def create_analysis(context, service, keyword, interim_fields):
# Determine if the sampling workflow is enabled
workflow_enabled = context.bika_setup.getSamplingWorkflowEnabled()
# Create the analysis
analysis = _createObjectByType("Analysis", context, keyword)
analysis.setService(service)
analysis.setInterimFields(interim_fields)
analysis.setMaxTimeAllowed(service.getMaxTimeAllowed())
analysis.unmarkCreationFlag()
analysis.reindexObject()
# Trigger the intitialization event of the new object
# zope.event.notify(ObjectInitializedEvent(analysis))
event.notify(ObjectInitializedEvent(analysis))
# Perform the appropriate workflow action
try:
workflow_action = 'sampling_workflow' if workflow_enabled \
else 'no_sampling_workflow'
context.portal_workflow.doActionFor(analysis, workflow_action)
except WorkflowException:
# The analysis may have been transitioned already!
# I am leaving this code here though, to prevent regression.
pass
# Return the newly created analysis
return analysis
def _add_services_to_ar(self, ar, analyses):
#Add Services
service_uids = [i.split(':')[0] for i in analyses]
new_analyses = ar.setAnalyses(service_uids)
ar.setRequestID(ar.getId())
ar.reindexObject()
event.notify(ObjectInitializedEvent(ar))
ar.at_post_create_script()
SamplingWorkflowEnabled = \
self.bika_setup.getSamplingWorkflowEnabled()
wftool = getToolByName(self, 'portal_workflow')
# Create sample partitions
parts = [{'services': [],
'container':[],
'preservation':'',
'separate':False}]
sample = ar.getSample()
parts_and_services = {}
for _i in range(len(parts)):
p = parts[_i]
part_prefix = sample.getId() + "-P"
if '%s%s' % (part_prefix, _i + 1) in sample.objectIds():
parts[_i]['object'] = sample['%s%s' % (part_prefix, _i + 1)]
parts_and_services['%s%s' % (part_prefix, _i + 1)] = \
p['services']
else:
part = _createObjectByType("SamplePartition", sample, tmpID())
parts[_i]['object'] = part
container = None
preservation = p['preservation']
parts[_i]['prepreserved'] = False
part.unmarkCreationFlag()
part.edit(
Container=container,
Preservation=preservation,
)
part._renameAfterCreation()
if SamplingWorkflowEnabled:
wftool.doActionFor(part, 'sampling_workflow')
else:
wftool.doActionFor(part, 'no_sampling_workflow')
parts_and_services[part.id] = p['services']
if SamplingWorkflowEnabled:
wftool.doActionFor(ar, 'sampling_workflow')
else:
wftool.doActionFor(ar, 'no_sampling_workflow')
# Add analyses to sample partitions
# XXX jsonapi create AR: right now, all new analyses are linked to the first samplepartition
if new_analyses:
analyses = list(part.getAnalyses())
analyses.extend(new_analyses)
part.edit(
Analyses=analyses,
)
for analysis in new_analyses:
analysis.setSamplePartition(part)
