def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
if self.destination_url == "":
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
skiplist = self.request.get('workflow_skiplist', [])
action, came_from = self._get_form_workflow_action()
# transition the context object.
if came_from == "workflow_action":
obj = self.context
# the only actions allowed on inactive/cancelled
# items are "reinstate" and "activate"
if not isActive(obj) and action not in ('reinstate', 'activate'):
message = self.context.translate(_('Item is inactive.'))
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.destination_url)
return
else:
if obj.UID() not in skiplist:
allowed_transitions = []
for t in workflow.getTransitionsFor(obj):
allowed_transitions.append(t['id'])
if action in allowed_transitions:
workflow.doActionFor(obj, action)
self.request.response.redirect(self.destination_url)
return
# transition selected items from the bika_listing/Table.
transitioned = []
selected_items = self._get_selected_items()
for uid, item in selected_items.items():
# the only action allowed on inactive items is "activate"
if not isActive(item) and action not in ('reinstate', 'activate'):
continue
if uid not in skiplist:
allowed_transitions = []
for t in workflow.getTransitionsFor(item):
allowed_transitions.append(t['id'])
if action in allowed_transitions:
try:
workflow.doActionFor(item, action)
transitioned.append(item.Title())
except WorkflowException:
pass
if len(transitioned) > 0:
message = self.context.translate(PMF('Changes saved.'))
self.context.plone_utils.addPortalMessage(message, 'info')
# automatic label printing
if action == 'receive' and 'receive' in self.context.bika_setup.getAutoPrintLabels():
q = "/sticker?size=%s&items=" % (self.context.bika_setup.getAutoLabelSize())
# selected_items is a list of UIDs (stickers for AR_add use IDs)
q += ",".join([i.getId() for i in selected_items.values()])
self.request.response.redirect(self.context.absolute_url() + q)
else:
self.request.response.redirect(self.destination_url)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
if self.destination_url == "":
self.destination_url = self.request.get_header(
"referer", self.context.absolute_url())
action, came_from = self._get_form_workflow_action()
# transition the context object (plone edit bar dropdown)
if came_from == "workflow_action":
obj = self.context
# the only actions allowed on inactive/cancelled
# items are "reinstate" and "activate"
if not isActive(obj) and action not in ('reinstate', 'activate'):
message = self.context.translate(_('Item is inactive.'))
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.destination_url)
return
if not skip(obj, action, peek=True):
allowed_transitions = []
for t in workflow.getTransitionsFor(obj):
allowed_transitions.append(t['id'])
if action in allowed_transitions:
workflow.doActionFor(obj, action)
self.request.response.redirect(self.destination_url)
return
# transition selected items from the bika_listing/Table.
transitioned = []
selected_items = self._get_selected_items()
for uid, item in selected_items.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 = []
for t in workflow.getTransitionsFor(item):
allowed_transitions.append(t['id'])
if action in allowed_transitions:
doActionFor(item, action)
transitioned.append(item.Title())
if len(transitioned) > 0:
message = self.context.translate(PMF('Changes saved.'))
self.context.plone_utils.addPortalMessage(message, 'info')
# automatic label printing
if action == 'receive' and 'receive' in self.portal.bika_setup.getAutoPrintLabels(
):
q = "/sticker?size=%s&items=" % (
self.portal.bika_setup.getAutoLabelSize())
# selected_items is a list of UIDs (stickers for AR_add use IDs)
q += ",".join([i.getId() for i in selected_items.values()])
self.request.response.redirect(self.context.absolute_url() + q)
else:
self.request.response.redirect(self.destination_url)
def getWSTemplates(self, contentFilter={}):
istate = contentFilter.get("inactive_state", None)
if istate == 'active':
templates = [p for p in self.context.bika_setup.objectValues("WSTemplate")
if isActive(p)]
elif istate == 'inactive':
templates = [p for p in self.context.objectValues("WorksheetTemplate")
if not isActive(p)]
else:
templates = [p for p in self.context.objectValues("WorksheetTemplate")]
return templates
def getARProfiles(self, contentFilter={}):
istate = contentFilter.get("inactive_state", None)
if istate == 'active':
profiles = [p for p in self.context.objectValues("ARProfile")
if isActive(p)]
elif istate == 'inactive':
profiles = [p for p in self.context.objectValues("ARProfile")
if not isActive(p)]
else:
profiles = [p for p in self.context.objectValues("ARProfile")]
return profiles
def getARProfiles(self, contentFilter={}):
istate = contentFilter.get("inactive_state", None)
if istate == 'active':
profiles = [p for p in self.context.objectValues("ARProfile")
if isActive(p)]
elif istate == 'inactive':
profiles = [p for p in self.context.objectValues("ARProfile")
if not isActive(p)]
else:
profiles = [p for p in self.context.objectValues("ARProfile")]
profiles.sort(lambda a,b:cmp(a.Title().lower(), b.Title().lower()))
return profiles
def getARTemplates(self, contentFilter={}):
istate = contentFilter.get("inactive_state", None)
if istate == 'active':
templates = [
p for p in self.context.objectValues("ARTemplate")
if isActive(p)
]
elif istate == 'inactive':
templates = [
p for p in self.context.objectValues("ARTemplate")
if not isActive(p)
]
else:
templates = [p for p in self.context.objectValues("ARTemplate")]
return templates
def __call__(self):
self.context_actions = {}
wf = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
translate = self.context.translate
# client contact required
active_contacts = [c for c in self.context.objectValues('Contact') if
wf.getInfoFor(c, 'inactive_state', '') == 'active']
if isActive(self.context):
if self.context.portal_type == "Client" and not active_contacts:
msg = _("Client contact required before request may be submitted")
addPortalMessage(msg)
else:
if mtool.checkPermission(AddAnalysisRequest, self.context):
self.context_actions[t(_('Add'))] = {
'url': self.context.absolute_url() + "/portal_factory/"
"AnalysisRequest/Request new analyses/ar_add",
'icon': '++resource++bika.lims.images/add.png'}
# in client context we can use a permission check for this transition
# in multi-client listings, we must rather check against user roles.
if mtool.checkPermission(ModifyPortalContent, self.context):
review_states = []
for review_state in self.review_states:
review_state['custom_actions'].extend(
[{'id': 'copy_to_new',
'title': _('Copy to new'),
'url': 'workflow_action?action=copy_to_new'}, ])
review_states.append(review_state)
self.review_states = review_states
return super(ClientAnalysisRequestsView, self).__call__()
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?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 __call__(self):
self.context_actions = {}
wf = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
PR = self.context.getPrimaryReferrer()
if isActive(self.context):
if mtool.checkPermission(AddAnalysisRequest, PR):
#client contact required
contacts = [
c for c in PR.objectValues('Contact')
if wf.getInfoFor(c, 'inactive_state', '') == 'active'
]
if contacts:
self.context_actions[self.context.translate(_('Add'))] = {
'url': PR.absolute_url() + "/ar_add",
'icon': '++resource++bika.lims.images/add.png'
}
else:
msg = _(
"Client contact required before request may be submitted"
)
addPortalMessage(self.context.translate(msg))
return super(AnalysisRequestsView, self).__call__()
def __call__(self):
self.context_actions = {}
wf = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
translate = self.context.translate
# client contact required
active_contacts = [
c for c in self.context.objectValues('Contact')
if wf.getInfoFor(c, 'inactive_state', '') == 'active'
]
if isActive(self.context):
if self.context.portal_type == "Client" and not active_contacts:
msg = _(
"Client contact required before request may be submitted")
addPortalMessage(msg)
else:
if mtool.checkPermission(AddAnalysisRequest, self.context):
self.context_actions[t(_('Add'))] = {
'url': self.context.absolute_url() + "/portal_factory/"
"AnalysisRequest/Request new analyses/ar_add",
'icon': '++resource++bika.lims.images/add.png'
}
return super(ClientAnalysisRequestsView, self).__call__()
def __call__(self):
self.context_actions = {}
wf = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
translate = self.context.translate
# client contact required
active_contacts = [c for c in self.context.objectValues('Contact') if
wf.getInfoFor(c, 'inactive_state', '') == 'active']
if isActive(self.context):
if self.context.portal_type == "Client" and not active_contacts:
msg = _("Client contact required before request may be submitted")
addPortalMessage(msg)
else:
if mtool.checkPermission(AddAnalysisRequest, self.context):
self.context_actions[t(_('Add'))] = {
'url': self.context.absolute_url() + "/portal_factory/"
"AnalysisRequest/Request new analyses/ar_add",
'icon': '++resource++bika.lims.images/add.png'}
# in client context we can use a permission check for this transition
# in multi-client listings, we must rather check against user roles.
if mtool.checkPermission(ModifyPortalContent, self.context):
review_states = []
for review_state in self.review_states:
review_state['custom_actions'].extend(
[{'id': 'copy_to_new',
'title': _('Copy to new'),
'url': 'workflow_action?action=copy_to_new'}, ])
review_states.append(review_state)
self.review_states = review_states
return super(ClientAnalysisRequestsView, self).__call__()
def workflow_action_publish(self):
action, came_from = WorkflowAction._get_form_workflow_action(self)
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
# AR publish preview
self.request.response.redirect(self.context.absolute_url() + "/publish")
def workflow_action_publish(self):
action, came_from = WorkflowAction._get_form_workflow_action(self)
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
# AR publish preview
self.request.response.redirect(self.context.absolute_url() + "/publish")
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, "portal_workflow")
if self.destination_url == "":
self.destination_url = self.request.get_header("referer", self.context.absolute_url())
skiplist = self.request.get("workflow_skiplist", [])
action, came_from = self._get_form_workflow_action()
# transition the context object.
if came_from == "workflow_action":
obj = self.context
# the only actions allowed on inactive/cancelled
# items are "reinstate" and "activate"
if not isActive(obj) and action not in ("reinstate", "activate"):
message = _("Item is inactive.")
