampled', 'sample_due']):
message = _("There are field analyses without submitted results.")
self.addMessage(message, 'info')
# Create QC Analyses View for this AR
show_cats = self.context.bika_setup.getCategoriseAnalysisServices()
qcview = self.createQCAnalyesView(ar,
self.request,
show_categories=show_cats)
qcview.allow_edit = False
qcview.show_select_column = False
qcview.show_workflow_action_buttons = False
qcview.form_id = "%s_qcanalyses"
qcview.review_states[0]['transitions'] = [{
'id': 'submit'
}, {
'id': 'retract'
}, {
'id': 'verify'
}]
self.qctable = qcview.contents_table()
# Create the ResultsInterpretation by department view
from dependencies.dependency import ARResultsInterpretationView
self.riview = ARResultsInterpretationView(ar, self.request)
# If a general retracted is done, rise a waring
if workflow.getInfoFor(ar, 'review_state') == 'sample_received':
allstatus = list()
for analysis in ar.getAnalyses():
status = workflow.getInfoFor(analysis.getObject(),
'review_state')
if status not in ['retracted', 'to_be_verified', 'verified']:
allstatus = []
break
else:
allstatus.append(status)
if len(allstatus) > 0:
self.addMessage("General Retract Done", 'warning')
# If is a retracted AR, show the link to child AR and show a warn msg
if workflow.getInfoFor(ar, 'review_state') == 'invalid':
childar = hasattr(ar, 'getChildAnalysisRequest') \
and ar.getChildAnalysisRequest() or None
message = _(
'These results have been withdrawn and are '
'listed here for trace-ability purposes. Please follow '
'the link to the retest')
if childar:
message = (message + " %s.") % childar.getRequestID()
else:
message = message + "."
self.addMessage(message, 'warning')
# If is an AR automatically generated due to a Retraction, show it's
# parent AR information
if hasattr(ar, 'getParentAnalysisRequest') \
and ar.getParentAnalysisRequest():
par = ar.getParentAnalysisRequest()
message = _(
'This Analysis Request has been '
'generated automatically due to '
'the retraction of the Analysis '
'Request ${retracted_request_id}.',
mapping={'retracted_request_id': par.getRequestID()})
self.addMessage(message, 'info')
self.renderMessages()
return self.template()
def __init__(self, context, request, **kwargs):
self.catalog = "bika_analysis_catalog"
self.contentFilter = dict(kwargs)
self.contentFilter['portal_type'] = 'Analysis'
self.contentFilter['sort_on'] = 'sortable_title'
self.context_actions = {}
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = False
self.show_column_toggles = False
self.pagesize = 999999
self.form_id = 'analyses_form'
self.portal = getToolByName(context, 'portal_url').getPortalObject()
self.portal_url = self.portal.absolute_url()
request.set('disable_plone.rightcolumn', 1)
# each editable item needs it's own allow_edit
# which is a list of field names.
self.allow_edit = False
self.columns = {
'Service': {
'title': _('Analysis'),
'sortable': False},
'Partition': {
'title': _("Partition"),
'sortable':False},
'Method': {
'title': _('Method'),
'sortable': False,
'toggle': True},
'Instrument': {
'title': _('Instrument'),
'sortable': False,
'toggle': True},
'Analyst': {
'title': _('Analyst'),
'sortable': False,
'toggle': True},
'state_title': {
'title': _('Status'),
'sortable': False},
'DetectionLimit': {
'title': _('DL'),
'sortable': False,
'toggle': False},
'Result': {
'title': _('Result'),
'input_width': '6',
'input_class': 'ajax_calculate numeric',
'sortable': False},
'Specification': {
'title': _('Specification'),
'sortable': False},
'ResultDM': {
'title': _('Dry'),
'sortable': False},
'Uncertainty': {
'title': _('+-'),
'sortable': False},
'retested': {
'title': "<img title='%s' src='%s/++resource++bika.lims.images/retested.png'/>"%\
(t(_('Retested')), self.portal_url),
'type':'boolean',
'sortable': False},
'Attachments': {
'title': _('Attachments'),
'sortable': False},
'CaptureDate': {
'title': _('Captured'),
'index': 'getResultCaptureDate',
'sortable':False},
'DueDate': {
'title': _('Due Date'),
'index': 'getDueDate',
'sortable':False},
}
self.review_states = [
{
'id':
'default',
'title':
_('All'),
'contentFilter': {},
'columns': [
'Service', 'Partition', 'DetectionLimit', 'Result',
'Specification', 'Method', 'Instrument', 'Analyst',
'Uncertainty', 'CaptureDate', 'DueDate', 'state_title'
]
},
]
if not context.bika_setup.getShowPartitions():
self.review_states[0]['columns'].remove('Partition')
super(AnalysesView, self).__init__(
context,
request,
show_categories=context.bika_setup.getCategoriseAnalysisServices(),
expand_all_categories=True)
def setupCatalogs(self, portal):