# If Preservation is required for some partitions,
# and the SamplingWorkflow is disabled, we need
# to transition to to_be_preserved manually.
if not SamplingWorkflowEnabled:
to_be_preserved = []
sample_due = []
lowest_state = 'sample_due'
for p in sample.objectValues('SamplePartition'):
if p.getPreservation():
lowest_state = 'to_be_preserved'
to_be_preserved.append(p)
else:
sample_due.append(p)
for p in to_be_preserved:
doActionFor(p, 'to_be_preserved')
for p in sample_due:
doActionFor(p, 'sample_due')
doActionFor(sample, lowest_state)
for analysis in ar.objectValues('Analysis'):
doActionFor(analysis, lowest_state)
doActionFor(ar, lowest_state)
def _submit_arimport_p(self):
""" load the profiles import layout """
ars = []
samples = []
valid_batch = False
client = self.aq_parent
contact_obj = None
cc_contact_obj = None
# validate contact
for contact in client.objectValues('Contact'):
if contact.getUsername() == self.getContactID():
contact_obj = contact
if self.getCCContactID() == None:
if contact_obj != None:
break
else:
if contact.getUsername() == self.getCCContactID():
cc_contact_obj = contact
if contact_obj != None:
break
if contact_obj == None:
valid_batch = False
# get Keyword to ServiceId Map
services = {}
service_uids = {}
for service in self.bika_setup_catalog(
portal_type = 'AnalysisService'):
obj = service.getObject()
keyword = obj.getKeyword()
if keyword:
services[keyword] = '%s:%s' % (obj.UID(), obj.getPrice())
service_uids[obj.UID()] = '%s:%s' % (obj.UID(), obj.getPrice())
samplepoints = self.bika_setup_catalog(
portal_type = 'SamplePoint',
Title = self.getSamplePoint())
if not samplepoints:
valid_batch = False
profiles = {}
aritems = self.objectValues('ARImportItem')
request = self.REQUEST
title = 'Submitting AR Import'
bar = ProgressBar(
self, request, title, description='')
event.notify(InitialiseProgressBar(bar))
row_count = 0
item_count = len(aritems)
prefix = 'Sample'
for aritem in aritems:
# set up analyses
ar_profile = None
analyses = []
row_count += 1
for profilekey in aritem.getAnalysisProfile():
this_profile = None
if not profiles.has_key(profilekey):
profiles[profilekey] = []
# there is no profilekey index
l_prox = self._findProfileKey(profilekey)
if l_prox:
profiles[profilekey] = \
[s.UID() for s in l_prox.getService()]
this_profile = l_prox
else:
#TODO This will not find it!!
# there is no profilekey index
c_prox = self.bika_setup_catalog(
portal_type = 'AnalysisProfile',
getClientUID = client.UID(),
getProfileKey = profilekey)
if c_prox:
obj = c_prox[0].getObject()
profiles[profilekey] = \
[s.UID() for s in obj.getService()]
this_profile = obj
if ar_profile is None:
ar_profile = obj
else:
ar_profile = None
profile = profiles[profilekey]
for analysis in profile:
if not service_uids.has_key(analysis):
service = tool.lookupObject(analysis)
keyword = service.getKeyword()
service_uids[obj.UID()] = '%s:%s' % (obj.UID(), obj.getPrice())
if keyword:
services[keyword] = '%s:%s' % (obj.UID(), obj.getPrice())
if service_uids.has_key(analysis):
if not service_uids[analysis] in analyses:
analyses.append(service_uids[analysis])
else:
valid_batch = False
for analysis in aritem.getAnalyses(full_objects=True):
if not services.has_key(analysis):
for service in self.bika_setup_catalog(
portal_type = 'AnalysisService',
getKeyword = analysis):
obj = service.getObject()
services[analysis] = '%s:%s' % (obj.UID(), obj.getPrice())
service_uids[obj.UID()] = '%s:%s' % (obj.UID(), obj.getPrice())
if services.has_key(analysis):
analyses.append(services[analysis])
else:
valid_batch = False
sampletypes = self.portal_catalog(
portal_type = 'SampleType',
sortable_title = aritem.getSampleType().lower(),
)
if not sampletypes:
valid_batch = False
return
sampletypeuid = sampletypes[0].getObject().UID()
if aritem.getSampleDate():
date_items = aritem.getSampleDate().split('/')
sample_date = DateTime(
int(date_items[2]), int(date_items[0]), int(date_items[1]))
else:
sample_date = None
sample_id = '%s-%s' % (prefix, tmpID())
sample = _createObjectByType("Sample", client, sample_id)
sample.unmarkCreationFlag()
sample.edit(
SampleID = sample_id,
ClientReference = aritem.getClientRef(),
ClientSampleID = aritem.getClientSid(),
SampleType = aritem.getSampleType(),
DateSampled = sample_date,
SamplingDate = sample_date,
DateReceived = DateTime(),
Remarks = aritem.getClientRemarks(),
)
sample._renameAfterCreation()
sample.setSamplePoint(self.getSamplePoint())
sample.setSampleID(sample.getId())
event.notify(ObjectInitializedEvent(sample))
sample.at_post_create_script()
sample_uid = sample.UID()
samples.append(sample_id)
aritem.setSample(sample_uid)
priorities = self.bika_setup_catalog(
portal_type = 'ARPriority',
sortable_title = aritem.Priority.lower(),
)
if len(priorities) < 1:
logger.warning(
