def for_key(cls, key, port):
return cls(
None,
key,
port,
current_time_stamp(),
current_time_stamp(),
CacheEntryStatus.loading,
None,
None,
None,
None,
)
def for_key(cls, key, port):
return cls(
None,
key,
port,
current_time_stamp(),
current_time_stamp(),
"loading",
None,
None,
None,
None,
)
def do_view(path, source_name=None):
source = matching_source(source_name)
match = cache.check_path(source, path)
if match is None:
lookup = source.lookup(path)
if lookup is None:
raise CellxgeneException(
f"Could not find item for path {path} in source {source.name}",
404,
)
key = CacheKey.for_lookup(source, lookup)
print(
f"view path={path}, source_name={source_name}, dataset={key.file_path}, annotation_file= {key.annotation_file_path}, key={key.descriptor}, source={key.source_name}"
)
with entry_lock:
match = cache.check_entry(key)
if match is None:
uascripts = get_extra_scripts()
match = cache.create_entry(key, uascripts)
match.timestamp = current_time_stamp()
if (match.status == CacheEntryStatus.loaded
or match.status == CacheEntryStatus.loading):
return match.serve_content(path)
elif match.status == CacheEntryStatus.error:
raise ProcessException.from_cache_entry(match)
def main():
logging.basicConfig(
level=logging.INFO,
format='%(asctime)s:%(name)s:%(levelname)s:%(message)s')
env.validate()
pruner = PruneProcessCache(cache)
background_thread = Thread(target=pruner)
background_thread.start()
app.launchtime = current_time_stamp()
app.run(host="0.0.0.0", port=env.gateway_port, debug=False)
def launch():
env.validate()
if not item_sources or not len(item_sources):
raise Exception("No data sources specified for Cellxgene Gateway")
global default_item_source
if default_item_source is None:
default_item_source = item_sources[0]
pruner = PruneProcessCache(cache)
background_thread = Thread(target=pruner)
background_thread.start()
app.launchtime = current_time_stamp()
def do_view(path):
key = get_key(path)
print(
f"view path={path}, dataset={key.dataset}, annotation_file= {key.annotation_file}, key={key.pathpart}"
)
with entry_lock:
match = cache.check_entry(key)
if match is None:
uascripts = get_extra_scripts()
match = cache.create_entry(key, uascripts)
match.timestamp = current_time_stamp()
if match.status == "loaded" or match.status == "loading":
return match.serve_content(path)
elif match.status == "error":
raise ProcessException.from_cache_entry(match)
def prune(self):
timestamp = util.current_time_stamp()
cutoff = timestamp - self.expire_seconds
processes_to_delete = [p for p in self.cache.entry_list if p.timestamp < cutoff]
processes_to_keep = [
p for p in self.cache.entry_list if not p.timestamp < cutoff
]
logger.debug(
f"Cutoff {cutoff} = timestamp {timestamp} - expire seconds {self.expire_seconds} , keeping {processes_to_keep}, pruning {processes_to_delete}"
)
for process in processes_to_delete:
try:
logger.info(f"pruning process {process.pid} ({process.key.dataset})")
self.cache.prune(process)
except Exception:
logger.exception(
"failed to prune process {process.pid} ({process.dataset})"
)