# an item should belong to only one catalog.
# that way looking it up means first looking up *the* catalog
# in which it is indexed, as well as making it cheaper to index.
def addIndex(cat, *args):
try:
cat.addIndex(*args)
except:
pass
def addColumn(cat, col):
try:
cat.addColumn(col)
except:
pass
# create lexicon
wordSplitter = Empty()
wordSplitter.group = 'Word Splitter'
wordSplitter.name = 'Unicode Whitespace splitter'
caseNormalizer = Empty()
caseNormalizer.group = 'Case Normalizer'
caseNormalizer.name = 'Unicode Case Normalizer'
stopWords = Empty()
stopWords.group = 'Stop Words'
stopWords.name = 'Remove listed and single char words'
elem = [wordSplitter, caseNormalizer, stopWords]
zc_extras = Empty()
zc_extras.index_type = 'Okapi BM25 Rank'
zc_extras.lexicon_id = 'Lexicon'
# bika_analysis_catalog
bac = getToolByName(portal, 'bika_analysis_catalog', None)
if bac == None:
logger.warning('Could not find the bika_analysis_catalog tool.')
return
try:
bac.manage_addProduct['ZCTextIndex'].manage_addLexicon(
'Lexicon', 'Lexicon', elem)
except:
logger.warning(
'Could not add ZCTextIndex to bika_analysis_catalog')
pass
at = getToolByName(portal, 'archetype_tool')
at.setCatalogsByType('Analysis', ['bika_analysis_catalog'])
at.setCatalogsByType('ReferenceAnalysis', ['bika_analysis_catalog'])
at.setCatalogsByType('DuplicateAnalysis', ['bika_analysis_catalog'])
addIndex(bac, 'path', 'ExtendedPathIndex', ('getPhysicalPath'))
addIndex(bac, 'allowedRolesAndUsers', 'KeywordIndex')
addIndex(bac, 'UID', 'FieldIndex')
addIndex(bac, 'Title', 'FieldIndex')
addIndex(bac, 'Description', 'ZCTextIndex', zc_extras)
addIndex(bac, 'id', 'FieldIndex')
addIndex(bac, 'Type', 'FieldIndex')
addIndex(bac, 'portal_type', 'FieldIndex')
addIndex(bac, 'created', 'DateIndex')
addIndex(bac, 'Creator', 'FieldIndex')
addIndex(bac, 'title', 'FieldIndex', 'Title')
addIndex(bac, 'sortable_title', 'FieldIndex')
addIndex(bac, 'description', 'FieldIndex', 'Description')
addIndex(bac, 'review_state', 'FieldIndex')
addIndex(bac, 'worksheetanalysis_review_state', 'FieldIndex')
addIndex(bac, 'cancellation_state', 'FieldIndex')
addIndex(bac, 'getDueDate', 'DateIndex')
addIndex(bac, 'getDateSampled', 'DateIndex')
addIndex(bac, 'getDateReceived', 'DateIndex')
addIndex(bac, 'getResultCaptureDate', 'DateIndex')
addIndex(bac, 'getDateAnalysisPublished', 'DateIndex')
addIndex(bac, 'getClientUID', 'FieldIndex')
addIndex(bac, 'getAnalyst', 'FieldIndex')
addIndex(bac, 'getClientTitle', 'FieldIndex')
addIndex(bac, 'getRequestID', 'FieldIndex')
addIndex(bac, 'getClientOrderNumber', 'FieldIndex')
addIndex(bac, 'getKeyword', 'FieldIndex')
addIndex(bac, 'getServiceTitle', 'FieldIndex')
addIndex(bac, 'getServiceUID', 'FieldIndex')
addIndex(bac, 'getCategoryUID', 'FieldIndex')
