def fiup(ctx, collection, path, registry, dest, pool_size):
"""Collect files in a study by COLLECTION (accession number) using a
PATH REGISTRY, and send to DEST."""
services = ctx.obj.get('services')
click.echo(click.style('Upload Registered Files by Accession Number',
underline=True, bold=True))
file_indexer = FileIndexer(pool_size=pool_size)
R = Redis(**services[registry])
O = Orthanc(**services[dest])
if collection != "ALL":
result = file_indexer.upload_collection(
collection=collection,
basepath=path,
registry=R,
dest=O
)
else:
items = file_indexer.items_on_path(basepath=path, registry=R)
click.echo('Expecting {} items on path'.format(len(items)))
result = file_indexer.upload_path(
basepath=path,
registry=R,
dest=O
)
click.echo(result)
def test_index(setup_redis):
print("Testing indexing speed")
R = Redis()
R.clear()
dcmfdx = FileIndexer(pool_size=15)
dcmfdx.index_path(
basepath=path,
registry=R,
rex="*",
recurse_style=recursion_style
)
"""
def test_redis_index(setup_redis):
R = Redis()
d = Dixel(meta={"FileName": "my_file"},
tags={"AccessionNumber": "100"})
R.add_to_collection(d, item_key="FileName")
logging.debug( R.collections() )
assert("100" in R.collections() )
logging.debug( R.collected_items("100") )
assert("my_file" in R.collected_items("100") )
def findex(ctx, path, registry, orthanc_db, regex, pool_size):
"""Inventory collections of files by accession number with a PATH REGISTRY for retrieval"""
services = ctx.obj.get('services')
click.echo(click.style('Register Files by Accession Number', underline=True, bold=True))
file_indexer = FileIndexer(pool_size=pool_size)
R = Redis(**services[registry])
result = file_indexer.index_path(
path,
registry=R,
rex=regex,
recurse_style="UNSTRUCTURED" if not orthanc_db else "ORTHANC"
)
click.echo(result)
def test_upload(setup_redis, setup_orthanc0):
print("Testing upload speed")
R = Redis()
O = Orthanc()
O.clear()
dcmfdx = FileIndexer(pool_size=15)
dcmfdx.upload_path(
basepath=path,
registry=R,
dest=O
)
pprint(O.gateway.statistics())
"""
def test_redis_ep(setup_redis):
logging.debug("Test Redis EP")
R = Redis()
logging.debug(R)
R.check()
t = Test(data={"myDateTime": datetime.now(), "foo": {'bar': 3}})
id = R.put(t)
s = R.get(id)
logging.debug(t)
logging.debug(s)
assert( t == s )
u = Test(data=42)
id2 = R.put(u)
v = R.get(id2)
logging.debug(u)
logging.debug(v)
assert( u == v )
R.update(id, u)
w = R.get(id)
assert( w == v )
assert( w != s )
assert( R.exists(id) )
R.delete(id)
assert( not R.exists(id) )
a = "one two three"
id2 = R.put(a)
b = R.get(id2)
assert( a == b )
def get_cache(self):
return Redis(**self.redis_conf)