网络分析期间出现 Cytoscape 错误 - java.lang.exception？

Question

我是第一次尝试使用 Cytoscape 和 ANIMO 应用程序，但我遇到了问题并卡住了。任何帮助将非常感激！！

我使用的是简单的测试网络（2-3 个节点），但是当我尝试分析网络时经常出现错误。如果我运行来自 shell 的 Cytoscape，我会得到以下信息：

karaf@Cytoscape 3.7.2()> SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.


animo.core.analyser.AnalysisException: Error during analysis: <pre>java.lang.Exception: [/Users/Carla/CytoscapeConfiguration/3/karaf_data/tmp/ANIMO7219678590825060215.xml] Verify result: 134
 empty result
HTTP/1.1 400 Bad Request
Date: Wed, 04 Mar 2020 16:48:28 GMT
Server: Apache/2.4
Content-Length: 226
Connection: close
Content-Type: text/html; charset=iso-8859-1

<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>400 Bad Request</title>
</head><body>
<h1>Bad Request</h1>
<p>Your browser sent a request that this server could not understand.<br />
</p>
</body></html>

 (current directory: /Applications/Cytoscape_v3.7.2/framework/.)

    at animo.core.analyser.uppaal.UppaalModelAnalyserSMC.analyze(UppaalModelAnalyserSMC.java:666)
    at animo.cytoscape.RunAction$RunTask.performNormalAnalysis(RunAction.java:141)
    at animo.cytoscape.RunAction$RunTask.run(RunAction.java:312)
    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)
</pre>
    at animo.core.analyser.uppaal.UppaalModelAnalyserSMC.analyze(UppaalModelAnalyserSMC.java:683)
    at animo.cytoscape.RunAction$RunTask.performNormalAnalysis(RunAction.java:141)
    at animo.cytoscape.RunAction$RunTask.run(RunAction.java:312)
    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.lang.Exception: [/Users/Carla/CytoscapeConfiguration/3/karaf_data/tmp/ANIMO7219678590825060215.xml] Verify result: 134
 empty result
HTTP/1.1 400 Bad Request
Date: Wed, 04 Mar 2020 16:48:28 GMT
Server: Apache/2.4
Content-Length: 226
Connection: close
Content-Type: text/html; charset=iso-8859-1

<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>400 Bad Request</title>
</head><body>
<h1>Bad Request</h1>
<p>Your browser sent a request that this server could not understand.<br />
</p>
</body></html>

 (current directory: /Applications/Cytoscape_v3.7.2/framework/.)

    at animo.core.analyser.uppaal.UppaalModelAnalyserSMC.analyze(UppaalModelAnalyserSMC.java:666)
    ... 9 more

我还运行故障排除脚本并得到了这个...

Target Cytoscape version: 3.7.2
Your shell is bash
Compatible OS version found: 10.14
 - Pass: OS Version = 10.14.6
 - Pass: Following Oracle JDK found:

/Library/Java/JavaVirtualMachines/jdk1.8.0_151.jdk
 - Pass: Current Java Version = 1.8.0_151
 - Pass: JAVA_HOME found: /Library/Java/JavaVirtualMachines/jdk1.8.0_151.jdk/Contents/Home
Checking connection to Cytoscape App Store...
5 packets transmitted, 0 packets received, 100.0% packet loss
Looks connection to App Store is unstable.
Please check firewall setting from System Preference.
traceroute result:
traceroute to apps.cytoscape.org (52.34.133.210), 64 hops max, 52 byte packets
 1  172.27.109.254 (172.27.109.254)  1.542 ms  1.095 ms  1.026 ms
 2  …

我检查了 Mac 上的防火墙选项，Cytoscape 设置为 "Allow incoming connections"。我是一个非常喜欢生物学的人，所以我不知道如何前进...

非常感谢您的帮助！！

厘米

Answer 1

感谢 berezovskyi 的建议。仅供参考，以防万一有人遇到困难，作者 (Stefano Schivo) 提出了一个有效的解决方案。解决方案是使用旧版本的 ANIMO、UPPAAL 和 Cytoscape。以下是协同工作的版本。

Cytoscape 3.4.0

Java1.8.0_151

ANIMO 3.4.0

UPPAAL 4.1.19

谢谢，CM

网络分析期间出现 Cytoscape 错误 - java.lang.exception？

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