'Invalid Priority: validation should have prevented this')
priority = ''
else:
priority = priorities[0].getObject()
ar_id = tmpID()
ar = _createObjectByType("AnalysisRequest", client, ar_id)
report_dry_matter = False
ar.unmarkCreationFlag()
ar.edit(
RequestID = ar_id,
Contact = self.getContact(),
CCContact = self.getCCContact(),
CCEmails = self.getCCEmailsInvoice(),
ClientOrderNumber = self.getOrderID(),
ReportDryMatter = report_dry_matter,
Profile = ar_profile,
Analyses = analyses,
Remarks = aritem.getClientRemarks(),
Priority = priority,
)
ar.setSample(sample_uid)
sample = ar.getSample()
ar.setSampleType(sampletypeuid)
ar_uid = ar.UID()
aritem.setAnalysisRequest(ar_uid)
ars.append(ar_id)
ar._renameAfterCreation()
progress_index = float(row_count)/float(item_count)*100.0
progress = ProgressState(request, progress_index)
event.notify(UpdateProgressEvent(progress))
self._add_services_to_ar(ar, analyses)
self.setDateApplied(DateTime())
self.reindexObject()
def _submit_arimport_c(self):
""" load the classic import layout """
ars = []
samples = []
valid_batch = True
client = self.aq_parent
contact_obj = None
cc_contact_obj = None
# validate contact
for contact in client.objectValues('Contact'):
if contact.getUsername() == self.getContactID():
contact_obj = contact
if self.getCCContactID() == None:
if contact_obj != None:
break
else:
if contact.getUsername() == self.getCCContactID():
cc_contact_obj = contact
if contact_obj != None:
break
if contact_obj == None:
valid_batch = False
# get Keyword to ServiceId Map
services = {}
for service in self.bika_setup_catalog(
portal_type = 'AnalysisService'):
obj = service.getObject()
keyword = obj.getKeyword()
if keyword:
services[keyword] = '%s:%s' % (obj.UID(), obj.getPrice())
samplepoints = self.bika_setup_catalog(
portal_type = 'SamplePoint',
Title = self.getSamplePoint())
if not samplepoints:
valid_batch = False
aritems = self.objectValues('ARImportItem')
request = self.REQUEST
title = 'Submitting AR Import'
bar = ProgressBar(
self, request, title, description='')
event.notify(InitialiseProgressBar(bar))
SamplingWorkflowEnabled = \
self.bika_setup.getSamplingWorkflowEnabled()
row_count = 0
item_count =len(aritems)
prefix = 'Sample'
for aritem in aritems:
row_count += 1
# set up analyses
analyses = []
for analysis in aritem.getAnalyses(full_objects=True):
if services.has_key(analysis):
analyses.append(services[analysis])
else:
valid_batch = False
sampletypes = self.portal_catalog(
portal_type = 'SampleType',
sortable_title = aritem.getSampleType().lower(),
)
if not sampletypes:
valid_batch = False
return
sampletypeuid = sampletypes[0].getObject().UID()
if aritem.getSampleDate():
date_items = aritem.getSampleDate().split('/')
sample_date = DateTime(
int(date_items[2]), int(date_items[1]), int(date_items[0]))
else:
sample_date = None
sample_id = '%s-%s' % (prefix, tmpID())
sample = _createObjectByType("Sample", client, sample_id)
sample.unmarkCreationFlag()
sample.edit(
SampleID = sample_id,
ClientReference = aritem.getClientRef(),
ClientSampleID = aritem.getClientSid(),
SampleType = aritem.getSampleType(),
DateSampled = sample_date,
SamplingDate = sample_date,
DateReceived = DateTime(),
)
sample._renameAfterCreation()
#sp_id = client.invokeFactory('SamplePoint', id=tmpID())
#sp = client[sp_id]
#sp.edit(title=self.getSamplePoint())
sample.setSamplePoint(self.getSamplePoint())
sample.setSampleID(sample.getId())
event.notify(ObjectInitializedEvent(sample))
sample.at_post_create_script()
sample_uid = sample.UID()
samples.append(sample_id)
aritem.setSample(sample_uid)
priorities = self.bika_setup_catalog(
portal_type = 'ARPriority',
sortable_title = aritem.Priority.lower(),
)
if len(priorities) < 1:
logger.warning(
'Invalid Priority: validation should have prevented this')
#Create AR
ar_id = tmpID()
ar = _createObjectByType("AnalysisRequest", client, ar_id)
if aritem.getReportDryMatter().lower() == 'y':
report_dry_matter = True
else:
report_dry_matter = False
ar.unmarkCreationFlag()
ar.edit(
RequestID = ar_id,
Contact = self.getContact(),
CCContact = self.getCCContact(),
CCEmails = self.getCCEmailsInvoice(),
ClientOrderNumber = self.getOrderID(),
ReportDryMatter = report_dry_matter,
Analyses = analyses,
Priority = priorities[0].getObject(),
)
ar.setSample(sample_uid)
sample = ar.getSample()
ar.setSampleType(sampletypeuid)
ar_uid = ar.UID()
aritem.setAnalysisRequest(ar_uid)
ars.append(ar_id)
ar._renameAfterCreation()
self._add_services_to_ar(ar, analyses)
progress_index = float(row_count)/float(item_count)*100.0
progress = ProgressState(request, progress_index)
event.notify(UpdateProgressEvent(progress))
#TODO REmove for production - just to look pretty
#time.sleep(1)
self.setDateApplied(DateTime())
self.reindexObject()
def create(self, context, request):
"""/@@API/create: Create new object.