addIndex(bac, 'getCategoryTitle', 'FieldIndex')
addIndex(bac, 'getPointOfCapture', 'FieldIndex')
addIndex(bac, 'getDateReceived', 'DateIndex')
addIndex(bac, 'getResultCaptureDate', 'DateIndex')
addIndex(bac, 'getSampleTypeUID', 'FieldIndex')
addIndex(bac, 'getSamplePointUID', 'FieldIndex')
addIndex(bac, 'getRawSamplePoints', 'KeywordsIndex')
addIndex(bac, 'getRawSampleTypes', 'KeywordIndex')
addIndex(bac, 'getRetested', 'FieldIndex')
addIndex(bac, 'getReferenceAnalysesGroupID', 'FieldIndex')
addColumn(bac, 'path')
addColumn(bac, 'UID')
addColumn(bac, 'id')
addColumn(bac, 'Type')
addColumn(bac, 'portal_type')
addColumn(bac, 'getObjPositionInParent')
addColumn(bac, 'Title')
addColumn(bac, 'Description')
addColumn(bac, 'title')
addColumn(bac, 'sortable_title')
addColumn(bac, 'description')
addColumn(bac, 'review_state')
addColumn(bac, 'cancellation_state')
addColumn(bac, 'getRequestID')
addColumn(bac, 'getReferenceAnalysesGroupID')
addColumn(bac, 'getResultCaptureDate')
addColumn(bac, 'Priority')
# bika_catalog
bc = getToolByName(portal, 'bika_catalog', None)
if bc == None:
logger.warning('Could not find the bika_catalog tool.')
return
try:
bc.manage_addProduct['ZCTextIndex'].manage_addLexicon(
'Lexicon', 'Lexicon', elem)
except:
logger.warning('Could not add ZCTextIndex to bika_catalog')
pass
at = getToolByName(portal, 'archetype_tool')
at.setCatalogsByType('Batch', ['bika_catalog', 'portal_catalog'])
at.setCatalogsByType('AnalysisRequest',
['bika_catalog', 'portal_catalog'])
at.setCatalogsByType('Sample', ['bika_catalog', 'portal_catalog'])
at.setCatalogsByType('SamplePartition',
['bika_catalog', 'portal_catalog'])
at.setCatalogsByType('ReferenceSample',
['bika_catalog', 'portal_catalog'])
at.setCatalogsByType('Report', [
'bika_catalog',
])
at.setCatalogsByType('Worksheet', ['bika_catalog', 'portal_catalog'])
addIndex(bc, 'path', 'ExtendedPathIndex', ('getPhysicalPath'))
addIndex(bc, 'allowedRolesAndUsers', 'KeywordIndex')
addIndex(bc, 'UID', 'FieldIndex')
addIndex(bc, 'SearchableText', 'ZCTextIndex', zc_extras)
addIndex(bc, 'Title', 'ZCTextIndex', zc_extras)
addIndex(bc, 'Description', 'ZCTextIndex', zc_extras)
addIndex(bc, 'id', 'FieldIndex')
addIndex(bc, 'getId', 'FieldIndex')
addIndex(bc, 'Type', 'FieldIndex')
addIndex(bc, 'portal_type', 'FieldIndex')
addIndex(bc, 'created', 'DateIndex')
addIndex(bc, 'Creator', 'FieldIndex')
addIndex(bc, 'getObjPositionInParent', 'GopipIndex')
addIndex(bc, 'title', 'FieldIndex', 'Title')
addIndex(bc, 'sortable_title', 'FieldIndex')
addIndex(bc, 'description', 'FieldIndex', 'Description')
addIndex(bc, 'review_state', 'FieldIndex')
addIndex(bc, 'inactive_state', 'FieldIndex')
addIndex(bc, 'worksheetanalysis_review_state', 'FieldIndex')
addIndex(bc, 'cancellation_state', 'FieldIndex')