self.context.plone_utils.addPortalMessage(message, "info")
self.request.response.redirect(self.destination_url)
return
else:
if obj.UID() not in skiplist:
workflow.doActionFor(obj, action)
self.request.response.redirect(self.destination_url)
return
# transition selected items from the bika_listing/Table.
transitioned = []
selected_items = self._get_selected_items()
for uid, item in selected_items.items():
# the only action allowed on inactive items is "activate"
if not isActive(item) and action not in ("reinstate", "activate"):
continue
if uid not in skiplist:
try:
workflow.doActionFor(item, action)
transitioned.append(item.Title())
except WorkflowException:
pass
if len(transitioned) > 0:
message = _("Changes saved.")
self.context.plone_utils.addPortalMessage(message, "info")
self.request.response.redirect(self.destination_url)
def __call__(self):
mtool = getToolByName(self.context, 'portal_membership')
checkPermission = mtool.checkPermission
if isActive(self.context):
if checkPermission(AddAnalysisSpec, self.context):
self.context_actions[_('Add')] = \
{'url': 'createObject?type_name=AnalysisSpec',
'permission': 'Add portal content',
'icon': '++resource++bika.lims.images/add.png'}
return super(ClientAnalysisSpecsView, self).__call__()
def getContacts(self, dl=True):
pairs = []
objects = []
for contact in self.aq_parent.objectValues('Contact'):
if isActive(contact) and contact.UID() != self.UID():
pairs.append((contact.UID(), contact.Title()))
if not dl:
objects.append(contact)
pairs.sort(lambda x, y: cmp(x[1].lower(), y[1].lower()))
return dl and DisplayList(pairs) or objects
def getContacts(self, dl=True):
pairs = []
objects = []
for contact in self.aq_parent.objectValues('Contact'):
if isActive(contact) and contact.UID() != self.UID():
pairs.append((contact.UID(), contact.Title()))
if not dl:
objects.append(contact)
pairs.sort(lambda x, y: cmp(x[1].lower(), y[1].lower()))
return dl and DisplayList(pairs) or objects
def getCCContacts(self):
"""Return a JSON value, containing all Contacts and their default CCs
for this client. This function is used to set form values for javascript.
"""
contact_data = []
for contact in self.objectValues('Contact'):
if isActive(contact):
this_contact_data = {'title': contact.Title(),
'uid': contact.UID(), }
ccs = []
for cc in contact.getCCContact():
if isActive(cc):
ccs.append({'title': cc.Title(),
'uid': cc.UID(),})
this_contact_data['ccs_json'] = json.dumps(ccs)
this_contact_data['ccs'] = ccs
contact_data.append(this_contact_data)
contact_data.sort(lambda x, y:cmp(x['title'].lower(),
y['title'].lower()))
return contact_data
def artemplates(self):
""" Return applicable client and Lab ARTemplate records
"""
res = []
templates = []
client = self.context.portal_type == 'AnalysisRequest' \
and self.context.aq_parent or self.context
for template in client.objectValues("ARTemplate"):
if isActive(template):
templates.append((template.Title(), template))
templates.sort(lambda x, y: cmp(x[0], y[0]))
res += templates
templates = []
for template in self.context.bika_setup.bika_artemplates.objectValues("ARTemplate"):
if isActive(template):
lab = t(_('Lab'))
title = to_utf8(template.Title())
templates.append(("%s: %s" % (lab, title), template))
templates.sort(lambda x, y: cmp(x[0], y[0]))
res += templates
return res
def analysisprofiles(self):
""" Return applicable client and Lab AnalysisProfile records
"""
res = []
profiles = []
client = self.context.portal_type == 'AnalysisRequest' \
and self.context.aq_parent or self.context
for profile in client.objectValues("AnalysisProfile"):
if isActive(profile):
profiles.append((profile.Title(), profile))
profiles.sort(lambda x, y: cmp(x[0], y[0]))
res += profiles
profiles = []
for profile in self.context.bika_setup.bika_analysisprofiles.objectValues("AnalysisProfile"):
if isActive(profile):
lab = t(_('Lab'))
title = to_utf8(profile.Title())
profiles.append(("%s: %s" % (lab, title), profile))
profiles.sort(lambda x, y: cmp(x[0], y[0]))
res += profiles
return res
def __call__(self):
self.context_actions = {}
bc = getToolByName(self.context, 'bika_catalog')
wf = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
if isActive(self.context):
if mtool.checkPermission(AddAnalysisRequest, self.portal):
self.context_actions[self.context.translate(_('Add new'))] = {
'url':self.context.absolute_url() + '/ar_add?col_count=1',
'icon': '++resource++bika.lims.images/add.png'}
return super(BatchAnalysisRequestsView, self).__call__()
def artemplates(self):
""" Return applicable client and Lab ARTemplate records
"""
res = []
templates = []
client = self.context.portal_type == 'AnalysisRequest' \
and self.context.aq_parent or self.context
for template in client.objectValues("ARTemplate"):
if isActive(template):
templates.append((template.Title(), template))
templates.sort(lambda x, y: cmp(x[0], y[0]))
res += templates
templates = []
for template in self.context.bika_setup.bika_artemplates.objectValues("ARTemplate"):
if isActive(template):
lab = t(_('Lab'))
title = to_utf8(template.Title())
templates.append(("%s: %s" % (lab, title), template))
templates.sort(lambda x, y: cmp(x[0], y[0]))
res += templates
return res
def analysisprofiles(self):
""" Return applicable client and Lab AnalysisProfile records
"""
res = []
profiles = []
client = self.context.portal_type == 'AnalysisRequest' \
and self.context.aq_parent or self.context
for profile in client.objectValues("AnalysisProfile"):
if isActive(profile):
profiles.append((profile.Title(), profile))
profiles.sort(lambda x, y: cmp(x[0], y[0]))
res += profiles
profiles = []
for profile in self.context.bika_setup.bika_analysisprofiles.objectValues("AnalysisProfile"):
if isActive(profile):
lab = t(_('Lab'))
title = to_utf8(profile.Title())
profiles.append(("%s: %s" % (lab, title), profile))
profiles.sort(lambda x, y: cmp(x[0], y[0]))
res += profiles
return res
def __call__(self):
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
w_tool = getToolByName(self.context, 'portal_workflow')
active_contacts = [
c for c in self.context.objectValues('Contact')
if w_tool.getInfoFor(c, 'inactive_state', '') == 'active'
]
if isActive(self.context):
if self.context.portal_type == "Client":
if not active_contacts:
msg = _(
"Client contact required before request may be submitted"
)
addPortalMessage(msg)
else:
if mtool.checkPermission(AddProject, self.context):
self.context_actions[_('Add')] = {
'url': 'createObject?type_name=Project',
'icon': '++resource++bika.lims.images/add.png'
}
if mtool.checkPermission(ManageProjects, self.context):
self.review_states[0]['transitions'].append({'id': 'deactivate'})
self.review_states.append({
'id':
'inactive',
'title':
_('Dormant'),
'contentFilter': {
'inactive_state': 'inactive'
},
'transitions': [
{
'id': 'activate'
},
],
'columns': ['Title', 'getClient', 'getStudyType']
})
self.review_states.append({
'id':
'all',
'title':
_('All'),
'contentFilter': {},
'transitions': [{
'id': 'empty'
}],
'columns': ['Title', 'getClient', 'getStudyType']
})
stat = self.request.get("%s_review_state" % self.form_id,
'default')
self.show_select_column = stat != 'all'
return BikaListingView.__call__(self)
def folderitems(self, full_objects=False):
items = BikaListingView.folderitems(self)
bsc = getToolByName(self.context, 'bika_setup_catalog')
brains = bsc(portal_type='SampleType', inactive_state='active')
biospecimen_types = [{
'ResultValue': brain.UID,
'ResultText': brain.title
} for brain in brains]
ret = []
for x, item in enumerate(items):
if not items[x].has_key('obj'):
continue
obj = items[x]['obj']
if not ISample.providedBy(obj):
continue
items[x]['Type'] = obj.getSampleType() and obj.getSampleType(
).Title() or ''
items[x]['Volume'] = obj.getField('Volume').get(obj)
items[x]['Unit'] = VOLUME_UNITS[0]['ResultText']
items[x]['SubjectID'] = obj.getField('SubjectID').get(obj)
kit = obj.getField('Kit').get(obj)
project = obj.getField('Project').get(obj)
items[x]['Kit'] = kit
items[x]['Project'] = project
if project:
items[x]['replace']['Project'] = \
'<a href="%s">%s</a>' % (project.absolute_url(),
project.Title())
if kit:
items[x]['replace']['Kit'] = \
'<a href="%s">%s</a>' % (kit.absolute_url(), kit.Title())
# TODO: IF STATUS IS RECEIVED EXECUTE THIS
# items[x]['replace']['Type'] = \
# '<a href="%s">%s</a>' % (obj.getSampleType().absolute_url(),
# obj.getSampleType().Title())
items[x]['Barcode'] = obj.getField('Barcode').get(obj)
items[x]['replace']['Title'] = "<a href='%s'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
# TODO: SPECIFY OBJ STATES WHERE USER CAN EDIT BARCODE
if self.allow_edit and isActive(self.context) and \
getSecurityManager().checkPermission(ManageProjects, obj):
if items[x]['review_state'] == "sample_registered":
items[x]['allow_edit'] = ['Type', 'Barcode']
items[x]['choices']['Type'] = biospecimen_types
elif items[x]['review_state'] == "sample_due":
items[x]['allow_edit'] = ['SubjectID', 'Volume', 'Unit']
if not items[x]['Unit']:
items[x]['choices']['Unit'] = VOLUME_UNITS
ret.append(item)
return ret
def __call__(self):
self.context_actions = {}
bc = getToolByName(self.context, 'bika_catalog')
wf = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
if isActive(self.context):
if mtool.checkPermission(AddAnalysisRequest, self.portal):
self.context_actions[self.context.translate(_('Add new'))] = {
'url': self.context.absolute_url() + '/ar_add?col_count=1',
'icon': '++resource++bika.lims.images/add.png'
}
return super(BatchAnalysisRequestsView, self).__call__()
def __call__(self):
