def test_iterator_count(self, class_entity_repo, ent0, ent1):
agg = class_entity_repo.get_aggregate(IMyEntity)
with pytest.raises(StopIteration):
next(agg.iterator())
agg.add(ent0)
assert next(agg.iterator()) is ent0
# Iterator heeds filtering.
agg.filter = eq(id=ent1.id)
with pytest.raises(StopIteration):
next(agg.iterator())
agg.add(ent1)
assert next(agg.iterator()) is ent1
# Iterator heeds ordering.
agg.filter = None
agg.order = asc('id')
assert isinstance(agg.order, AscendingOrderSpecification)
assert next(agg.iterator()) is ent0
# Iterator heeds slice.
assert len(list(agg.iterator())) == 2
agg.slice = slice(0, 1)
assert len(list(agg.iterator())) == 1
# Count ignores slice.
assert agg.count() == 2
# Count heeds filtering.
agg.filter = eq(id=1)
assert agg.count() == 1
def test_basics(self, class_entity_repo):
agg = class_entity_repo.get_aggregate(IMyEntity)
child_agg = class_entity_repo.get_aggregate(IMyEntityChild)
new_child0 = self._make_child(child_agg)
new_parent1 = MyEntityParent()
new_ent1 = MyEntity()
new_ent1.parent = new_parent1
new_child1 = MyEntityChild()
child_rel_agg = self._make_rel_agg(class_entity_repo, new_ent1)
assert len(list(child_agg.iterator())) == 1
assert len(list(agg.iterator())) == 1
assert len(list(child_rel_agg.iterator())) == 0
# Adding to a relationship aggregate .....
child_rel_agg.add(new_child1)
# ....... adds to root aggregates:
assert len(list(child_agg.iterator())) == 2
# ....... adds (along the cascade) to parent root aggregate:
assert len(list(agg.iterator())) == 2
# ....... appends to children:
assert new_ent1.children == [new_child1]
# get by ID and slug, filtering.
assert child_rel_agg.get_by_id(new_child1.id).id == new_child1.id
assert \
child_rel_agg.get_by_slug(new_child1.slug).slug == new_child1.slug
child_rel_agg.filter = eq(id=2)
assert child_rel_agg.get_by_id(new_child1.id) is None
assert child_rel_agg.get_by_slug(new_child1.slug) is None
# update.
upd_child0 = MyEntityChild(id=0)
txt = 'FROBNIC'
upd_child0.text = txt
child_rel_agg.update(upd_child0)
assert new_child0.text == txt
def __get_empty_rack_barcode_params(self, count, tube_rack_specs_matrix):
rack_agg = get_root_aggregate(ITubeRack)
rack_agg.filter = eq(total_containers=0, specs=tube_rack_specs_matrix)
rack_agg.slice = slice(0, count)
if count == 1:
params = dict(rack=str(next(rack_agg.iterator()).barcode))
else:
params = dict([('rack%d' % (cnt + 1, ), str(rack.barcode))
for (cnt, rack) in enumerate(rack_agg.iterator())])
return params
def __get_empty_racks(self, count):
rack_specs_agg = get_root_aggregate(ITubeRackSpecs)
rs_matrix = rack_specs_agg.get_by_slug('matrix0500')
is_managed = get_item_status_managed()
rack_agg = get_root_aggregate(ITubeRack)
rack_agg.filter = eq(total_containers=0,
specs=rs_matrix,
status=is_managed)
rack_agg.slice = slice(0, count)
return list(iter(rack_agg))
def __get_empty_rack_barcode_params(self, count, tube_rack_specs_matrix):
rack_agg = get_root_aggregate(ITubeRack)
rack_agg.filter = eq(total_containers=0, specs=tube_rack_specs_matrix)
rack_agg.slice = slice(0, count)
if count == 1:
params = dict(rack=str(next(rack_agg.iterator()).barcode))
else:
params = dict([('rack%d' % (cnt + 1,), str(rack.barcode))
for (cnt, rack) in enumerate(rack_agg.iterator())])
return params
def run(self):
self.add_info('Running molecule design registrar.')