addIndex(bc, 'getAnalysisCategory', 'KeywordIndex')
addIndex(bc, 'getAnalysisService', 'KeywordIndex')
addIndex(bc, 'getAnalyst', 'FieldIndex')
addIndex(bc, 'getAnalysts', 'KeywordIndex')
addIndex(bc, 'BatchDate', 'DateIndex')
addIndex(bc, 'getClientOrderNumber', 'FieldIndex')
addIndex(bc, 'getClientReference', 'FieldIndex')
addIndex(bc, 'getClientSampleID', 'FieldIndex')
addIndex(bc, 'getClientTitle', 'FieldIndex')
addIndex(bc, 'getClientUID', 'FieldIndex')
addIndex(bc, 'getContactTitle', 'FieldIndex')
addIndex(bc, 'getDateDisposed', 'DateIndex')
addIndex(bc, 'getDateExpired', 'DateIndex')
addIndex(bc, 'getDateOpened', 'DateIndex')
addIndex(bc, 'getDatePublished', 'DateIndex')
addIndex(bc, 'getDateReceived', 'DateIndex')
addIndex(bc, 'getDateSampled', 'DateIndex')
addIndex(bc, 'getDisposalDate', 'DateIndex')
addIndex(bc, 'getDueDate', 'DateIndex')
addIndex(bc, 'getExpiryDate', 'DateIndex')
addIndex(bc, 'getInvoiced', 'FieldIndex')
addIndex(bc, 'getPreserver', 'FieldIndex')
addIndex(bc, 'getProfilesTitle', 'FieldIndex')
addIndex(bc, 'getReferenceDefinitionUID', 'FieldIndex')
addIndex(bc, 'getRequestID', 'FieldIndex')
addIndex(bc, 'getSampleID', 'FieldIndex')
addIndex(bc, 'getSamplePointTitle', 'FieldIndex')
addIndex(bc, 'getSamplePointUID', 'FieldIndex')
addIndex(bc, 'getSampler', 'FieldIndex')
addIndex(bc, 'getSampleTypeTitle', 'FieldIndex')
addIndex(bc, 'getSampleTypeUID', 'FieldIndex')
addIndex(bc, 'getSampleUID', 'FieldIndex')
addIndex(bc, 'getSamplingDate', 'DateIndex')
addIndex(bc, 'getServiceTitle', 'FieldIndex')
addIndex(bc, 'getWorksheetTemplateTitle', 'FieldIndex')
addIndex(bc, 'Priority', 'FieldIndex')
addIndex(bc, 'BatchUID', 'FieldIndex')
addColumn(bc, 'path')
addColumn(bc, 'UID')
addColumn(bc, 'id')
addColumn(bc, 'Type')
addColumn(bc, 'portal_type')
addColumn(bc, 'creator')
addColumn(bc, 'Created')
addColumn(bc, 'Title')
addColumn(bc, 'Description')
addColumn(bc, 'sortable_title')
addColumn(bc, 'review_state')
addColumn(bc, 'inactive_state')
addColumn(bc, 'cancellation_state')
addColumn(bc, 'getAnalysts')
addColumn(bc, 'getSampleID')
addColumn(bc, 'getRequestID')
addColumn(bc, 'getClientOrderNumber')
addColumn(bc, 'getClientReference')
addColumn(bc, 'getClientSampleID')
addColumn(bc, 'getContactTitle')
addColumn(bc, 'getClientTitle')
addColumn(bc, 'getProfilesTitle')
addColumn(bc, 'getSamplePointTitle')
addColumn(bc, 'getSampleTypeTitle')
addColumn(bc, 'getAnalysisCategory')
addColumn(bc, 'getAnalysisService')
addColumn(bc, 'getDatePublished')
addColumn(bc, 'getDateReceived')
addColumn(bc, 'getDateSampled')
addColumn(bc, 'review_state')
# bika_setup_catalog
bsc = getToolByName(portal, 'bika_setup_catalog', None)
if bsc == None:
logger.warning('Could not find the setup catalog tool.')
