def get_batched(context, portal_type=None, uid=None, endpoint=None, **kw):
"""Get batched results
"""
# TODO: to move to baobab lims jsonapi -----
pm = getToolByName(context, 'portal_membership')
roles = pm.getAuthenticatedMember().getRoles()
if 'EMS' in roles or uid == "allowSharing":
uid = None
if portal_type == 'Sample':
kw['object_provides'] = ISharableSample.__identifier__
req.get_request().form["catalog"] = "portal_catalog"
else:
raise Unauthorized(
"You don't have access permission to {}".format(portal_type))
# TODO: ------
# fetch the catalog results
results = get_search_results(portal_type=portal_type, uid=uid, **kw)
# fetch the batch params from the request
size = req.get_batch_size()
start = req.get_batch_start()
# check for existing complete flag
complete = req.get_complete(default=_marker)
if complete is _marker:
# if the uid is given, get the complete information set
complete = uid and True or False
# return a batched record
return get_batch(results,
size,
start,
endpoint=endpoint,
complete=complete)
def create_sample_type(container, portal_type, **data):
"""
create a sample type
:param container:
:param portal_type
:param data:
:return: sample type object
"""
container = get_object(container)
request = req.get_request()
retention_days = int(data.pop('RetentionDays', '0'))
retention_hours = int(data.pop('RetentionHours', '0'))
retention_minutes = int(data.pop('RetentionMinutes', '0'))
retention_period = {
'days': retention_days,
'hours': retention_hours,
'minutes': retention_minutes
}
data['RetentionPeriod'] = retention_period
values = {
"title": data.get('title', ''),
"description": data.get("description", ""),
"RetentionPeriod": retention_period,
"Hazardous": data.get("Hazardous"),
"Prefix": data.get('Prefix'),
"MinimumVolume": data.get('MinimumVolume'),
}
return create_smp_type(container, request, values)
def get_batched(context, portal_type=None, uid=None, endpoint=None, **kw):
"""Get batched results
"""
# TODO: to move to baobab lims jsonapi -----
pm = getToolByName(context, 'portal_membership')
roles = pm.getAuthenticatedMember().getRoles()
if 'EMS' in roles or uid == "allowSharing":
uid = None
if portal_type == 'Sample':
kw['object_provides'] = ISharableSample.__identifier__
req.get_request().form["catalog"] = "portal_catalog"
else:
raise Unauthorized("You don't have access permission to {}".format(portal_type))
# TODO: ------
# fetch the catalog results
results = get_search_results(portal_type=portal_type, uid=uid, **kw)
# fetch the batch params from the request
size = req.get_batch_size()
start = req.get_batch_start()
# check for existing complete flag
complete = req.get_complete(default=_marker)
if complete is _marker:
# if the uid is given, get the complete information set
complete = uid and True or False
# return a batched record
return get_batch(results, size, start, endpoint=endpoint,
complete=complete)
def make_prev_url(self):
if self.batch.previous is not None:
return None
request = req.get_request()
params = request.form
params["b_start"] = max(self.batch.numpages - 2, 0) * self.batch.size
return "%s?%s" % (request.URL, urllib.urlencode(params))
def make_next_url(self):
if self.batch.next is not None:
return None
request = req.get_request()
params = request.form
params["b_start"] = self.batch.numpages * self.batch.size
return "%s?%s" % (request.URL, urllib.urlencode(params))
def make_next_url(self):
if not self.batch.has_next:
return None
request = req.get_request()
params = request.form
params["b_start"] = self.batch.pagenumber * self.batch.pagesize
return "%s?%s" % (request.URL, urllib.urlencode(params))
def make_prev_url(self):
if not self.batch.has_previous:
return None
request = req.get_request()
params = request.form
pagesize = self.batch.pagesize
pagenumber = self.batch.pagenumber
params["b_start"] = max(pagenumber - 2, 0) * pagesize
return "%s?%s" % (request.URL, urllib.urlencode(params))
def create_analysisrequest(container, **data):
"""Create a minimun viable AnalysisRequest
:param container: A single folderish catalog brain or content object
:type container: ATContentType/DexterityContentType/CatalogBrain
"""
container = get_object(container)
request = req.get_request()
# we need to resolve the SampleType to a full object
sample_type = data.get("SampleType", None)
if sample_type is None:
fail(400, "Please provide a SampleType")
# TODO We should handle the same values as in the DataManager for this field
# (UID, path, objects, dictionaries ...)
results = search(portal_type="SampleType", title=sample_type)
values = {
"Analyses": data.get("Analyses", []),
"SampleType": results and get_object(results[0]) or None,
}
return create_ar(container, request, values)
def create_analysisrequest(container, **data):
"""Create a minimun viable AnalysisRequest
:param container: A single folderish catalog brain or content object
:type container: ATContentType/DexterityContentType/CatalogBrain
"""
container = get_object(container)
request = req.get_request()
# we need to resolve the SampleType to a full object
sample_type = data.get("SampleType", None)
if sample_type is None:
fail(400, "Please provide a SampleType")
# TODO We should handle the same values as in the DataManager for this field
# (UID, path, objects, dictionaries ...)
results = search(portal_type="SampleType", title=sample_type)
values = {
"Analyses": data.get("Analyses", []),
"SampleType": results and get_object(results[0]) or None,
}
return create_ar(container, request, values)
def create_sample(container, **data):
"""
create a sample from here that doesnt go via api create
:param container:
:param data:
:return: Sample object
"""
container = get_object(container)
request = req.get_request()
# we need to resolve the SampleType to a full object
sample_type = data.get("SampleType", None)
if sample_type is None:
fail(400, "Please provide a SampleType")
# TODO We should handle the same values as in the DataManager for this field
# (UID, path, objects, dictionaries ...)
sample_type_results = search(portal_type="SampleType", title=sample_type)
if not sample_type_results:
sample_type_results = search(portal_type="SampleType", uid=sample_type)
# StorageLocation
storage_location = data.get("StorageLocation", None)
if storage_location is None:
fail(400, "Please provide a StorageLocation")
linked_sample_list = search(portal_type="Sample",
title=data.get('LinkedSample', ''))
linked_sample = linked_sample_list and linked_sample_list[0].getObject(
) or None
try:
volume = str(data.get('Volume'))
float_volume = float(volume)
if not float_volume:
fail(400, "Please provide a correct Volume")
except:
raise
# TODO We should handle the same values as in the DataManager for this field
# (UID, path, objects, dictionaries ...)
storage_location_results = search(portal_type='StoragePosition',
Title=storage_location)
if not storage_location_results:
storage_location_results = search(portal_type='StoragePosition',
uid=storage_location)
# set the values and call the create function
values = {
"title":
data.get('title', ''),
"description":
data.get("description", ""),
"Project":
container, #because the container is in fact the project this sample belongs to.
"AllowSharing":
data.get('AllowSharing', 0),
"StorageLocation":
storage_location_results and get_object(storage_location_results[0])
or None,
"SampleType":
sample_type_results and get_object(sample_type_results[0]) or None,
"SubjectID":
data.get("SubjectID", ""),
"Barcode":
data.get("Barcode", ""),
"Volume":
volume,
"Unit":
data.get("Unit", ""),
"LinkedSample":
linked_sample,
"DateCreated":
data.get("DateCreated", ""),
}
api_source = data.get('APISource', None)
if api_source:
values['APISource'] = api_source
return create_smp(container, request, values)