self.__check_new_molecule_designs()
cs_agg = get_root_aggregate(IChemicalStructure)
md_agg = get_root_aggregate(IMoleculeDesign)
cs_keys = set()
new_css = set()
new_mds = set()
# Build keys for all new chemical structures.
for mdris in self.__new_mdris:
# By definition, all mdris for a given hash have the same
# structures, so we just take the first.
for cs in mdris[0].chemical_structures:
cs_keys.add((cs.structure_type_id, cs.representation))
# FIXME: Build a single filtering spec here (see FIXME above).
cs_map = {}
for cs_key in cs_keys:
sti, rpr = cs_key
spec = eq(structure_type_id=sti,
representation=rpr)
cs_agg.filter = spec
try:
cs = cs_agg.iterator().next()
except StopIteration:
continue
else:
cs_map[cs_key] = cs
self.add_debug('Creating %d new molecule designs.'
% len(self.__new_mdris))
for mdris in self.__new_mdris:
md_structs = []
# By definition, all mdris for a given hash have the same
# structures, so we just take the first.
for struct in mdris[0].chemical_structures:
key = (struct.structure_type_id, struct.representation)
if not key in cs_map:
# New chemical structure - add and use for the design.
cs_agg.add(struct)
new_css.add(struct)
md_structs.append(struct)
cs_map[key] = struct
else:
# Use existing structure for the design.
md_structs.append(cs_map[key])
# Create the new design.
md = MoleculeDesign.create_from_data(
dict(molecule_type=mdris[0].molecule_type,
chemical_structures=md_structs))
md_agg.add(md)
new_mds.add(md)
# Update registration items.
for mdri in mdris:
mdri.molecule_design = md
self.return_value = dict(molecule_designs=new_mds,
chemical_structures=new_css)
def from_indices(cls, row_index, column_index):
"""
Returns a RackPosition from the row index and column index.
:Note: Try not to use this method if you can avoid it as it takes
as it takes a lot of time if you try to fetch a larger number
of rack positions one by one. Use the rack position cache in the
:mod:`semiconstants` module instead, if possible.
:param row_index: the row of the container (this is 0 based).
:type row_index: :class:`int`
:param column_index: the column of the container (this 0 based).
:type column_index: :class:`int`
:return: The wanted rack position.
:rtype: :class:`RackPosition`
"""
agg = get_root_aggregate(IRackPosition)
agg.filter = eq(_row_index=row_index) & eq(_column_index=column_index)
return list(agg.iterator())[0]
def from_indices(cls, row_index, column_index):
"""
Returns a RackPosition from the row index and column index.
:Note: Try not to use this method if you can avoid it as it takes
as it takes a lot of time if you try to fetch a larger number
of rack positions one by one. Use the rack position cache in the
:mod:`semiconstants` module instead, if possible.
:param row_index: the row of the container (this is 0 based).
:type row_index: :class:`int`
:param column_index: the column of the container (this 0 based).
:type column_index: :class:`int`
:return: The wanted rack position.
:rtype: :class:`RackPosition`
"""
agg = get_root_aggregate(IRackPosition)
agg.filter = eq(_row_index=row_index) & eq(_column_index=column_index)
return list(agg.iterator())[0]
def run(self):
rack_agg = get_root_aggregate(IRack)
is_agg = get_root_aggregate(IItemStatus)
status = is_agg.get_by_slug(self.STATUS)
cnt_specs_agg = get_root_aggregate(IContainerSpecs)
cnt_specs = cnt_specs_agg.get_by_slug(self.SPECS)
tubes = []
for scan_fn in glob.glob("%s/*.txt" % self.__scanfile_directory):
strm = open(scan_fn, 'r')
try:
prs = RackScanningParser(strm, parent=self)
prs.run()
finally:
strm.close()
if prs.has_errors():
raise RuntimeError('Could not parse rack scan file "%s". '
'Error messages: %s' %
(scan_fn, self.get_messages()))
rack_agg.filter = eq(barcode=prs.rack_barcode)
try:
rack = rack_agg.iterator().next()
except StopIteration:
self.add_error('Rack with barcode "%s" does not exist.' %
prs.rack_barcode)
continue
if not rack.specs.has_tubes:
self.add_error('Rack with barcode "%s" is not a tube '
'rack.' % rack.barcode)
continue
for pos_label, barcode in prs.position_map.iteritems():
if barcode is None:
continue
pos = get_rack_position_from_label(pos_label)