return
try:
bsc.manage_addProduct['ZCTextIndex'].manage_addLexicon(
'Lexicon', 'Lexicon', elem)
except:
logger.warning('Could not add ZCTextIndex to bika_setup_catalog')
pass
at = getToolByName(portal, 'archetype_tool')
at.setCatalogsByType('Department', [
'bika_setup_catalog',
])
at.setCatalogsByType('Container', [
'bika_setup_catalog',
])
at.setCatalogsByType('ContainerType', [
'bika_setup_catalog',
])
at.setCatalogsByType('AnalysisCategory', [
'bika_setup_catalog',
])
at.setCatalogsByType('AnalysisService',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('AnalysisSpec', [
'bika_setup_catalog',
])
at.setCatalogsByType('SampleCondition', ['bika_setup_catalog'])
at.setCatalogsByType('SampleMatrix', [
'bika_setup_catalog',
])
at.setCatalogsByType('SampleType',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('SamplePoint',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('StorageLocation',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('SamplingDeviation', [
'bika_setup_catalog',
])
at.setCatalogsByType('Instrument', [
'bika_setup_catalog',
])
at.setCatalogsByType('InstrumentType', [
'bika_setup_catalog',
])
at.setCatalogsByType('Method',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('Multifile', ['bika_setup_catalog'])
at.setCatalogsByType('AttachmentType', [
'bika_setup_catalog',
])
at.setCatalogsByType('Calculation',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('AnalysisProfile',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('ARTemplate',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('LabProduct',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('LabContact',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('Manufacturer',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('Preservation', [
'bika_setup_catalog',
])
at.setCatalogsByType('ReferenceDefinition',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('SRTemplate',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('SubGroup', [
'bika_setup_catalog',
])
at.setCatalogsByType('Supplier',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('Unit', [
'bika_setup_catalog',
])
at.setCatalogsByType('WorksheetTemplate',
['bika_setup_catalog', 'portal_catalog'])
at.setCatalogsByType('BatchLabel', [
'bika_setup_catalog',
])
at.setCatalogsByType('ARPriority', [
'bika_setup_catalog',
])
addIndex(bsc, 'path', 'ExtendedPathIndex', ('getPhysicalPath'))
addIndex(bsc, 'allowedRolesAndUsers', 'KeywordIndex')
addIndex(bsc, 'UID', 'FieldIndex')
addIndex(bsc, 'SearchableText', 'ZCTextIndex', zc_extras)
addIndex(bsc, 'Title', 'ZCTextIndex', zc_extras)
addIndex(bsc, 'Description', 'ZCTextIndex', zc_extras)
addIndex(bsc, 'id', 'FieldIndex')
addIndex(bsc, 'getId', 'FieldIndex')
addIndex(bsc, 'Type', 'FieldIndex')
addIndex(bsc, 'portal_type', 'FieldIndex')
addIndex(bsc, 'created', 'DateIndex')
addIndex(bsc, 'Creator', 'FieldIndex')
addIndex(bsc, 'getObjPositionInParent', 'GopipIndex')
addIndex(bsc, 'title', 'FieldIndex', 'Title')
addIndex(bsc, 'sortable_title', 'FieldIndex')
addIndex(bsc, 'description', 'FieldIndex', 'Description')
addIndex(bsc, 'review_state', 'FieldIndex')
addIndex(bsc, 'inactive_state', 'FieldIndex')
addIndex(bsc, 'cancellation_state', 'FieldIndex')
addIndex(bsc, 'getAccredited', 'FieldIndex')
addIndex(bsc, 'getAnalyst', 'FieldIndex')
addIndex(bsc, 'getInstrumentType', 'FieldIndex')
addIndex(bsc, 'getInstrumentTypeName', 'FieldIndex')
addIndex(bsc, 'getBlank', 'FieldIndex')