self.context_actions = {}
bc = getToolByName(self.context, "bika_catalog")
wf = getToolByName(self.context, "portal_workflow")
mtool = getToolByName(self.context, "portal_membership")
addPortalMessage = self.context.plone_utils.addPortalMessage
if isActive(self.context):
if mtool.checkPermission(AddAnalysisRequest, self.portal):
self.context_actions[self.context.translate(_("Add new"))] = {
"url": self.context.absolute_url() + "/ar_add?col_count=1",
"icon": "++resource++bika.lims.images/add.png",
}
return super(BatchAnalysisRequestsView, self).__call__()
def getContacts(self, dl=True):
pc = getToolByName(self, 'portal_catalog')
bc = getToolByName(self, 'bika_catalog')
bsc = getToolByName(self, 'bika_setup_catalog')
pairs = []
objects = []
for contact in self.objectValues('Contact'):
if isActive(contact):
pairs.append((contact.UID(), contact.Title()))
if not dl:
objects.append(contact)
pairs.sort(lambda x, y:cmp(x[1].lower(), y[1].lower()))
return dl and DisplayList(pairs) or objects
def workflow_action_publish(self):
action, came_from = WorkflowAction._get_form_workflow_action(self)
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
# AR publish preview
uids = self.request.form.get('uids', [self.context.UID()])
items = ",".join(uids)
self.request.response.redirect(self.context.portal_url() +
"/analysisrequests/publish?items=" +
items)
def __call__(self):
mtool = getToolByName(self.context, 'portal_membership')
checkPermission = mtool.checkPermission
if isActive(self.context):
if checkPermission(AddAnalysisSpec, self.context):
self.context_actions[_('Add')] = \
{'url': 'createObject?type_name=AnalysisSpec',
'icon': '++resource++bika.lims.images/add.png'}
if checkPermission("Modify portal content", self.context):
self.context_actions[_('Set to lab defaults')] = \
{'url': 'set_to_lab_defaults',
'icon': '++resource++bika.lims.images/analysisspec.png'}
return super(ClientAnalysisSpecsView, self).__call__()
def getCCs(self):
items = []
for contact in self.getContacts(dl=False):
item = {"uid": contact.UID(), "title": contact.Title()}
ccs = []
if hasattr(contact, "getCCContact"):
for cc in contact.getCCContact():
if isActive(cc):
ccs.append({"title": cc.Title(), "uid": cc.UID()})
item["ccs_json"] = json.dumps(ccs)
item["ccs"] = ccs
items.append(item)
items.sort(lambda x, y: cmp(x["title"].lower(), y["title"].lower()))
return items
def __call__(self):
mtool = getToolByName(self.context, "portal_membership")
checkPermission = mtool.checkPermission
if isActive(self.context):
if checkPermission(AddAnalysisSpec, self.context):
self.context_actions[_("Add")] = {
"url": "createObject?type_name=AnalysisSpec",
"icon": "++resource++bika.lims.images/add.png",
}
if checkPermission(ManageClients, self.context):
self.context_actions[_("Set to lab defaults")] = {
"url": "set_to_lab_defaults",
"icon": "++resource++bika.lims.images/analysisspec.png",
}
return super(ClientAnalysisSpecsView, self).__call__()
def getCCContacts(self):
"""Return a JSON value, containing all Contacts and their default CCs
for this client. This function is used to set form values for javascript.
"""
contact_data = []
for contact in self.objectValues('Contact'):
if isActive(contact):
this_contact_data = {
'title': contact.Title(),
'uid': contact.UID(),
}
ccs = []
for cc in contact.getCCContact():
if isActive(cc):
ccs.append({
'title': cc.Title(),
'uid': cc.UID(),
})
this_contact_data['ccs_json'] = json.dumps(ccs)
this_contact_data['ccs'] = ccs
contact_data.append(this_contact_data)
contact_data.sort(
lambda x, y: cmp(x['title'].lower(), y['title'].lower()))
return contact_data
def getCCs(self):
items = []
for contact in self.getContacts(dl=False):
item = {'uid': contact.UID(), 'title': contact.Title()}
ccs = []
if hasattr(contact, 'getCCContact'):
for cc in contact.getCCContact():
if isActive(cc):
ccs.append({'title': cc.Title(),
'uid': cc.UID(),})
item['ccs_json'] = json.dumps(ccs)
item['ccs'] = ccs
items.append(item)
items.sort(lambda x, y:cmp(x['title'].lower(), y['title'].lower()))
return items
def __call__(self):
mtool = getToolByName(self.context, 'portal_membership')
checkPermission = mtool.checkPermission
if isActive(self.context):
if checkPermission(AddAnalysisSpec, self.context):
self.context_actions[_('Add')] = \
{'url': 'createObject?type_name=AnalysisSpec',
'icon': '++resource++bika.lims.images/add.png'}
#
# @lemoene with the changes made in AR-specs, I dont know how much
# sense this makes anymore.
# if checkPermission("Modify portal content", self.context):
# self.context_actions[_('Set to lab defaults')] = \
# {'url': 'set_to_lab_defaults',
# 'icon': '++resource++bika.lims.images/analysisspec.png'}
return super(ClientAnalysisSpecsView, self).__call__()
def __call__(self):
mtool = getToolByName(self.context, 'portal_membership')
checkPermission = mtool.checkPermission
if isActive(self.context):
if checkPermission(AddAnalysisSpec, self.context):
self.context_actions[_('Add')] = \
{'url': 'createObject?type_name=AnalysisSpec',
'icon': '++resource++bika.lims.images/add.png'}
#
# @lemoene with the changes made in AR-specs, I dont know how much
# sense this makes anymore.
# if checkPermission("Modify portal content", self.context):
# self.context_actions[_('Set to lab defaults')] = \
# {'url': 'set_to_lab_defaults',
# 'icon': '++resource++bika.lims.images/analysisspec.png'}
return super(ClientAnalysisSpecsView, self).__call__()
def __init__(self, context, request):
super(ClientAnalysisSpecsView, self).__init__(context, request)
bsc = getToolByName(context, 'bika_setup_catalog')
wf = getToolByName(context, 'portal_workflow')
self.contentFilter = {
'portal_type': 'AnalysisSpec',
'getClientUID': context.UID(),
'path': {
"query": "/".join(context.getPhysicalPath()),
"level": 0
}
}
self.contentsMethod = bsc
checkPermission = self.context.portal_membership.checkPermission
self.context_actions = {}
if isActive(self.context):
if checkPermission(AddAnalysisSpec, self.context):
self.context_actions[translate(_('Add'))] = \
{'url': 'createObject?type_name=AnalysisSpec',
'icon': '++resource++bika.lims.images/add.png'}
if checkPermission(ManageClients, self.context):
self.context_actions[translate(_('Set to lab defaults'))] = \
{'url': 'set_to_lab_defaults',
'icon': '++resource++bika.lims.images/analysisspec.png'}
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = True
self.pagesize = 50
self.icon = "++resource++bika.lims.images/analysisspec_big.png"
self.title = _("Analysis Specifications")
self.columns = {
'SampleType': {
'title': _('Sample Type'),
'index': 'getSampleTypeTitle'
},
}
self.review_states = [
{
'id': 'all',
'title': _('All'),
'columns': ['SampleType'],
},
]
def __call__(self):
plone.protect.CheckAuthenticator(self.request.form)
rc = getToolByName(self.context, REFERENCE_CATALOG)
uid = self.request.form.keys() and self.request.form.keys()[0] or None
if not uid:
return
contact = rc.lookupObject(uid)
cc_uids = []
cc_titles = []
for cc in contact.getCCContact():
active = isActive(contact)
if not active:
continue
cc_uids.append(cc.UID())
cc_titles.append(cc.Title())
return json.dumps([",".join(cc_uids),
",".join(cc_titles)])
def __call__(self):
self.context_actions = {}
wf = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
# client contact required
active_contacts = [c for c in self.context.objectValues('Contact') if
wf.getInfoFor(c, 'inactive_state', '') == 'active']
if isActive(self.context):
if self.context.portal_type == "Client" and not active_contacts:
msg = _("Client contact required before request may be submitted")
addPortalMessage(self.context.translate(msg))
else:
if mtool.checkPermission(AddAnalysisRequest, self.context):
self.context_actions[self.context.translate(_('Add'))] = {
'url':'ar_add',
'icon': '++resource++bika.lims.images/add.png'}
return super(ClientAnalysisRequestsView, self).__call__()
def folderitems(self, full_objects=False):
items = BikaListingView.folderitems(self)
bsc = getToolByName(self.context, 'bika_setup_catalog')
brains = bsc(portal_type='SampleType', inactive_state='active')
biospecimen_types = [
{
'ResultValue': brain.UID,
'ResultText': brain.title
}
for brain in brains
]
ret = []
for x, item in enumerate(items):
if not items[x].has_key('obj'):
continue
obj = items[x]['obj']
if not IBiospecimen.providedBy(obj):
continue
items[x]['Type'] = obj.getSampleType() and obj.getSampleType().Title() or ''
items[x]['Volume'] = obj.getField('Volume').get(obj)
items[x]['Unit'] = VOLUME_UNITS[0]['ResultText']
items[x]['SubjectID'] = obj.getField('SubjectID').get(obj)
kit = obj.getField('Kit').get(obj)
items[x]['Kit'] = kit
items[x]['Project'] = obj.aq_parent
if kit:
items[x]['replace']['Kit'] = \
'<a href="%s">%s</a>' % (kit.absolute_url(), kit.Title())
items[x]['replace']['Project'] = \
'<a href="%s">%s</a>' % (kit.aq_parent.absolute_url(),
kit.aq_parent.Title())
items[x]['Barcode'] = obj.getField('Barcode').get(obj)
items[x]['replace']['Title'] = "<a href='%s'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
# TODO: SPECIFY OBJ STATES WHERE USER CAN EDIT BARCODE
if self.allow_edit and isActive(self.context) and \
getSecurityManager().checkPermission(ManageAliquots, obj) and \
items[x]['review_state'] == "sample_due":
items[x]['allow_edit'] = ['Type', 'SubjectID', 'Barcode', 'Volume', 'Unit']
items[x]['choices']['Type'] = biospecimen_types
items[x]['choices']['Unit'] = VOLUME_UNITS
ret.append(item)
return ret
def getCCs(self):
"""Return a JSON value, containing all Contacts and their default CCs.