# FIXME: Enable this test once pulling a tube by barcode is
# fast.
# if tube_agg.get_by_slug(barcode):
# self.add_error('Tube with barcode "%s" already '
# 'exists.' % barcode)
# continue
if not rack.is_empty(pos):
self.add_error('Trying to place a tube in an occupied '
'position (%s on rack %s).' %
(pos_label, rack.barcode))
continue
tube = Tube.create_from_rack_and_position(
cnt_specs, status, barcode, rack, pos)
tubes.append(tube)
self.add_info('Creating tube with barcode %s at '
'position %s in rack %s.' %
(barcode, pos_label, rack.barcode))
if not self.has_errors():
self.return_value = tubes
def run(self):
rack_agg = get_root_aggregate(IRack)
is_agg = get_root_aggregate(IItemStatus)
status = is_agg.get_by_slug(self.STATUS)
cnt_specs_agg = get_root_aggregate(IContainerSpecs)
cnt_specs = cnt_specs_agg.get_by_slug(self.SPECS)
tubes = []
for scan_fn in glob.glob("%s/*.txt" % self.__scanfile_directory):
strm = open(scan_fn, 'r')
try:
prs = RackScanningParser(strm, parent=self)
prs.run()
finally:
strm.close()
if prs.has_errors():
raise RuntimeError('Could not parse rack scan file "%s". '
'Error messages: %s'
% (scan_fn, self.get_messages()))
rack_agg.filter = eq(barcode=prs.rack_barcode)
try:
rack = rack_agg.iterator().next()
except StopIteration:
self.add_error('Rack with barcode "%s" does not exist.'
% prs.rack_barcode)
continue
if not rack.specs.has_tubes:
self.add_error('Rack with barcode "%s" is not a tube '
'rack.' % rack.barcode)
continue
for pos_label, barcode in prs.position_map.iteritems():
if barcode is None:
continue
pos = get_rack_position_from_label(pos_label)
# FIXME: Enable this test once pulling a tube by barcode is
# fast.
# if tube_agg.get_by_slug(barcode):
# self.add_error('Tube with barcode "%s" already '
# 'exists.' % barcode)
# continue
if not rack.is_empty(pos):
self.add_error('Trying to place a tube in an occupied '
'position (%s on rack %s).' %
(pos_label, rack.barcode))
continue
tube = Tube.create_from_rack_and_position(cnt_specs, status,
barcode, rack, pos)
tubes.append(tube)
self.add_info('Creating tube with barcode %s at '
'position %s in rack %s.' %
(barcode, pos_label, rack.barcode))
if not self.has_errors():
self.return_value = tubes
def create_from_data(cls, data):
# We reuse molecule design sets that have the same members.
agg = get_root_aggregate(cls)
mds = data.pop('molecule_designs')
rpr_str = MoleculeDesignPool.make_member_hash_string(mds)
agg.filter = eq(member_hash=md5(rpr_str).hexdigest())
md_pools = list(agg.iterator())
if len(md_pools) == 0:
# New molecule design pool.
md_pool = cls(molecule_designs=mds, **data)
else:
md_pool, = md_pools # Must be exactly one matching pool here.