addIndex(bsc, 'getCalculationTitle', 'FieldIndex')
addIndex(bsc, 'getCalculationUID', 'FieldIndex')
addIndex(bsc, 'getCalibrationExpiryDate', 'FieldIndex')
addIndex(bsc, 'getCategoryTitle', 'FieldIndex')
addIndex(bsc, 'getCategoryUID', 'FieldIndex')
addIndex(bsc, 'getClientUID', 'FieldIndex')
addIndex(bsc, 'getDepartmentTitle', 'FieldIndex')
addIndex(bsc, 'getDuplicateVariation', 'FieldIndex')
addIndex(bsc, 'getFormula', 'FieldIndex')
addIndex(bsc, 'getFullname', 'FieldIndex')
addIndex(bsc, 'getHazardous', 'FieldIndex')
addIndex(bsc, 'getInstrumentTitle', 'FieldIndex')
addIndex(bsc, 'getKeyword', 'FieldIndex')
addIndex(bsc, 'getManagerName', 'FieldIndex')
addIndex(bsc, 'getManagerPhone', 'FieldIndex')
addIndex(bsc, 'getManagerEmail', 'FieldIndex')
addIndex(bsc, 'getMaxTimeAllowed', 'FieldIndex')
addIndex(bsc, 'getModel', 'FieldIndex')
addIndex(bsc, 'getName', 'FieldIndex')
addIndex(bsc, 'getPointOfCapture', 'FieldIndex')
addIndex(bsc, 'getPrice', 'FieldIndex')
addIndex(bsc, 'getSamplePointTitle', 'KeywordIndex')
addIndex(bsc, 'getSamplePointUID', 'FieldIndex')
addIndex(bsc, 'getSampleTypeTitle', 'KeywordIndex')
addIndex(bsc, 'getSampleTypeUID', 'FieldIndex')
addIndex(bsc, 'getServiceTitle', 'FieldIndex')
addIndex(bsc, 'getServiceUID', 'FieldIndex')
addIndex(bsc, 'getTotalPrice', 'FieldIndex')
addIndex(bsc, 'getUnit', 'FieldIndex')
addIndex(bsc, 'getVATAmount', 'FieldIndex')
addIndex(bsc, 'getVolume', 'FieldIndex')
addIndex(bsc, 'sortKey', 'FieldIndex')
addIndex(bsc, 'getMethodID', 'FieldIndex')
addIndex(bsc, 'getDocumentID', 'FieldIndex')
addColumn(bsc, 'path')
addColumn(bsc, 'UID')
addColumn(bsc, 'id')
addColumn(bsc, 'getId')
addColumn(bsc, 'Type')
addColumn(bsc, 'portal_type')
addColumn(bsc, 'getObjPositionInParent')
addColumn(bsc, 'Title')
addColumn(bsc, 'Description')
addColumn(bsc, 'title')
addColumn(bsc, 'sortable_title')
addColumn(bsc, 'description')
addColumn(bsc, 'review_state')
addColumn(bsc, 'inactive_state')
addColumn(bsc, 'cancellation_state')
addColumn(bsc, 'getAccredited')
addColumn(bsc, 'getInstrumentType')
addColumn(bsc, 'getInstrumentTypeName')
addColumn(bsc, 'getBlank')
addColumn(bsc, 'getCalculationTitle')
addColumn(bsc, 'getCalculationUID')
addColumn(bsc, 'getCalibrationExpiryDate')
addColumn(bsc, 'getCategoryTitle')
addColumn(bsc, 'getCategoryUID')
addColumn(bsc, 'getClientUID')
addColumn(bsc, 'getDepartmentTitle')
addColumn(bsc, 'getDuplicateVariation')
addColumn(bsc, 'getFormula')
addColumn(bsc, 'getFullname')
addColumn(bsc, 'getHazardous')
addColumn(bsc, 'getInstrumentTitle')
addColumn(bsc, 'getKeyword')
addColumn(bsc, 'getManagerName')
addColumn(bsc, 'getManagerPhone')
addColumn(bsc, 'getManagerEmail')
addColumn(bsc, 'getMaxTimeAllowed')
addColumn(bsc, 'getModel')
addColumn(bsc, 'getName')
addColumn(bsc, 'getPointOfCapture')
addColumn(bsc, 'getPrice')
addColumn(bsc, 'getSamplePointTitle')
addColumn(bsc, 'getSamplePointUID')
addColumn(bsc, 'getSampleTypeTitle')
addColumn(bsc, 'getSampleTypeUID')
addColumn(bsc, 'getServiceTitle')
addColumn(bsc, 'getServiceUID')
addColumn(bsc, 'getTotalPrice')
addColumn(bsc, 'getUnit')
addColumn(bsc, 'getVATAmount')
addColumn(bsc, 'getVolume')
def setupPortalContent(self, portal):
""" Setup Bika site structure """
wf = getToolByName(portal, 'portal_workflow')
obj = portal._getOb('front-page')
alsoProvides(obj, IHaveNoBreadCrumbs)
mp = obj.manage_permission
mp(permissions.View, ['Anonymous'], 1)
# remove undesired content objects
del_ids = []