Required parameters:
- obj_type = portal_type of new object.
- obj_path = path of new object, from plone site root. - Not required for
obj_type=AnalysisRequest
Optionally:
- obj_id = ID of new object.
All other parameters in the request are matched against the object's
Schema. If a matching field is found in the schema, then the value is
taken from the request and sent to the field's mutator.
Reference fields may have their target value(s) specified with a
delimited string query syntax, containing the portal_catalog search:
<FieldName>=index1:value1|index2:value2
eg to set the Client of a batch:
...@@API/update?obj_path=<path>...
...&Client=title:<client_title>&...
And, to set a multi-valued reference, these both work:
...@@API/update?obj_path=<path>...
...&InheritedObjects:list=title:AR1...
...&InheritedObjects:list=title:AR2...
...@@API/update?obj_path=<path>...
...&InheritedObjects[]=title:AR1...
...&InheritedObjects[]=title:AR2...
The Analysis_Specification parameter is special, it mimics
the format of the python dictionaries, and only service Keyword
can be used to reference services. Even if the keyword is not
actively required, it must be supplied:
<service_keyword>:min:max:error tolerance
The function returns a dictionary as a json string:
{
runtime: Function running time.
error: true or string(message) if error. false if no error.
success: true or string(message) if success. false if no success.
}
>>> portal = layer['portal']
>>> portal_url = portal.absolute_url()
>>> from plone.app.testing import SITE_OWNER_NAME
>>> from plone.app.testing import SITE_OWNER_PASSWORD
Simple AR creation, no obj_path parameter is required:
>>> browser = layer['getBrowser'](portal, loggedIn=True, username=SITE_OWNER_NAME, password=SITE_OWNER_PASSWORD)
>>> browser.open(portal_url+"/@@API/create", "&".join([
... "obj_type=AnalysisRequest",
... "Client=portal_type:Client|id:client-1",
... "SampleType=portal_type:SampleType|title:Apple Pulp",
... "Contact=portal_type:Contact|getFullname:Rita Mohale",
... "Services:list=portal_type:AnalysisService|title:Calcium",
... "Services:list=portal_type:AnalysisService|title:Copper",
... "Services:list=portal_type:AnalysisService|title:Magnesium",
... "SamplingDate=2013-09-29",
... "Specification=portal_type:AnalysisSpec|title:Apple Pulp",
... ]))
>>> browser.contents
'{..."success": true...}'
If some parameters are specified and are not located as existing fields or properties
of the created instance, the create should fail:
>>> browser = layer['getBrowser'](portal, loggedIn=True, username=SITE_OWNER_NAME, password=SITE_OWNER_PASSWORD)
>>> browser.open(portal_url+"/@@API/create?", "&".join([
... "obj_type=Batch",
... "obj_path=/batches",
... "title=Test",
... "Thing=Fish"
... ]))
>>> browser.contents
'{...The following request fields were not used: ...Thing...}'
Now we test that the AR create also fails if some fields are spelled wrong
>>> browser = layer['getBrowser'](portal, loggedIn=True, username=SITE_OWNER_NAME, password=SITE_OWNER_PASSWORD)
>>> browser.open(portal_url+"/@@API/create", "&".join([
... "obj_type=AnalysisRequest",
... "thing=Fish",
... "Client=portal_type:Client|id:client-1",
... "SampleType=portal_type:SampleType|title:Apple Pulp",
... "Contact=portal_type:Contact|getFullname:Rita Mohale",
... "Services:list=portal_type:AnalysisService|title:Calcium",
... "Services:list=portal_type:AnalysisService|title:Copper",
... "Services:list=portal_type:AnalysisService|title:Magnesium",
... "SamplingDate=2013-09-29"
... ]))
>>> browser.contents
'{...The following request fields were not used: ...thing...}'
"""
savepoint = transaction.savepoint()
self.context = context
self.request = request
self.unused = [x for x in self.request.form.keys()]
self.used("form.submitted")
self.used("__ac_name")
self.used("__ac_password")
# always require obj_type
self.require("obj_type")
obj_type = self.request['obj_type']
self.used("obj_type")