This function is used to set form values for javascript.
"""
items = []
for contact in self.getContacts(dl=False):
item = {'uid': contact.UID(), 'title': contact.Title()}
ccs = []
if hasattr(contact, 'getCCContact'):
for cc in contact.getCCContact():
if isActive(cc):
ccs.append({
'title': cc.Title(),
'uid': cc.UID(),
})
item['ccs_json'] = json.dumps(ccs)
item['ccs'] = ccs
items.append(item)
items.sort(lambda x, y: cmp(x['title'].lower(), y['title'].lower()))
return items
def __call__(self):
self.context_actions = {}
wf = getToolByName(self.context, "portal_workflow")
mtool = getToolByName(self.context, "portal_membership")
addPortalMessage = self.context.plone_utils.addPortalMessage
# client contact required
active_contacts = [
c for c in self.context.objectValues("Contact") if wf.getInfoFor(c, "inactive_state", "") == "active"
]
if isActive(self.context):
if self.context.portal_type == "Client" and not active_contacts:
msg = _("Client contact required before request may be submitted")
addPortalMessage(self.context.translate(msg))
else:
if mtool.checkPermission(AddAnalysisRequest, self.context):
self.context_actions[self.context.translate(_("Add"))] = {
"url": "ar_add",
"icon": "++resource++bika.lims.images/add.png",
}
return super(ClientAnalysisRequestsView, self).__call__()
def __call__(self):
self.context_actions = {}
wf = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
PR = self.context.getPrimaryReferrer()
if isActive(self.context):
if mtool.checkPermission(AddAnalysisRequest, PR):
#client contact required
contacts = [c for c in PR.objectValues('Contact') if
wf.getInfoFor(c, 'inactive_state', '') == 'active']
if contacts:
self.context_actions[self.context.translate(_('Add'))] = {
'url': PR.absolute_url() + "/portal_factory/"
"AnalysisRequest/Request new analyses/ar_add",
'icon': '++resource++bika.lims.images/add.png'}
else:
msg = _("Client contact required before request may be submitted")
addPortalMessage(self.context.translate(msg))
return super(AnalysisRequestsView, self).__call__()
def folderitems(self, full_objects=False):
items = BikaListingView.folderitems(self)
bsc = getToolByName(self.context, 'bika_setup_catalog')
brains = bsc(portal_type='SampleType', inactive_state='active')
aliquot_types = [
{
'ResultValue': brain.UID,
'ResultText': brain.title
}
for brain in brains
]
ret = []
for x, item in enumerate(items):
if not items[x].has_key('obj'):
continue
obj = items[x]['obj']
if not IAliquot.providedBy(obj):
continue
items[x]['replace']['Biospecimen'] = \
"<a href='%s'>%s</a>" % (obj.getField('LinkedSample').get(obj).absolute_url(),
obj.getField('LinkedSample').get(obj).Title())
items[x]['AliquotType'] = obj.getSampleType() and obj.getSampleType().Title() or ''
items[x]['Volume'] = items[x]['Volume'] = obj.getField('Volume').get(obj)
items[x]['Unit'] = VOLUME_UNITS[0]['ResultText']
items[x]['replace']['Title'] = "<a href='%s'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
if self.context.portal_type == 'Aliquots':
items[x]['replace']['Project'] = \
'<a href="%s">%s</a>' % (obj.aq_parent.absolute_url(),
obj.aq_parent.Title())
if self.allow_edit and isActive(self.context) and \
getSecurityManager().checkPermission("Modify portal content", obj) and \
items[x]['review_state'] == "sample_due":
items[x]['allow_edit'] = ['AliquotType', 'Volume', 'Unit']
items[x]['choices']['AliquotType'] = aliquot_types
items[x]['choices']['Unit'] = VOLUME_UNITS
ret.append(item)
return ret
def folderitems(self, full_objects=False):
items = BikaListingView.folderitems(self)
bsc = getToolByName(self.context, 'bika_setup_catalog')
brains = bsc(portal_type='SampleType', inactive_state='active')
aliquot_types = [{
'ResultValue': brain.UID,
'ResultText': brain.title
} for brain in brains]
ret = []
for x, item in enumerate(items):
if not items[x].has_key('obj'):
continue
obj = items[x]['obj']
if not IAliquot.providedBy(obj):
continue
items[x]['replace']['Biospecimen'] = \
"<a href='%s'>%s</a>" % (obj.getField('LinkedSample').get(obj).absolute_url(),
obj.getField('LinkedSample').get(obj).Title())
items[x]['AliquotType'] = obj.getSampleType(
) and obj.getSampleType().Title() or ''
items[x]['Volume'] = items[x]['Volume'] = obj.getField(
'Volume').get(obj)
items[x]['Unit'] = VOLUME_UNITS[0]['ResultText']
items[x]['replace']['Title'] = "<a href='%s'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
if self.context.portal_type == 'Aliquots':
items[x]['replace']['Project'] = \
'<a href="%s">%s</a>' % (obj.aq_parent.absolute_url(),
obj.aq_parent.Title())
if self.allow_edit and isActive(self.context) and \
getSecurityManager().checkPermission("Modify portal content", obj) and \
items[x]['review_state'] == "sample_due":
items[x]['allow_edit'] = ['AliquotType', 'Volume', 'Unit']
items[x]['choices']['AliquotType'] = aliquot_types
items[x]['choices']['Unit'] = VOLUME_UNITS
ret.append(item)
return ret
def __call__(self):
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
w_tool = getToolByName(self.context, 'portal_workflow')
active_contacts = [c for c in self.context.objectValues('Contact') if
w_tool.getInfoFor(c, 'inactive_state', '') == 'active']
if isActive(self.context):
if self.context.portal_type == "Client":
if not active_contacts:
msg = _("Client contact required before request may be submitted")
addPortalMessage(msg)
else:
if mtool.checkPermission(AddProject, self.context):
self.context_actions[_('Add')] = {
'url': 'createObject?type_name=Project',
'icon': '++resource++bika.lims.images/add.png'
}
if mtool.checkPermission(ManageProjects, self.context):
self.review_states[0]['transitions'].append({'id': 'deactivate'})
self.review_states.append(
{'id': 'inactive',
'title': _('Dormant'),
'contentFilter': {'inactive_state': 'inactive'},
'transitions': [{'id': 'activate'}, ],
'columns': ['Title',
'getClient',
'getStudyType']})
self.review_states.append(
{'id': 'all',
'title': _('All'),
'contentFilter': {},
'transitions': [{'id': 'empty'}],
'columns': ['Title',
'getClient',
'getStudyType']})
stat = self.request.get("%s_review_state" % self.form_id, 'default')
self.show_select_column = stat != 'all'
return super(ProjectsView, self).__call__()
def workflow_action_publish(self):
action, came_from = WorkflowAction._get_form_workflow_action(self)
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
# publish entire AR.
self.context.setDatePublished(DateTime())
transitioned = self.doPublish(self.context,
self.request,
action,
[self.context, ])()
if len(transitioned) == 1:
message = _(
'${items} published.',
mapping={'items': safe_unicode(', '.join(transitioned))})
else:
message = _("No items were published")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
self.request.response.redirect(self.destination_url)
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():
# Do not save data for analyses that are not selected.
if uid not in selected_analyses:
continue
analysis = selected_analyses[uid]