for obj_id in ['Members', 'news', 'events']:
if obj_id in portal.objectIds():
del_ids.append(obj_id)
if del_ids:
portal.manage_delObjects(ids=del_ids)
# index objects - importing through GenericSetup doesn't
for obj_id in (
'clients',
'batches',
'invoices',
'pricelists',
'bika_setup',
'methods',
'analysisrequests',
'referencesamples',
'samples',
'supplyorders',
'worksheets',
'reports',
'queries',
'arimports',
):
try:
obj = portal._getOb(obj_id)
obj.unmarkCreationFlag()
obj.reindexObject()
except:
pass
bika_setup = portal._getOb('bika_setup')
for obj_id in ('bika_analysiscategories', 'bika_analysisservices',
'bika_arpriorities', 'bika_attachmenttypes',
'bika_batchlabels', 'bika_calculations',
'bika_departments', 'bika_containers',
'bika_containertypes', 'bika_preservations',
'bika_instruments', 'bika_instrumenttypes',
'bika_analysisspecs', 'bika_analysisprofiles',
'bika_artemplates', 'bika_labcontacts',
'bika_labproducts', 'bika_manufacturers',
'bika_sampleconditions', 'bika_samplematrices',
'bika_samplingdeviations', 'bika_samplepoints',
'bika_sampletypes', 'bika_srtemplates',
'bika_storagelocations', 'bika_subgroups',
'bika_suppliers', 'bika_referencedefinitions',
'bika_worksheettemplates'):
try:
obj = bika_setup._getOb(obj_id)
obj.unmarkCreationFlag()
obj.reindexObject()
except:
pass
lab = bika_setup.laboratory
lab.edit(title=_('Laboratory'))
lab.unmarkCreationFlag()
lab.reindexObject()
def isManagementAllowed(self):
mtool = getToolByName(self.context, 'portal_membership')
return mtool.checkPermission(ManageWorksheets, self.context)
def read(context, request):
tag = AuthenticatorView(context, request).authenticator()
pattern = '<input .*name="(\w+)".*value="(\w+)"'
_authenticator = re.match(pattern, tag).groups()[1]
ret = {
"url": router.url_for("read", force_external=True),
"success": True,
"error": False,
"objects": [],
"_authenticator": _authenticator,
}
debug_mode = True #App.config.getConfiguration().debug_mode "Commented by Yasir"
catalog_name = request.get("catalog_name", "portal_catalog")
if not catalog_name:
raise ValueError("bad or missing catalog_name: " + catalog_name)
catalog = getToolByName(context, catalog_name)
indexes = catalog.indexes()
contentFilter = {}
for index in indexes:
if index in request:
if index == 'review_state' and "{" in request[index]:
continue
contentFilter[index] = safe_unicode(request[index])
if "%s[]" % index in request:
value = request["%s[]" % index]
contentFilter[index] = [safe_unicode(v) for v in value]
if 'limit' in request:
try:
contentFilter['sort_limit'] = int(request["limit"])
except ValueError:
pass
sort_on = request.get('sort_on', 'id')
contentFilter['sort_on'] = sort_on
# sort order
sort_order = request.get('sort_order', '')
if sort_order:
contentFilter['sort_order'] = sort_order
else:
sort_order = 'ascending'
contentFilter['sort_order'] = 'ascending'
include_fields = get_include_fields(request)
if debug_mode:
logger.info("contentFilter: " + str(contentFilter))
# Get matching objects from catalog
proxies = catalog(**contentFilter)
# batching items
page_nr = int(request.get("page_nr", 0))
try:
page_size = int(request.get("page_size", 10))
except ValueError:
page_size = 10
# page_size == 0: show all
if page_size == 0:
page_size = len(proxies)
first_item_nr = page_size * page_nr
if first_item_nr > len(proxies):
first_item_nr = 0
page_proxies = proxies[first_item_nr:first_item_nr + page_size]
for proxy in page_proxies:
obj_data = {}
# Place all proxy attributes into the result.
obj_data.update(load_brain_metadata(proxy, include_fields))
# Place all schema fields ino the result.
obj = proxy.getObject()
obj_data.update(load_field_values(obj, include_fields))
obj_data['path'] = "/".join(obj.getPhysicalPath())
# call any adapters that care to modify this data.
adapters = getAdapters((obj, ), IJSONReadExtender)
for name, adapter in adapters:
adapter(request, obj_data)
ret['objects'].append(obj_data)
ret['total_objects'] = len(proxies)
ret['first_object_nr'] = first_item_nr
last_object_nr = first_item_nr + len(page_proxies)
if last_object_nr > ret['total_objects']:
last_object_nr = ret['total_objects']
ret['last_object_nr'] = last_object_nr
if debug_mode:
logger.info("{0} objects returned".format(len(ret['objects'])))
return ret
def _transitions(self):
workflow = getToolByName(self.context, 'portal_workflow')
return workflow.listActionInfos(object=self.context, max=1)
def workflow_script_unassign(self):
if skip(self, "unassign"):
return
workflow = getToolByName(self, 'portal_workflow')
self.reindexObject(idxs=[
"review_state",
])
rc = getToolByName(self, REFERENCE_CATALOG)
wsUID = self.REQUEST['context_uid']
ws = rc.lookupObject(wsUID)
# May need to promote the Worksheet's review_state
# if all other analyses are at a higher state than this one was.
# (or maybe retract it if there are no analyses left)
# Note: duplicates, controls and blanks have 'assigned' as a review_state.
can_submit = True
can_attach = True
can_verify = True
ws_empty = False
analyses = ws.getAnalyses()
# We flag this worksheet as empty if there is ONE UNASSIGNED
# analysis left: worksheet.removeAnalysis() hasn't removed it from
# the layout yet at this stage.
if len(analyses) == 1 \
and workflow.getInfoFor(analyses[0], 'review_state') == 'unassigned':
ws_empty = True
for a in analyses:
ws_empty = False
a_state = workflow.getInfoFor(a, 'review_state')
if a_state in \
('assigned', 'sample_due', 'sample_received',):
can_submit = False
else:
if not ws.getAnalyst():
can_submit = False
if a_state in \
('assigned', 'sample_due', 'sample_received', 'attachment_due',):
can_attach = False
if a_state in \
('assigned', 'sample_due', 'sample_received', 'attachment_due', 'to_be_verified',):
can_verify = False
if not ws_empty:
# Note: WS adds itself to the skiplist so we have to take it off again
# to allow multiple promotions (maybe by more than one self).
if can_submit and workflow.getInfoFor(ws,
'review_state') == 'open':
workflow.doActionFor(ws, 'submit')
skip(ws, 'submit', unskip=True)
if can_attach and workflow.getInfoFor(
ws, 'review_state') == 'attachment_due':
workflow.doActionFor(ws, 'attach')
skip(ws, 'attach', unskip=True)
if can_verify and workflow.getInfoFor(
ws, 'review_state') == 'to_be_verified':
self.REQUEST["workflow_skiplist"].append('verify all analyses')
workflow.doActionFor(ws, 'verify')
skip(ws, 'verify', unskip=True)
else:
if workflow.getInfoFor(ws, 'review_state') != 'open':
workflow.doActionFor(ws, 'retract')
skip(ws, 'retract', unskip=True)