# AnalysisRequest shortcut: creates Sample, Partition, AR, Analyses.
if obj_type == "AnalysisRequest":
try:
return self._create_ar(context, request)
except:
savepoint.rollback()
raise
# Other object types require explicit path as their parent
self.require("obj_path")
obj_path = self.request['obj_path']
if not obj_path.startswith("/"):
obj_path = "/" + obj_path
self.used("obj_path")
site_path = request['PATH_INFO'].replace("/@@API/create", "")
parent = context.restrictedTraverse(str(site_path + obj_path))
# normal permissions still apply for this user
if not getSecurityManager().checkPermission(AccessJSONAPI, parent):
msg = "You don't have the '{0}' permission on {1}".format(
AccessJSONAPI, parent.absolute_url())
raise Unauthorized(msg)
obj_id = request.get("obj_id", "")
_renameAfterCreation = False
if not obj_id:
_renameAfterCreation = True
obj_id = tmpID()
self.used(obj_id)
ret = {
"url": router.url_for("create", force_external=True),
"success": True,
"error": False,
}
try:
obj = _createObjectByType(obj_type, parent, obj_id)
obj.unmarkCreationFlag()
if _renameAfterCreation:
renameAfterCreation(obj)
ret['obj_id'] = obj.getId()
used_fields = set_fields_from_request(obj, request)
for field in used_fields:
self.used(field)
obj.reindexObject()
obj.aq_parent.reindexObject()
event.notify(ObjectInitializedEvent(obj))
obj.at_post_create_script()
except:
savepoint.rollback()
raise
if self.unused:
raise BadRequest("The following request fields were not used: %s. Request aborted." % self.unused)
return ret
def _create_ar(self, context, request):
"""Creates AnalysisRequest object, with supporting Sample, Partition
and Analysis objects. The client is retrieved from the obj_path
key in the request.
Required request parameters:
- Contact: One client contact Fullname. The contact must exist
in the specified client. The first Contact with the specified
value in it's Fullname field will be used.
- SampleType_<index> - Must be an existing sample type.
Optional request parameters:
- CCContacts: A list of contact Fullnames, which will be copied on
all messages related to this AR and it's sample or results.
- CCEmails: A list of email addresses to include as above.
- Sample_id: Create a secondary AR with an existing sample. If
unspecified, a new sample is created.
- Specification: a lookup to set Analysis specs default values
for all analyses
- Analysis_Specification: specs (or overrides) per analysis, using
a special lookup format.
&Analysis_Specification:list=<Keyword>:min:max:error&...