return md_pool
def test_get_by_id_and_slug(self, class_entity_repo, ent0):
agg = class_entity_repo.get_aggregate(IMyEntity)
agg.add(ent0)
assert agg.get_by_id(0) is ent0
assert agg.get_by_slug('0') is ent0
assert agg.get_by_id(-1) is None
assert agg.get_by_slug('-1') is None
agg.filter = eq(id=1)
assert agg.get_by_id(0) is None
assert agg.get_by_slug('0') is None
with pytest.raises(ValueError) as cm:
agg.add(object())
exp_msg = 'Invalid data type for traversal'
assert str(cm.value).startswith(exp_msg)
def test_filter_order_slice(self):
ent0 = MyEntity(id=0)
ent1 = MyEntity(id=1)
ent2 = MyEntity(id=2)
cache = EntityCache(entities=[])
cache.add(ent0)
cache.add(ent1)
cache.add(ent2)
filter_expr = EvalFilterExpression(~eq(id=0))
order_expr = EvalOrderExpression(asc('id'))
slice_key = slice(1, 2)
self.assert_equal(list(cache.retrieve(filter_expression=filter_expr,
order_expression=order_expr,
slice_key=slice_key)),
[ent2])
def test_nested_attribute(self, class_entity_repo, ent0, ent1, ent2):
agg = class_entity_repo.get_aggregate(IMyEntity)
agg.add(ent0)
agg.add(ent1)
agg.add(ent2)
assert len(list(agg.iterator())) == 3
agg.filter = eq(**{'parent.text':'222'})
assert len(list(agg.iterator())) == 1
agg.filter = None
assert len(list(agg.iterator())) == 3
agg.order = asc('parent.text')
assert next(agg.iterator()) is ent2
# With nested filter and order.
agg.filter = gt(**{'parent.text':'000'})
assert next(agg.iterator()) is ent1
# With nested filter, order, and slice.
agg.slice = slice(1, 2)
assert next(agg.iterator()) is ent0
def test_filter_order_slice(self, class_configurator):
class_configurator.begin()
try:
ent0 = MyEntity(id=0)
ent1 = MyEntity(id=1)
ent2 = MyEntity(id=2)
cache = EntityCache(entities=[])
cache.add(ent0)
cache.add(ent1)
cache.add(ent2)
filter_expr = EvalFilterExpression(~eq(id=0))
order_expr = EvalOrderExpression(asc('id'))
slice_key = slice(1, 2)
assert list(cache.retrieve(filter_expression=filter_expr,
order_expression=order_expr,
slice_key=slice_key)) \
== [ent2]
finally:
class_configurator.end()
def get_iso(cls, value):
agg = get_root_aggregate(IStockSampleCreationIso)
agg.filter = eq(label=value)
return list(agg.iterator())[0]
def get_iso_request(cls, value):
ir_agg = get_root_aggregate(IStockSampleCreationIsoRequest)
ir_agg.filter = eq(label=value)
return ir_agg.iterator().next()
def test_not(self):
spec = ~eq(number_attr=1)
self.assert_true(isinstance(spec, NegationFilterSpecification))
self.assert_true(spec.is_satisfied_by(self.candidate))
def test_or(self):
spec = eq(number_attr=1) | eq(text_attr='attr')
self.assert_true(isinstance(spec, DisjunctionFilterSpecification))
self.assert_true(spec.is_satisfied_by(self.candidate))
def test_or(self):
spec = eq(number_attr=1) | eq(text_attr='attr')
self.assert_true(isinstance(spec, DisjunctionFilterSpecification))
self.assert_true(spec.is_satisfied_by(self.candidate))
def get_iso(cls, value):
agg = get_root_aggregate(IStockSampleCreationIso)
agg.filter = eq(label=value)
return list(agg.iterator())[0]
def __check_new_supplier_molecule_designs(self):
self.add_debug('Checking for new supplier molecule designs.')
smd_agg = get_root_aggregate(ISupplierMoleculeDesign)
# FIXME: We should really build a single filtering spec here like so:
# spec = reduce(or_,
# [eq(supplier=sri.supplier, product_id=sri.product_id)
# for in in self.sample_registration_items])
# However, this leads to "maximum recursion depth exceeded"
# problems with the current everest.
exst_smd_map = {}
for sri in self.registration_items:
smd_spec = eq(supplier=sri.supplier,
product_id=sri.product_id,
is_current=True)
smd_agg.filter = smd_spec
try:
smd = next(smd_agg.iterator())
except StopIteration:
continue
else:
exst_smd_map[(smd.supplier, smd.product_id)] = smd
new_smd_sri_map = {}
for sri in self.registration_items:
mdpri = sri.molecule_design_pool_registration_item
# Set the molecule type.
mdpri.molecule_type = sri.molecule_type
key = (sri.supplier, sri.product_id)
if key in exst_smd_map:
# Update sample registration item.
smd = exst_smd_map[key]
sri.supplier_molecule_design = smd
if not smd.molecule_design_pool is None:
# Compare found design information against existing design
# information.
mdris = mdpri.molecule_design_registration_items
found_md_hashes = \
sorted([MoleculeDesign.make_structure_hash(
mdri.chemical_structures)
for mdri in mdris])
exist_mds = smd.molecule_design_pool.molecule_designs
exist_md_hashes = sorted([md.structure_hash
for md in exist_mds])
if found_md_hashes != exist_md_hashes:
msg = 'For product ID "%s" and supplier "%s", a ' \
'supplier molecule design exists which has ' \
'different design information than the one ' \
'included in the current registration.' \
% (sri.product_id, sri.supplier.name)
self.add_error(msg)
continue
else:
# FIXME: Should this be a warning instead?
msg = 'For product ID "%s" and supplier "%s", a ' \
'supplier molecule design was found which does ' \
'not have an associated molecule design pool.' \
% (sri.product_id, sri.supplier.name)
self.add_error(msg)
continue
else:
# We use a map here so that multiple sample registration items
# with the same supplier molecule design information create
# only a single new supplier molecule design.
new_smd_sri_map.setdefault(key, []).append(sri)
# Store new supplier molecule design registration items for later use.
self.__new_smd_sri_map = new_smd_sri_map
def test_not(self, specification_candidate): #pylint: disable=W0621
spec = ~eq(number_attr=NUMBER_VALUE - 1)
assert isinstance(spec, NegationFilterSpecification)
assert spec.is_satisfied_by(specification_candidate)
def get_iso_request(cls, value):
ir_agg = get_root_aggregate(IStockSampleCreationIsoRequest)
ir_agg.filter = eq(label=value)
return ir_agg.iterator().next()
def __get_rack(self, barcode):
rack_agg = get_root_aggregate(IRack)
rack_agg.filter = eq(barcode=barcode)
return next(rack_agg.iterator())
def test_eq_generator(self):
spec = eq(number_attr=0) & eq(text_attr='attr')
self.assert_true(spec.is_satisfied_by(self.candidate))
def test_not(self):
spec = ~eq(number_attr=1)
self.assert_true(isinstance(spec, NegationFilterSpecification))
self.assert_true(spec.is_satisfied_by(self.candidate))
def view_member(view_collection): #pylint: disable=W0621
view_collection.filter = eq(id=0)
return next(iter(view_collection))
def __get_target_rack(self, barcode):
rack_agg = get_root_aggregate(IRack)
rack_agg.filter = eq(barcode=barcode)
return next(rack_agg.iterator())
def test_eq_generator(self):
spec = eq(number_attr=0) & eq(text_attr='attr')
self.assert_true(spec.is_satisfied_by(self.candidate))
def test_multiple_keywords(self):
spec = eq(number_attr=0, text_attr='attr')
self.assert_true(isinstance(spec, ConjunctionFilterSpecification))
self.assert_true(spec.is_satisfied_by(self.candidate))
def test_multiple_keywords(self):
spec = eq(number_attr=0, text_attr='attr')
self.assert_true(isinstance(spec, ConjunctionFilterSpecification))
self.assert_true(spec.is_satisfied_by(self.candidate))
def view_member(view_collection): #pylint: disable=W0621
view_collection.filter = eq(id=0)
return next(iter(view_collection))
def test_or(self, specification_candidate): #pylint: disable=W0621
spec = eq(number_attr=NUMBER_VALUE - 1) | eq(text_attr=TEXT_VALUE)
assert isinstance(spec, DisjunctionFilterSpecification)
assert spec.is_satisfied_by(specification_candidate)
def filter_by(self, **kw):
spec = eq(**kw)
visitor_cls = get_filter_specification_visitor(self.expression_kind)
vst = visitor_cls(self._entity_class)
spec.accept(vst)
return vst.filter_query(self)
def filter_by(self, **kw):
spec = eq(**kw)
visitor_cls = get_filter_specification_visitor(self.expression_kind)
vst = visitor_cls(self._entity_class)
spec.accept(vst)
return vst.filter_query(self)