# never save any part of rows with empty result values.
# https://jira.bikalabs.com/browse/LIMS-1944:
if not result:
continue
# ignore result if analysis object no longer exists
if not analysis:
continue
# Prevent saving data if the analysis is already transitioned
if not (checkPermission(EditResults, analysis)
or checkPermission(EditFieldResults, analysis)):
title = safe_unicode(analysis.getService().Title())
msgid = _('Result for ${analysis} could not be saved because '
'it was already submitted by another user.',
mapping={'analysis': title})
message = safe_unicode(t(msgid))
self.context.plone_utils.addPortalMessage(message)
continue
# 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
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')
# LIMS-2366: Finally, when we are done processing all applicable
# analyses, we must attempt to initiate the submit transition on the
# AR itself. This is for the case where "general retraction" has been
# done, or where the last "received" analysis has been removed, and
# the AR is in state "received" while there are no "received" analyses
# left to trigger the parent transition.
if self.context.portal_type == 'Sample':
ar = self.context.getAnalysisRequests()[0]
elif self.context.portal_type == 'Analysis':
ar = self.context.aq_parent
else:
ar = self.context
doActionFor(ar, '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 folderitems(self):
bsc = getToolByName(self.context, 'bika_setup_catalog')
analysis_categories = bsc(portal_type="AnalysisCategory",
sort_on="sortable_title")
analysis_categories_order = dict([
(b.Title, "{:04}".format(a))
for a, b in enumerate(analysis_categories)
])
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)
member = mtool.getAuthenticatedMember()
self.interim_fields = {}
self.interim_columns = {}
self.specs = {}
show_methodinstr_columns = False
dmk = self.context.bika_setup.getResultsDecimalMark()
for item in items:
if 'obj' not in item:
logger.warn(
"Missing 'obj' key in Analysis item '{}'".format(item))
continue
# self.contentsMethod may return brains or objects.
obj = api.get_object(item["obj"])
if workflow.getInfoFor(obj, 'review_state') == 'retracted' \
and not checkPermission(ViewRetractedAnalyses, self.context):
logger.info("Skipping retracted analysis {}".format(
obj.getId()))
continue
result = obj.getResult()
service = obj.getService()
calculation = service.getCalculation()
unit = service.getUnit()
keyword = service.getKeyword()
if self.show_categories:
cat = obj.getService().getCategoryTitle()
cat_order = analysis_categories_order.get(cat)
item['category'] = cat
if (cat, cat_order) not in self.categories:
self.categories.append((cat, cat_order))
# 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'] = \
formatDecimalMark(interim_fields[x]['value'], dmk)
self.interim_fields[obj.UID()] = interim_fields
item['service_uid'] = service.UID()
item['Service'] = service.Title()
item['Keyword'] = keyword
item['Unit'] = format_supsub(unit) if unit else ''
item['Result'] = ''
item['formatted_result'] = ''
item['interim_fields'] = interim_fields
item['Remarks'] = obj.getRemarks()
item['Uncertainty'] = ''
item['DetectionLimit'] = ''
item['retested'] = obj.getRetested()
item['class']['retested'] = 'center'
item['result_captured'] = self.ulocalized_time(
obj.getResultCaptureDate(), long_format=0)
item['calculation'] = calculation and True or False
try:
item['Partition'] = obj.getSamplePartition().getId()
except AttributeError:
item['Partition'] = ''
if obj.portal_type == "ReferenceAnalysis":
item['DueDate'] = self.ulocalized_time(
obj.aq_parent.getExpiryDate(), long_format=0)
else:
item['DueDate'] = self.ulocalized_time(obj.getDueDate(),
long_format=1)
cd = obj.getResultCaptureDate()
item['CaptureDate'] = cd and self.ulocalized_time(
cd, long_format=1) or ''
item['Attachments'] = ''
item['allow_edit'] = []
tblrowclass = item.get('table_row_class')
if obj.portal_type == 'ReferenceAnalysis':
item['st_uid'] = obj.aq_parent.UID()
item['table_row_class'] = ' '.join(
[tblrowclass, 'qc-analysis'])
elif obj.portal_type == 'DuplicateAnalysis' and \
obj.getAnalysis().portal_type == 'ReferenceAnalysis':
item['st_uid'] = obj.aq_parent.UID()
item['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 ''
item['st_uid'] = st_uid
if checkPermission(ManageBika, self.context):
# service_uid = service.UID()
# latest = rc.lookupObject(service_uid).version_id
item['Service'] = service.Title()
item['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:
item['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()]:
item['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 item['calculation'] or \
(item['calculation'] and self.interim_fields[obj.UID()]):
item['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()
item['Analyst'] = analyst
item['choices']['Analyst'] = self.getAnalysts()
else:
item['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.icon
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>"
item['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:
item['Result'] = result
scinot = self.context.bika_setup.getScientificNotationResults()
item['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(
) is True:
unc = obj.getUncertainty(result)
item['allow_edit'].append('Uncertainty')
item['Uncertainty'] = unc if unc else ''
item['before']['Uncertainty'] = '± '
item['after'][
'Uncertainty'] = '<em class="discreet" style="white-space:nowrap;"> %s</em>' % item[
'Unit']
item['structure'] = False
elif fu:
item['Uncertainty'] = fu
item['before']['Uncertainty'] = '± '
item['after'][
'Uncertainty'] = '<em class="discreet" style="white-space:nowrap;"> %s</em>' % item[
'Unit']
item['structure'] = True
# 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() is 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:
item['Specification'] = ""
if 'Result' in item['allow_edit']:
item['allow_edit'].remove('Result')
item['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 = ""
item['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
item[f['keyword']] = f
item['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()
item['replace']['DueDate'] = \
self.ulocalized_time(duedate, long_format=1)
if item['review_state'] not in [
'to_be_sampled', 'to_be_preserved', 'sample_due',
'published'
]:
if (resultdate and resultdate > duedate) \
or (not resultdate and DateTime() > duedate):
item['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")))
after_icons = []
# Submitting user may not verify results unless the user is labman
# or manager and the AS has isSelfVerificationEnabled set to True
if item['review_state'] == 'to_be_verified':
# If multi-verification required, place an informative icon
numverifications = obj.getNumberOfRequiredVerifications()
if numverifications > 1:
# More than one verification required, place an icon
# Get the number of verifications already done:
done = obj.getNumberOfVerifications()
pending = numverifications - done
ratio = float(done) / float(numverifications) \
if done > 0 else 0
scale = '' if ratio < 0.25 else '25' \
if ratio < 0.50 else '50' \
if ratio < 0.75 else '75'
anchor = "<a href='#' title='%s %s %s' " \
"class='multi-verification scale-%s'>%s/%s</a>"
anchor = anchor % (t(
_("Multi-verification required")), str(pending),
t(_("verification(s) pending")), scale,
str(done), str(numverifications))
after_icons.append(anchor)
username = member.getUserName()
allowed = ploneapi.user.has_permission(VerifyPermission,
username=username)
if allowed and not obj.isUserAllowedToVerify(member):
after_icons.append(
"<img src='++resource++bika.lims.images/submitted-by-current-user.png' title='%s'/>"
% (t(
_("Cannot verify, submitted or verified by current user before"
))))
elif allowed:
if obj.getSubmittedBy() == member.getUser().getId():
after_icons.append(
"<img src='++resource++bika.lims.images/warning.png' title='%s'/>"
%
(t(_("Can verify, but submitted by current user")))
)
# If analysis Submitted and Verified by the same person, then warning icon will appear.
submitter = obj.getSubmittedBy()
if submitter and obj.wasVerifiedByUser(submitter):
after_icons.append(
"<img src='++resource++bika.lims.images/warning.png' title='%s'/>"
% (t(
_("Submited and verified by the same user- " +
submitter))))
# add icon for assigned analyses in AR views
if self.context.portal_type == 'AnalysisRequest':
obj = item['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]
after_icons.append(
"<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)
}))))
item['after']['state_title'] = ' '.join(after_icons)
# 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
if self.show_categories:
self.categories = map(lambda x: x[0],
sorted(self.categories, key=lambda x: x[1]))
else:
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 folderitems(self, full_objects=False):