"""
wftool = getToolByName(context, 'portal_workflow')
bc = getToolByName(context, 'bika_catalog')
bsc = getToolByName(context, 'bika_setup_catalog')
pc = getToolByName(context, 'portal_catalog')
ret = {
"url": router.url_for("create", force_external=True),
"success": True,
"error": False,
}
SamplingWorkflowEnabled = context.bika_setup.getSamplingWorkflowEnabled()
for field in [
'Client',
'SampleType',
'Contact',
'SamplingDate',
'Services']:
self.require(field)
self.used(field)
try:
client = resolve_request_lookup(context, request, 'Client')[0].getObject()
except IndexError:
raise Exception("Client not found")
# Sample_id
if 'Sample' in request:
try:
sample = resolve_request_lookup(context, request, 'Sample')[0].getObject()
except IndexError:
raise Exception("Sample not found")
else:
# Primary AR
sample = _createObjectByType("Sample", client, tmpID())
sample.unmarkCreationFlag()
fields = set_fields_from_request(sample, request)
for field in fields:
self.used(field)
sample._renameAfterCreation()
sample.setSampleID(sample.getId())
event.notify(ObjectInitializedEvent(sample))
sample.at_post_create_script()
if SamplingWorkflowEnabled:
wftool.doActionFor(sample, 'sampling_workflow')
else:
wftool.doActionFor(sample, 'no_sampling_workflow')
ret['sample_id'] = sample.getId()
parts = [{'services': [],
'container': [],
'preservation': '',
'separate': False}]
specs = self.get_specs_from_request()
ar = _createObjectByType("AnalysisRequest", client, tmpID())
ar.unmarkCreationFlag()
fields = set_fields_from_request(ar, request)
for field in fields:
self.used(field)
ar.setSample(sample.UID())
ar._renameAfterCreation()
ret['ar_id'] = ar.getId()
brains = resolve_request_lookup(context, request, 'Services')
service_uids = [p.UID for p in brains]
new_analyses = ar.setAnalyses(service_uids, specs=specs)
ar.setRequestID(ar.getId())
ar.reindexObject()
event.notify(ObjectInitializedEvent(ar))
ar.at_post_create_script()
# Create sample partitions
parts_and_services = {}
for _i in range(len(parts)):
p = parts[_i]
part_prefix = sample.getId() + "-P"
if '%s%s' % (part_prefix, _i + 1) in sample.objectIds():
parts[_i]['object'] = sample['%s%s' % (part_prefix, _i + 1)]
parts_and_services['%s%s' % (part_prefix, _i + 1)] = p['services']
part = parts[_i]['object']
else:
part = _createObjectByType("SamplePartition", sample, tmpID())
parts[_i]['object'] = part
container = None
preservation = p['preservation']
parts[_i]['prepreserved'] = False
part.edit(
Container=container,
Preservation=preservation,
)
part.processForm()
if SamplingWorkflowEnabled:
wftool.doActionFor(part, 'sampling_workflow')
else:
wftool.doActionFor(part, 'no_sampling_workflow')
parts_and_services[part.id] = p['services']
if SamplingWorkflowEnabled:
wftool.doActionFor(ar, 'sampling_workflow')
else:
wftool.doActionFor(ar, 'no_sampling_workflow')
# Add analyses to sample partitions
# XXX jsonapi create AR: right now, all new analyses are linked to the first samplepartition
if new_analyses:
analyses = list(part.getAnalyses())
analyses.extend(new_analyses)
part.edit(
Analyses=analyses,
)
for analysis in new_analyses:
analysis.setSamplePartition(part)
# If Preservation is required for some partitions,
# and the SamplingWorkflow is disabled, we need
# to transition to to_be_preserved manually.
if not SamplingWorkflowEnabled:
to_be_preserved = []
sample_due = []
lowest_state = 'sample_due'
for p in sample.objectValues('SamplePartition'):
if p.getPreservation():
lowest_state = 'to_be_preserved'
to_be_preserved.append(p)
else:
sample_due.append(p)
for p in to_be_preserved:
doActionFor(p, 'to_be_preserved')
for p in sample_due:
doActionFor(p, 'sample_due')
doActionFor(sample, lowest_state)
for analysis in ar.objectValues('Analysis'):
doActionFor(analysis, lowest_state)
doActionFor(ar, lowest_state)
# receive secondary AR
if request.get('Sample_id', ''):
doActionFor(ar, 'sampled')
doActionFor(ar, 'sample_due')
not_receive = ['to_be_sampled', 'sample_due', 'sampled',
'to_be_preserved']
sample_state = wftool.getInfoFor(sample, 'review_state')
if sample_state not in not_receive:
doActionFor(ar, 'receive')
for analysis in ar.getAnalyses(full_objects=1):
doActionFor(analysis, 'sampled')
doActionFor(analysis, 'sample_due')
if sample_state not in not_receive:
doActionFor(analysis, 'receive')
if self.unused:
raise BadRequest("The following request fields were not used: %s. Request aborted." % self.unused)
return ret
