def test_list_duplicate_ids(self):
from libcellml import Annotator, CellmlElementType, Parser
model_string = file_contents("annotator/lots_of_duplicate_ids.cellml")
parser = Parser()
annotator = Annotator()
model = parser.parseModel(model_string)
annotator.setModel(model)
id_list = annotator.duplicateIds()
expected_ids = ('duplicateId1', 'duplicateId2', 'duplicateId3',
'duplicateId4')
self.assertEqual(expected_ids, id_list)
# Get the collections by duplicated id.
c2v1 = model.component("component2").variable("variable1")
c2v2 = model.component("component2").variable("variable2")
c3v1 = model.component("component2").component("component3").variable(
"variable1")
c3v2 = model.component("component2").component("component3").variable(
"variable2")
c4v1 = model.component("component4").variable("variable1")
c4v2 = model.component("component4").variable("variable2")
expected_items = {
"duplicateId1": (
(CellmlElementType.UNITS, model.units("units2")),
(CellmlElementType.IMPORT, model.importSource(0)),
(CellmlElementType.MAP_VARIABLES, (c4v1, c2v1)),
(CellmlElementType.COMPONENT, model.component("component2")),
(CellmlElementType.CONNECTION, (c2v1, c3v1)),
(CellmlElementType.TEST_VALUE,
model.component("component2").reset(0)),
(CellmlElementType.COMPONENT_REF,
model.component("component2").component("component3")),
(CellmlElementType.VARIABLE,
model.component("component2").component(
"component3").variable("variable2")),
),
"duplicateId2": (
(CellmlElementType.MODEL, model),
(CellmlElementType.UNITS, model.units("units1")),
(CellmlElementType.UNITS, model.units("blob")),
(CellmlElementType.CONNECTION, (c4v2, c2v2)),
(CellmlElementType.VARIABLE, c4v2),
(CellmlElementType.COMPONENT_REF,
model.component("component2")),
(CellmlElementType.RESET,
model.component("component2").reset(0)),
(CellmlElementType.VARIABLE, c3v1),
),
"duplicateId3": (
(CellmlElementType.IMPORT, model.importSource(1)),
(CellmlElementType.UNITS, model.units("units3")),
(CellmlElementType.VARIABLE, c4v1),
(CellmlElementType.VARIABLE, c2v2),
(CellmlElementType.MAP_VARIABLES, (c2v2, c4v2)),
(CellmlElementType.COMPONENT,
model.component("component2").component("component3")),
(CellmlElementType.ENCAPSULATION, model),
),
"duplicateId4": (
(CellmlElementType.UNIT, ((model.units("units2"), 0))),
(CellmlElementType.COMPONENT, model.component("component1")),
(CellmlElementType.COMPONENT, model.component("component4")),
(CellmlElementType.MAP_VARIABLES, (c2v1, c3v1)),
(CellmlElementType.VARIABLE, c2v1),
(CellmlElementType.MAP_VARIABLES, (c2v2, c4v2)),
(CellmlElementType.RESET_VALUE,
model.component("component2").reset(0)),
)
}
for id in expected_ids:
items_with_id = annotator.items(id)
count = 0
for item in items_with_id:
self.assertEqual(item[0], expected_items[id][count][0])
# SWIG copies the pointers so can't expect a comparison to be true. Not sure how to
# compare these ...
# self.assertEqual(item[1], expected_items[id][count][1])
count = count + 1
# Retrieve the issues from the annotator and print to the terminal.
print_issues(annotator)
# end 3.b
# Recorded 1 issues:
# Issue [0] is a WARNING:
# description: The id 'polo' occurs 6 times in the model so a unique item cannot be located.
# stored item type: UNDEFINED
# Since the id is not unique, we need to retrieve a vector of all items
# with that id to investigate them.
# 3.c
# Use the items function to retrieve the vector of items with id 'polo',
# and iterate through it printing the different types to the terminal.
polo_items = annotator.items('polo')
print('The items with an id of "polo" have types of:')
index = 0
for item in polo_items:
print(' - [{}] {}'.format(index,
cellmlElementTypeAsString(item.type())))
index += 1
# end 3.c
# The items with an id of 'polo' have types of:
# - [0] UNITS
# - [1] UNITS
# - [2] UNIT
# - [3] VARIABLE
# - [4] RESET
# STEP 5
# Handling duplicate ID strings.
# Find any duplicated ID strings inside the model.
duplicatedIds = annotator.duplicateIds()
print('There are {} duplicated ids in the model.'.format(
len(duplicatedIds)))
for i in duplicatedIds:
print(' - ' + i)
print()
# Retrieve all items with the given id string. This returns a std.vector
# of AnyItems which will need to be cast into libcellml items before they
# can be used. Note that duplicated ids are not valid CellML, and need
# to be fixed before the model can be used.
allItemsWithDuplicateId1 = annotator.items('duplicateId1')
# A new id string which is automatically generated and unique can be
# assigned to these items.
print(
'Before assigning automatic ids there are {} items with an id of "duplicateId1".'
.format(annotator.itemCount('duplicateId1')))
for item in allItemsWithDuplicateId1:
annotator.assignId(item)
# Now there are no more items with the duplicated id 'duplicateId1'
# remaining in the model.
allItemsWithDuplicateId1 = annotator.items('duplicateId1')
print(
'After assigning automatic ids there are {} items with an id of "duplicateId1".'
.format(annotator.itemCount('duplicateId1')))