# Show only ISharable samples for EMS. Skip others.
pm = getToolByName(self.context, 'portal_membership')
roles = pm.getAuthenticatedMember().getRoles()
#print roles
if 'EMS' in roles:
self.contentFilter['object_provides'] = ISharableSample.__identifier__
items = BikaListingView.folderitems(self)
bsc = getToolByName(self.context, 'bika_setup_catalog')
brains = bsc(portal_type='SampleType', inactive_state='active')
biospecimen_types = [
{
'ResultValue': brain.UID,
'ResultText': brain.title
}
for brain in brains
]
ret = []
for x, item in enumerate(items):
if not items[x].has_key('obj'):
continue
obj = items[x]['obj']
if not ISample.providedBy(obj):
continue
items[x]['Type'] = obj.getSampleType() and obj.getSampleType().Title() or ''
items[x]['Volume'] = obj.getField('Volume').get(obj)
items[x]['Unit'] = obj.getField('Unit').get(obj)
items[x]['SubjectID'] = obj.getField('SubjectID').get(obj)
project = obj.getField('Project').get(obj)
if not project:
project = obj.aq_parent
items[x]['Project'] = project
storage_location = obj.getField('StorageLocation').get(obj)
if storage_location:
items[x]['StorageLocation'] = storage_location.Title()
if project:
items[x]['replace']['Project'] = \
'<a href="%s">%s</a>' % (project.absolute_url(),
project.Title())
items[x]['Barcode'] = obj.getField('Barcode').get(obj)
items[x]['replace']['Title'] = "<a href='%s'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
frozen_time = obj.getField('FrozenTime').get(obj)
if frozen_time:
try:
items[x]['FrozenTime'] = frozen_time.strftime("%Y-%m-%d %H:%M")
except:
items[x]['FrozenTime'] = str(frozen_time)
batch = obj.getField('Batch').get(obj)
try:
items[x]['CFGTime'] = batch.getField('CfgDateTime').get(batch).strftime("%Y/%m/%d %H:%M")
except:
items[x]['CFGTime'] = ''
try:
items[x]['SamplingTime'] = obj.getField('SamplingDate').get(obj).strftime("%Y/%m/%d %H:%M")
except:
items[x]['SamplingTime'] = ''
if self.allow_edit and isActive(self.context) and \
getSecurityManager().checkPermission(ModifyPortalContent, obj):
if items[x]['review_state'] == "sample_registered":
items[x]['allow_edit'] = ['Type', 'Barcode', 'FrozenTime']
items[x]['choices']['Type'] = biospecimen_types
elif items[x]['review_state'] == "sample_due":
# items[x]['allow_edit'] = ['SubjectID', 'Volume', 'Unit']
items[x]['allow_edit'] = ['Volume', 'Unit']
if not items[x]['Unit']:
items[x]['choices']['Unit'] = VOLUME_UNITS
elif items[x]['review_state'] == "sample_shipped":
# items[x]['allow_edit'] = ['SubjectID', 'Volume']
items[x]['allow_edit'] = ['Volume']
ret.append(item)
return ret
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]['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:
if self.context.portal_type == 'AnalysisRequest':
sample = self.context.getSample()
st_uid = sample.getSampleType().UID()
items[i]['st_uid'] = st_uid
if st_uid not in self.specs:
proxies = bsc(portal_type = 'AnalysisSpec',
getSampleTypeUID = st_uid)
elif self.context.portal_type == "Worksheet":
if obj.portal_type == "DuplicateAnalysis":
sample = obj.getAnalysis().getSample()
elif obj.portal_type == "RejectAnalysis":
sample = obj.getAnalysis().getSample()
else:
sample = obj.aq_parent.getSample()
st_uid = sample.getSampleType().UID()
items[i]['st_uid'] = st_uid
if st_uid not in self.specs:
proxies = bsc(portal_type = 'AnalysisSpec',
getSampleTypeUID = st_uid)
elif self.context.portal_type == 'Sample':
st_uid = self.context.getSampleType().UID()
items[i]['st_uid'] = st_uid
if st_uid not in self.specs:
proxies = bsc(portal_type = 'AnalysisSpec',
getSampleTypeUID = st_uid)
else:
proxies = []
if st_uid not in self.specs:
for spec in (p.getObject() for p in proxies):
if spec.getClientUID() == obj.getClientUID():
client_or_lab = 'client'
elif spec.getClientUID() == self.context.bika_setup.bika_analysisspecs.UID():
client_or_lab = 'lab'
else:
continue
for keyword, results_range in \
spec.getResultsRangeDict().items():
# hidden form field 'specs' keyed by sampletype uid:
# {st_uid: {'lab/client':{keyword:{min,max,error}}}}
if st_uid in self.specs:
if client_or_lab in self.specs[st_uid]:
self.specs[st_uid][client_or_lab][keyword] = results_range
else:
self.specs[st_uid][client_or_lab] = {keyword: results_range}
else:
self.specs[st_uid] = {client_or_lab: {keyword: results_range}}
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)
items[i]['Uncertainty'] = format_uncertainty(obj, result, decimalmark=dmk, sciformat=int(scinot))
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 __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
self.context = aq_inner(self.context)
workflow = getToolByName(self.context, 'portal_workflow')
checkPermission = self.context.portal_membership.checkPermission
context = self.context
context_url = context.absolute_url()
# use came_from to decide which UI action was clicked.
# "workflow_action" is the action name specified in the
# portal_workflow transition url.
came_from = "workflow_action"
action = form.get(came_from, '')
if not action and not form.get('bika_listing_filter_bar_submit', ''):
# workflow_action_button is the action name specified in
# the bika_listing_view table buttons.
came_from = "workflow_action_button"
action = form.get('workflow_action_id', '')
if not action:
if self.destination_url == "":
self.destination_url = self.request.get_header("referer",
context_url)
self.request.response.redirect(self.destination_url)
return
if action == "sample":
objects = AnalysisRequestWorkflowAction._get_selected_items(self)
transitioned = {'to_be_preserved': [], 'sample_due': []}
dsfn = 'getDateSampled'
for obj_uid, obj in objects.items():
if obj.portal_type == "AnalysisRequest":
ar = obj
sample = obj.getSample()
else:
# If it is a Sample, then fieldname is DateSampled
dsfn = 'DateSampled'
sample = obj
ar = sample.aq_parent
# can't transition inactive items
if workflow.getInfoFor(sample, 'inactive_state', '') == 'inactive':
continue
# grab this object's Sampler and DateSampled from the form
# (if the columns are available and edit controls exist)
if 'getSampler' in form:
try:
Sampler = form['getSampler'][0][obj_uid].strip()
except KeyError:
continue
Sampler = Sampler and Sampler or ''
sample.setSampler(Sampler)
sample.reindexObject()
if dsfn in form:
try:
DateSampled = form[dsfn][0][obj_uid].strip()
except KeyError:
continue
DateSampled = DateSampled and DateTime(DateSampled) or ''
sample.setDateSampled(DateSampled)
sample.reindexObject()
# write them to the sample
if not sample.getSampler():
# Make the message more specific if the reason for not
# transitioning is that no Sampler has been selected
message = _('Sampler is required for the Sampling transition of ${sample}',
mapping={'sample': sample.Title()})
self.context.plone_utils.addPortalMessage(message, 'info')
continue
if not sample.getDateSampled():
continue
Sampler = sample.getSampler()
DateSampled = sample.getDateSampled()
sample.reindexObject()
ars = sample.getAnalysisRequests()
# Analyses and AnalysisRequets have calculated fields
# that are indexed; re-index all these objects.
for ar in ars:
ar.reindexObject()
analyses = sample.getAnalyses({'review_state': 'to_be_sampled'})
for a in analyses:
a.getObject().reindexObject()
# transition the object if both values are present
if Sampler and DateSampled:
workflow.doActionFor(sample, action)
new_state = workflow.getInfoFor(sample, 'review_state')
doActionFor(ar, action)
transitioned[new_state].append(sample.Title())
message = None
for state in transitioned:
tlist = transitioned[state]
if len(tlist) > 1:
if state == 'to_be_preserved':
message = _('${items} are waiting for preservation.',
mapping={'items': ', '.join(tlist)})
else:
message = _('${items} are waiting to be received.',
mapping={'items': ', '.join(tlist)})
self.context.plone_utils.addPortalMessage(message, 'info')
elif len(tlist) == 1:
if state == 'to_be_preserved':
message = _('${item} is waiting for preservation.',
mapping={'item': ', '.join(tlist)})
else:
message = _('${item} is waiting to be received.',
mapping={'item': ', '.join(tlist)})
self.context.plone_utils.addPortalMessage(message, 'info')
if not message:
message = _('No changes made.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.request.get_header("referer",
context_url)
self.request.response.redirect(self.destination_url)
elif action == "preserve":
objects = AnalysisRequestWorkflowAction._get_selected_items(self)
transitioned = {}
not_transitioned = []
Preserver = str()
DatePreserved = str()
for obj_uid, obj in objects.items():
if obj.portal_type == "AnalysisRequest":
ar = obj
sample = obj.getSample()
else:
sample = obj
ar = sample.aq_parent
# can't transition inactive items
if workflow.getInfoFor(sample, 'inactive_state', '') == 'inactive':
continue
if not checkPermission(PreserveSample, sample):
continue
# grab this object's Preserver and DatePreserved from the form
# (if the columns are available and edit controls exist)
if 'getPreserver' in form and 'getDatePreserved' in form:
try:
Preserver = form['getPreserver'][0][obj_uid].strip()
DatePreserved = form['getDatePreserved'][0][obj_uid].strip()
except KeyError:
continue
Preserver = Preserver and Preserver or ''
DatePreserved = DatePreserved and DateTime(DatePreserved) or ''
else:
continue
for sp in sample.objectValues("SamplePartition"):
if workflow.getInfoFor(sp, 'review_state') == 'to_be_preserved':
sp.setDatePreserved(DatePreserved)
sp.setPreserver(Preserver)
for sp in sample.objectValues("SamplePartition"):
if workflow.getInfoFor(sp, 'review_state') == 'to_be_preserved':
if Preserver and DatePreserved:
doActionFor(sp, action)
transitioned[sp.aq_parent.Title()] = sp.Title()
else:
not_transitioned.append(sp)
if len(transitioned.keys()) > 1:
message = _('${items}: partitions are waiting to be received.',
mapping={'items': ', '.join(transitioned.keys())})
else:
message = _('${item}: ${part} is waiting to be received.',
mapping={'item': ', '.join(transitioned.keys()),
'part': ', '.join(transitioned.values()), })
self.context.plone_utils.addPortalMessage(message, 'info')
# And then the sample itself
if Preserver and DatePreserved and not not_transitioned:
doActionFor(sample, action)
# message = _('${item} is waiting to be received.',
# mapping = {'item': sample.Title()})
# message = t(message)
# self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.request.get_header(
"referer", self.context.absolute_url())
self.request.response.redirect(self.destination_url)
elif action in ('prepublish', 'publish', 'republish'):
