def __init__(self):
"""
options should contain the following name-value pairs as a dict:
Create a new instance of Annotator.
In order to specify the input and output creators and datasources, use the set and addDatasource methods.
"""
self._inputCreator = None
self._outputRenderer = None
self._datasources = []
self.logger = logging.getLogger(__name__)
self._manualAnnotations = dict()
self._defaultAnnotations = dict()
self._isMulticore = None
self._numCores = None
self._cacheManager = CacheManager()
self._cacheManager.initialize(None, "not_used")
self._cache_stats = {"miss": 0, "hit": 0}
self._is_skip_no_alts = False
self._annotating_type = None
self._annotate_func_ptr = Annotator.ANNOTATING_FUNC_DICT.get(
self._annotating_type, _annotate_mut)
pass
def initialize_cache_manager(self, runSpec):
"""Do not bother calculating the db_dir_key if the cache is not being used. """
cache_url = runSpec.get_cache_url()
if cache_url is not None and cache_url != "":
db_dir_key = self.create_db_dir_key()
self._cacheManager = CacheManager()
self._cacheManager.initialize(cache_url, db_dir_key, is_read_only=runSpec.get_is_read_only_cache())
else:
db_dir_key = "never_used"
self._cacheManager = None
def test_cached_annots_dummy_cache(self):
"""Test dummy cache. Also, tests a simple store and retrieve, which should be None."""
cm = CacheManager()
fake_db_dir_key = "blah"
cm.initialize(None, fake_db_dir_key, is_read_only=False)
m = MutationDataFactory.default_create()
m.createAnnotation("blah1", "val1", annotationSource="INPUT")
m.createAnnotation("blah2", "val5", annotationSource="some_datasource")
cm.store_annotations_in_cache(m)
annots = cm.retrieve_cached_annotations(m)
self.assertTrue(annots is None)
def test_cached_annots(self):
"""Test to make sure that we are not storing annotations that should not be cached. Also, tests a simple store and retrieve."""
cache_file = "out/shove.managertest.annots.cache"
cm = CacheManager()
fake_db_dir_key = "blah"
cm.initialize("file://" + cache_file,
fake_db_dir_key,
is_read_only=False)
m = MutationDataFactory.default_create()
m.createAnnotation("blah1", "val1", annotationSource="INPUT")
m.createAnnotation("blah2", "val5", annotationSource="some_datasource")
cm.store_annotations_in_cache(m)
annots = cm.retrieve_cached_annotations(m)
self.assertTrue(len(annots.keys()) == 1)
self.assertTrue(annots["blah2"].getValue() == "val5")