def get_specs_from_request(self):
"""Specifications for analyses are given on the request in *Spec
>>> portal = layer['portal']
>>> portal_url = portal.absolute_url()
>>> from plone.app.testing import SITE_OWNER_NAME
>>> from plone.app.testing import SITE_OWNER_PASSWORD
>>> 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",
... "AR_Specification=portal_type:AnalysisSpec|title:Apple Pulp",
... "Analysis_Specification:list=Cu:5:10:10",
... "Analysis_Specification:list=Mg:6:11:11"
... ]))
>>> browser.contents
'{...The following request fields were not used: ...thing...}'
"""
context = self.context
request = self.request
brains = resolve_request_lookup(context, request, "AR_Specification")
kwspecs = brains[0].getObject().getResultsRangeDict() if brains else {}
Analysis_Specification = self.request.get("Analysis_Specification", "")
self.used("AR_Specification")
self.used("Analysis_Specification")
if not kwspecs and not Analysis_Specification:
return {}
specs = {}
bsc = getToolByName(context, "bika_setup_catalog")
for k, v in kwspecs.items():
uid = bsc(portal_type="AnalysisService", getKeyword=k)[0].UID
specs[uid] = v
if Analysis_Specification:
for string in Analysis_Specification:
keyword, Min, Max, error = string.split(":")
brains = bsc(portal_type="AnalysisService", getKeyword=keyword)
if not brains:
raise BadRequest("Service not found: %s" % keyword)
specs[brains[0].UID] = {
"min": Min,
"max": Max,
"error": error,
}
return specs
def get_specs_from_request(self):
"""Specifications for analyses are given on the request in *Spec
>>> portal = layer['portal']
>>> portal_url = portal.absolute_url()
>>> from plone.app.testing import SITE_OWNER_NAME
>>> from plone.app.testing import SITE_OWNER_PASSWORD
>>> 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",
... "AR_Specification=portal_type:AnalysisSpec|title:Apple Pulp",
... "Analysis_Specification:list=Cu:5:10:10",
... "Analysis_Specification:list=Mg:6:11:11"
... ]))
>>> browser.contents
'{...The following request fields were not used: ...thing...}'
"""
context = self.context
request = self.request
brains = resolve_request_lookup(context, request, "AR_Specification")
kwspecs = brains[0].getObject().getResultsRangeDict() if brains else {}
Analysis_Specification = self.request.get("Analysis_Specification", "")
self.used("AR_Specification")
self.used("Analysis_Specification")
if not kwspecs and not Analysis_Specification:
return {}
specs = {}
bsc = getToolByName(context, "bika_setup_catalog")
for k, v in kwspecs.items():
uid = bsc(portal_type="AnalysisService", getKeyword=k)[0].UID
specs[uid] = v
if Analysis_Specification:
for string in Analysis_Specification:
keyword, Min, Max, error = string.split(":")
brains = bsc(portal_type="AnalysisService", getKeyword=keyword)
if not brains:
raise BadRequest("Service not found: %s" % keyword)
specs[brains[0].UID] = {"min": Min, "max": Max, "error": error}
return specs
def get_specs_from_request(self, dicts_to_dict_rr=None):
"""Specifications for analyses are given on the request in *Spec
>>> portal = layer['portal']
>>> portal_url = portal.absolute_url()
>>> from plone.app.testing import SITE_OWNER_NAME
>>> from plone.app.testing import SITE_OWNER_PASSWORD
>>> 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",
... 'ResultsRange=[{"keyword":"Cu","min":5,"max":10,"error":10},{"keyword":"Mg","min":6,"max":11,"error":11}]',
... ]))
>>> browser.contents
'{..."success": true...}'
"""
# valid output for ResultsRange goes here.
specs = []
context = self.context
request = self.request
brains = resolve_request_lookup(context, request, "Specification")
spec_rr = brains[0].getObject().getResultsRange() if brains else {}
spec_rr = dicts_to_dict(spec_rr, 'keyword')
#
bsc = getToolByName(context, "bika_setup_catalog")
req_rr = request.get('ResultsRange', "[]")
try:
req_rr = json.loads(req_rr)
except:
raise BadRequest("Invalid value for ResultsRange (%s)"%req_rr)
req_rr = dicts_to_dict(req_rr, 'keyword')
#
spec_rr.update(req_rr)
return spec_rr.values()
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