# We pass a list of AR objects to Publish.
# it returns a list of AR IDs which were actually published.
objects = AnalysisRequestWorkflowAction._get_selected_items(self)
its = []
for uid, obj in objects.items():
if isActive(obj):
its.append(uid)
its = ",".join(its)
q = "/publish?items=" + its
self.destination_url = self.context.absolute_url() + q
self.request.response.redirect(self.destination_url)
else:
AnalysisRequestWorkflowAction.__call__(self)
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 submit(self):
""" Saves the form
"""
form = self.request.form
remarks = form.get('Remarks', [{}])[0]
results = form.get('Result', [{}])[0]
retested = form.get('retested', {})
methods = form.get('Method', [{}])[0]
instruments = 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]
selected = WorkflowAction._get_selected_items(self)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
sm = getSecurityManager()
hasInterims = {}
# XXX combine data from multiple bika listing tables.
item_data = {}
if 'item_data' in form:
if type(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'])
# Iterate for each selected analysis and save its data as needed
for uid, analysis in selected.items():
allow_edit = sm.checkPermission(EditResults, analysis)
analysis_active = isActive(analysis)
# Need to save remarks?
if uid in remarks and allow_edit and analysis_active:
analysis.setRemarks(remarks[uid])
# Retested?
if uid in retested and allow_edit and analysis_active:
analysis.setRetested(retested[uid])
# 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)
if analysis.meta_type == 'ReferenceAnalysis':
instrument.setDisposeUntilNextCalibrationTest(
False)
# 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 and uid in dlimits and dlimits[uid]:
analysis.setDetectionLimitOperand(dlimits[uid])
# Need to save results?
if uid in results and results[uid] and allow_edit \
and analysis_active:
interims = item_data.get(uid, [])
analysis.setInterimFields(interims)
analysis.setResult(results[uid])
analysis.reindexObject()
can_submit = True
deps = analysis.getDependencies() \
if hasattr(analysis, 'getDependencies') else []
for dependency in deps:
if workflow.getInfoFor(dependency, 'review_state') in \
('to_be_sampled', 'to_be_preserved',
'sample_due', 'sample_received'):
can_submit = False
break
if can_submit:
# doActionFor transitions the analysis to verif pending,
# so must only be done when results are submitted.
doActionFor(analysis, 'submit')
# Maybe some analyses need to be retracted due to a QC failure
# Done here because don't know if the last selected analysis is
# a valid QC for the instrument used in previous analyses.
# If we add this logic in subscribers.analyses, there's the
# possibility to retract analyses before the QC being reached.
self.retractInvalidAnalyses()
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.request.get_header(
"referer", self.context.absolute_url())
self.request.response.redirect(self.destination_url)
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 ''
body = _("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}",
mapping={"request_link":aranchor,
"new_request_link":naranchor,
"remarks": addremarks,
"lab_address": lab_address})
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):
# Do generic bika.lims stuff
_AnalysisRequestWorkflowAction.__call__(self)
# Do bika-health specific actions when submit
action = _AnalysisRequestWorkflowAction._get_form_workflow_action(self)
addPortalMessage = self.context.plone_utils.addPortalMessage
if action[0] == 'submit' and isActive(self.context):
inpanicanalyses = []
workflow = getToolByName(self.context, 'portal_workflow')
translate = self.context.translate
rc = getToolByName(self.context, REFERENCE_CATALOG)
uc = getToolByName(self.context, 'uid_catalog')
# retrieve the results from database and check if
# the values are exceeding panic levels
alerts = {}
for uid in self.request.form.get('Result', [{}])[0].keys():
analysis = rc.lookupObject(uid)
analysis = analysis.getObject() if hasattr(analysis, 'getObject') else analysis
if not analysis:
continue
astate = workflow.getInfoFor(analysis, 'review_state')
if astate == 'retracted':
continue
alerts.update(ResultOutOfRange(analysis)())
if alerts:
message = translate(_('Some results exceeded the '
'panic levels that may '
'indicate an imminent '
'life-threatening condition'
))
addPortalMessage(message, 'warning')
self.request.response.redirect(self.context.absolute_url())
# If panic levels alert email enabled, send an email to
# labmanagers
bs = self.context.bika_setup
if hasattr(bs, 'getEnablePanicAlert') \
and bs.getEnablePanicAlert():
laboratory = self.context.bika_setup.laboratory
lab_address = "<br/>".join(laboratory.getPrintAddress())
managers = self.context.portal_groups.getGroupMembers('LabManagers')
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = _("Panic alert")
mime_msg['From'] = formataddr(
(encode_header(laboratory.getName()),
laboratory.getEmailAddress()))
to = []
for manager in managers:
user = self.portal.acl_users.getUser(manager)
uemail = user.getProperty('email')
ufull = user.getProperty('fullname')
to.append(formataddr((encode_header(ufull), uemail)))
mime_msg['To'] = ','.join(to)
strans = []
ars = {}
for analysis_uid, alertlist in alerts:
analysis = uc(analysis_uid).getObject()
for alert in alertlist:
ars[analysis.aq_parent.Title()] = 1
strans.append("- {0}, {1}: {2}".format(
analysis.Title(),
translate(_("Result")),
analysis.getResult()))
ars = ", ".join(ars.keys())
stran = "<br/>".join(strans)
text = translate(_(
"Some results from ${items} exceeded the panic levels "
"that may indicate an imminent life-threatening "
"condition: <br/><br/>{analysisresults}<br/><br/>"
"<b>Please, check the Analysis Request if you "
"want to re-test the analysis or immediately "
"alert the client.</b><br/><br/>{lab_address}",
mapping={'items': ars,
'analysisresults': stran,
'lab_address': lab_address}))
msg_txt = MIMEText(safe_unicode(text).encode('utf-8'),
_subtype='html')
mime_msg.preamble = 'This is a multi-part MIME message.'
mime_msg.attach(msg_txt)
try:
host = getToolByName(self.context, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except Exception as msg:
ar = inpanicanalyses[0].getRequestID()
logger.error("Panic level email %s: %s" %
(ar, str(msg)))
message = translate(
_('Unable to send an email to alert lab '
'managers that some analyses exceeded the '
'panic levels') + (": %s" % str(msg)))
addPortalMessage(message, 'warning')
def folderitems(self):
rc = getToolByName(self.context, REFERENCE_CATALOG)
bsc = getToolByName(self.context, 'bika_setup_catalog')
workflow = getToolByName(self.context, 'portal_workflow')
portal = getToolByName(self.context, 'portal_url').getPortalObject()
translate = self.context.translation_service.translate
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)
context_active = isActive(self.context)
items = super(AnalysesView, self).folderitems(full_objects=True)
self.interim_fields = {}
self.interim_columns = {}
self.specs = {}
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']
result = obj.getResult()
service = obj.getService()
calculation = service.getCalculation()
unit = service.getUnit()
keyword = service.getKeyword()
precision = service.getPrecision()
# Check for InterimFields attribute on our object,
interim_fields = hasattr(obj, 'getInterimFields') \
and obj.getInterimFields() or []
self.interim_fields[obj.UID()] = interim_fields
items[i]['Keyword'] = keyword
items[i]['Unit'] = unit and unit or ''
items[i]['Result'] = ''
items[i]['formatted_result'] = ''
items[i]['interim_fields'] = interim_fields
items[i]['Uncertainty'] = ''
items[i]['retested'] = obj.getRetested()
items[i]['class']['retested'] = 'center'
items[i]['calculation'] = calculation and True or False
items[i]['Partition'] = obj.getSamplePartition().Title()
if obj.portal_type == "ReferenceAnalysis":
items[i]['DueDate'] = ''
items[i]['CaptureDate'] = ''
else:
items[i]['DueDate'] = obj.getDueDate()
cd = obj.getResultCaptureDate()
items[i]['CaptureDate'] = cd and TimeOrDate(self.context,
cd) or ''
items[i]['Attachments'] = ''
# calculate specs
if obj.portal_type == 'ReferenceAnalysis':
items[i]['st_uid'] = obj.aq_parent.UID()
else:
if self.context.portal_type == 'AnalysisRequest':
sample = self.context.getSample()
st_uid = sample.getSampleType().UID()
items[i]['st_uid'] = st_uid
if st_uid not in self.specs:
proxies = bsc(portal_type='AnalysisSpec',
getSampleTypeUID=st_uid)
elif self.context.portal_type == "Worksheet":
if obj.portal_type == "DuplicateAnalysis":
sample = obj.getAnalysis().getSample()
else:
sample = obj.aq_parent.getSample()
st_uid = sample.getSampleType().UID()
items[i]['st_uid'] = st_uid
if st_uid not in self.specs:
proxies = bsc(portal_type='AnalysisSpec',
getSampleTypeUID=st_uid)
elif self.context.portal_type == 'Sample':
st_uid = self.context.getSampleType().UID()
items[i]['st_uid'] = st_uid
if st_uid not in self.specs:
proxies = bsc(portal_type='AnalysisSpec',
getSampleTypeUID=st_uid)
else:
proxies = []
if st_uid not in self.specs:
for spec in (p.getObject() for p in proxies):
client_or_lab = ""
if spec.getClientUID() == obj.getClientUID():
client_or_lab = 'client'
elif spec.getClientUID(
) == self.context.bika_setup.bika_analysisspecs.UID():
client_or_lab = 'lab'
else:
continue
for keyword, results_range in \
spec.getResultsRangeDict().items():
# hidden form field 'specs' keyed by sampletype uid:
# {st_uid: {'lab/client':{keyword:{min,max,error}}}}
if st_uid in self.specs:
if client_or_lab in self.specs[st_uid]:
self.specs[st_uid][client_or_lab][
keyword] = results_range
else:
self.specs[st_uid][client_or_lab] = {
keyword: results_range
}
else:
self.specs[st_uid] = {
client_or_lab: {
keyword: results_range
}
}
method = service.getMethod()
items[i]['Method'] = method and method.Title() or ''
if method:
items[i]['replace']['Method'] = "<a href='%s'>%s</a>" % \
(method.absolute_url(), method.Title())
# Show version number of out-of-date objects
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"
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:
items[i]['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)) )
if can_edit_analysis:
items[i]['allow_edit'] = [
'Result',
]
# 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')
# 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
items[i]['formatted_result'] = result
if result != '':
if 'Result' in items[i]['choices'] and items[i]['choices'][
'Result']:
items[i]['formatted_result'] = \
[r['ResultText'] for r in items[i]['choices']['Result'] \
if str(r['ResultValue']) == str(result)][0]
else:
try:
items[i]['formatted_result'] = precision and \
str("%%.%sf" % precision) % float(result) or result
except:
items[i]['formatted_result'] = result
indet = translate(_('Indet'))
if result == indet:
# 'Indeterminate' results flag a specific error
Indet = translate(_("Indeterminate result"))
items[i]['after']['Result'] = \
'<img width="16" height="16" title="%s"' % Indet + \
'src="%s/++resource++bika.lims.images/exclamation.png"/>' % \
(portal.absolute_url())
else:
# result being un-floatable, is an error.
msg = translate(_("Invalid result"))
items[i]['after']['Result'] = \
'<img width="16" height="16" title="%s"' % msg + \
'src="%s/++resource++bika.lims.images/exclamation.png"/>' % \
(portal.absolute_url())
items[i]['Uncertainty'] = obj.getUncertainty(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'/>" % (
portal.absolute_url(), icon)
attachments += '<a href="%s/at_download/AttachmentFile"/>%s</a>' % (
attachment.absolute_url(), af.filename)
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>"
if hasattr(obj, 'result_in_range'):
items[i]['result_in_range'] = obj.result_in_range(
result, self.chosen_spec)
else:
items[i]['result_in_range'] = (True, None)
if not can_view_result or \
(not items[i]['Result'] and not can_edit_analysis):
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"/>' % \
(portal.absolute_url())
# 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:
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
if items[i]['obj'].portal_type != "DuplicateAnalysis":
if (not calculation or (calculation and not calculation.getDependentServices())) and \
items[i]['review_state'] not in ['to_be_sampled', 'to_be_preserved', 'sample_due', 'published'] and \
items[i]['DueDate'] < DateTime():
DueDate = TimeOrDate(self.context,
item['DueDate'],
long_format=0)
if self.context.portal_type == 'AnalysisRequest':
items[i]['replace']['DueDate'] = '%s <img width="16" height="16" src="%s/++resource++bika.lims.images/late.png" title="%s"/>' % \
(DueDate, portal.absolute_url(),
translate(_("Due Date")) + ": %s"%DueDate)
else:
items[i]['replace']['DueDate'] = '%s <img width="16" height="16" src="%s/++resource++bika.lims.images/late.png" title="%s"/>' % \
(DueDate, portal.absolute_url(),
translate(_("Late Analysis")))
else:
items[i]['replace']['DueDate'] = TimeOrDate(
self.context, item['DueDate'])
# add icon for assigned analyses in AR views
if self.context.portal_type == 'AnalysisRequest' and \
workflow.getInfoFor(items[i]['obj'], 'worksheetanalysis_review_state') == 'assigned':
ws = items[i]['obj'].getBackReferences('WorksheetAnalysis')[0]
items[i]['after']['state_title'] = \
"<a href='%s'><img src='++resource++bika.lims.images/worksheet.png' title='Assigned: %s'/></a>" % \
(ws.absolute_url(), 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.
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 always enabled for worksheets,
# never enabled for reference sample contexts, and refers to
# getReportDryMatter in ARs.
# XXX It should be enabled only if any of the ARs present asked for DM.
if items and \
(self.context.portal_type == 'Worksheet' or \
(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.json_specs = json.dumps(self.specs)
self.json_interim_fields = json.dumps(self.interim_fields)
return items
def __call__(self):
# Do generic bika.lims stuff
BaseClass.__call__(self)
# Do bika-health specific actions when submit
action = BaseClass._get_form_workflow_action(self)
addPortalMessage = self.context.plone_utils.addPortalMessage
if action[0] == 'submit' and isActive(self.context):
inpanicanalyses = []
workflow = getToolByName(self.context, 'portal_workflow')
translate = self.context.translate
rc = getToolByName(self.context, REFERENCE_CATALOG)
uc = getToolByName(self.context, 'uid_catalog')
# retrieve the results from database and check if
# the values are exceeding panic levels
alerts = {}
for uid in self.request.form.get('Result', [{}])[0].keys():
analysis = rc.lookupObject(uid)
analysis = analysis.getObject() if hasattr(analysis, 'getObject') else analysis
if not analysis:
continue
astate = workflow.getInfoFor(analysis, 'review_state')
if astate == 'retracted':
continue
alerts.update(ResultOutOfRange(analysis)())
if alerts:
message = translate(_('Some results exceeded the '
'panic levels that may '
'indicate an imminent '
'life-threatening condition'
))
addPortalMessage(message, 'warning')
self.request.response.redirect(self.context.absolute_url())
# If panic levels alert email enabled, send an email to
# labmanagers
bs = self.context.bika_setup
if hasattr(bs, 'getEnablePanicAlert') \
and bs.getEnablePanicAlert():
laboratory = self.context.bika_setup.laboratory
lab_address = "<br/>".join(laboratory.getPrintAddress())
managers = self.context.portal_groups.getGroupMembers('LabManagers')
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = _("Panic alert")
mime_msg['From'] = formataddr(
(encode_header(laboratory.getName()),
laboratory.getEmailAddress()))
to = []
for manager in managers:
user = self.portal.acl_users.getUser(manager)
uemail = user.getProperty('email')
ufull = user.getProperty('fullname')
to.append(formataddr((encode_header(ufull), uemail)))
mime_msg['To'] = ','.join(to)
strans = []
ars = {}
for analysis_uid, alertlist in alerts:
analysis = uc(analysis_uid).getObject()
for alert in alertlist:
ars[analysis.aq_parent.Title()] = 1
strans.append("- {0}, {1}: {2}".format(
analysis.getService().Title(),
translate(_("Result")),
analysis.getResult()))
ars = ", ".join(ars.keys())
stran = "<br/>".join(strans)
text = translate(_(
"Some results from ${items} exceeded the panic levels "
"that may indicate an imminent life-threatening "
"condition: <br/><br/>{analysisresults}<br/><br/>"
"<b>Please, check the Analysis Request if you "
"want to re-test the analysis or immediately "
"alert the client.</b><br/><br/>{lab_address}",
mapping={'items': ars,
'analysisresults': stran,
'lab_address': lab_address}))
msg_txt = MIMEText(safe_unicode(text).encode('utf-8'),
_subtype='html')
mime_msg.preamble = 'This is a multi-part MIME message.'
mime_msg.attach(msg_txt)
try:
host = getToolByName(self.context, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except Exception as msg:
ar = inpanicanalyses[0].getRequestID()
logger.error("Panic level email %s: %s" %
(ar, str(msg)))
message = translate(
_('Unable to send an email to alert lab '
'managers that some analyses exceeded the '
'panic levels') + (": %s" % str(msg)))
addPortalMessage(message, 'warning')
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
bsc = getToolByName(self.context, 'bika_setup_catalog')
bac = getToolByName(self.context, 'bika_analysis_catalog')
action, came_from = WorkflowAction._get_form_workflow_action(self)
# XXX combine data from multiple bika listing tables.
item_data = {}
if 'item_data' in form:
if type(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'])
if action == 'submit' and self.request.form.has_key("Result"):
selected_analyses = WorkflowAction._get_selected_items(self)
results = {}
hasInterims = {}
# first save results for entire form
for uid, result in self.request.form['Result'][0].items():
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
if not(getSecurityManager().checkPermission(EditResults, analysis)):
# or changes no longer allowed
continue
if not isActive(analysis):
# or it's cancelled
continue
results[uid] = result
service = analysis.getService()
interimFields = item_data[uid]
if len(interimFields) > 0:
hasInterims[uid] = True
else:
hasInterims[uid] = False
unit = service.getUnit()
analysis.edit(
Result = result,
InterimFields = interimFields,
Retested = form.has_key('retested') and \
form['retested'].has_key(uid),
Unit = unit and unit or '')
# discover which items may be submitted
submissable = []
for uid, analysis in selected_analyses.items():
if uid not in results:
continue
can_submit = True
if hasattr(analysis, 'getDependencies'):
dependencies = analysis.getDependencies()
for dependency in dependencies:
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
for dependency in dependencies:
if workflow.getInfoFor(dependency, 'review_state') in \
('to_be_sampled', 'to_be_preserved',
'sample_due', 'sample_received'):
can_submit = False
if can_submit:
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')
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
self.request.response.redirect(self.destination_url)
## assign
elif action == 'assign':
if not(getSecurityManager().checkPermission(EditWorksheet, self.context)):
self.request.response.redirect(self.context.absolute_url())
return
selected_analyses = WorkflowAction._get_selected_items(self)
selected_analysis_uids = selected_analyses.keys()
if selected_analyses:
for uid in selected_analysis_uids:
analysis = rc.lookupObject(uid)
# Double-check the state first
if (workflow.getInfoFor(analysis, 'worksheetanalysis_review_state') == 'unassigned'
and workflow.getInfoFor(analysis, 'review_state') == 'sample_received'
and workflow.getInfoFor(analysis, 'cancellation_state') == 'active'):
self.context.addAnalysis(analysis)
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
## unassign
elif action == 'unassign':
if not(getSecurityManager().checkPermission(EditWorksheet, self.context)):
self.request.response.redirect(self.context.absolute_url())
return
selected_analyses = WorkflowAction._get_selected_items(self)
selected_analysis_uids = selected_analyses.keys()
for analysis_uid in selected_analysis_uids:
try:
analysis = bac(UID=analysis_uid)[0].getObject()
except IndexError:
# Duplicate analyses are removed when their analyses
# get removed, so indexerror is expected.
continue
if skip(analysis, action, peek=True):
continue
self.context.removeAnalysis(analysis)
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
## verify
elif action == 'verify':
# default bika_listing.py/WorkflowAction, but then go to view screen.
self.destination_url = self.context.absolute_url()
WorkflowAction.__call__(self)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
