Loading interactions from String-db

[Denis Puthier]

Dear all,

I'm trying to use stringApp plugin from Cytoscape. I'm wondering whether the server is up as I'm getting some messages that seem to indicate that the connection cannot be established. The error message inside Cytoscape is "Loading interactions from String-db" with a 'do-not-enter signs'.  The message from the console is written below.

- Cytoscape version: 3.7.2

- stringApp: 1.5.0

Best

[Denis Puthier]

Sorry,

Here is the message from the console:

java.io.IOException: Server returned HTTP response code: 503 for URL: https://api11.jensenlab.org/network

at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)

at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

at java.lang.reflect.Constructor.newInstance(Constructor.java:423)

at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1944)

at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1939)

at java.security.AccessController.doPrivileged(Native Method)

at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1938)

at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1508)

at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)

at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:263)

at edu.ucsf.rbvi.stringApp.internal.io.HttpUtils.postJSON(HttpUtils.java:144)

at edu.ucsf.rbvi.stringApp.internal.tasks.LoadInteractions.run(LoadInteractions.java:93)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:352)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

at java.lang.Thread.run(Thread.java:748)

Caused by: java.io.IOException: Server returned HTTP response code: 503 for URL: https://api11.jensenlab.org/network

at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1894)

at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)

at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480)

at sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(HttpsURLConnectionImpl.java:347)

at edu.ucsf.rbvi.stringApp.internal.io.HttpUtils.executeWithRedirect(HttpUtils.java:432)

at edu.ucsf.rbvi.stringApp.internal.io.HttpUtils.postJSON(HttpUtils.java:136)

... 8 more

java.lang.NullPointerException: null

at edu.ucsf.rbvi.stringApp.internal.utils.ModelUtils.getEnrichmentSettings(ModelUtils.java:1520) ~[?:?]

at edu.ucsf.rbvi.stringApp.internal.model.StringNetwork.setNetwork(StringNetwork.java:65) ~[?:?]

at edu.ucsf.rbvi.stringApp.internal.model.StringManager.addStringNetwork(StringManager.java:369) ~[?:?]

at edu.ucsf.rbvi.stringApp.internal.utils.ModelUtils.createNetworkFromJSON(ModelUtils.java:486) ~[?:?]

at edu.ucsf.rbvi.stringApp.internal.tasks.LoadInteractions.run(LoadInteractions.java:96) ~[?:?]

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321) ~[87:org.cytoscape.work-swing-impl:3.7.2]

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:352) [87:org.cytoscape.work-swing-impl:3.7.2]

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:?]

at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:?]

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:?]

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:?]

at java.lang.Thread.run(Thread.java:748) [?:?]

java.lang.NullPointerException

at edu.ucsf.rbvi.stringApp.internal.utils.ModelUtils.getEnrichmentSettings(ModelUtils.java:1520)

at edu.ucsf.rbvi.stringApp.internal.model.StringNetwork.setNetwork(StringNetwork.java:65)

at edu.ucsf.rbvi.stringApp.internal.model.StringManager.addStringNetwork(StringManager.java:369)

at edu.ucsf.rbvi.stringApp.internal.utils.ModelUtils.createNetworkFromJSON(ModelUtils.java:486)

at edu.ucsf.rbvi.stringApp.internal.tasks.LoadInteractions.run(LoadInteractions.java:96)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:352)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

at java.lang.Thread.run(Thread.java:748)

[Nadezhda Doncheva]

Hi Denis,

We are aware of the issue. The back-end server is currently down and we are working on it. I hope it will be up again latest tomorrow.

Best wishes,

Nadya

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[Nadezhda Doncheva]

Hi Denis,

It is back online now :)

Best,

Nadya

[put...@gmail.com]

Dear all,

I'm trying to use stringApp plugin from Cytoscape. I'm wondering whether the server is up as I'm getting some messages that seem to indicate that the connection cannot be established. The error message inside Cytoscape is "Loading interactions from String-db" with a 'do-not-enter signs'.  The message from the console is written below.

- Cytoscape version: 3.7.2

- stringApp: 1.5.0

Best