The OSGi/Karaf container could not download its features, so its services never started
Tools built on Karaf (Cytoscape among them) resolve their feature list over the network at boot. If that fetch fails the JVM still starts and the process looks alive — but everything layered on top, including any REST/API port, never loads. That is exactly why the process shows up in ps while the port refuses connections.
First check the machine can reach the repository at all (curl -I https://repo1.maven.org/maven2/); inside Docker this is usually DNS or a proxy that broke without you changing anything. Then check the version in your properties/config file matches the version actually installed — a config carried over from an older image points the resolver at an artifact that does not exist.