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[protege-discussion] WebProtege and 3.4.1 login issue

Brad Cox bcox at virtualschool.edu
Sun Aug 2 11:55:48 PDT 2009


The instructions didn't say if this needs a running servlet engine.  
Previous was without one. With tomcat 5 running, I get the default  
tomcat page. Is that what I should expect?

On Aug 2, 2009, at 2:49 PM, Brad Cox wrote:

> FYI I downloaded the new webprotege and tried to compile it. I think  
> I followed the instructions right, but get these errors at compile  
> time:
>
> Description	Resource	Path	Location	Type
> java.io.FileWriter is not supported by Google App Engine's Java  
> runtime environment	
> ProjectConfigurationServiceImpl.java	/web-protege-trunk/src/edu/ 
> stanford/bmir/protege/web/server	line 128	Google App Engine Java  
> Problem
> The appengine-web.xml file does not exist	WEB-INF	/web-protege-trunk/ 
> war	Unknown	Google App Engine Problem
> java.rmi.Naming is not supported by Google App Engine's Java runtime  
> environment	
> ProjectManager.java	/web-protege-trunk/src/edu/stanford/bmir/protege/ 
> web/server	line 199	Google App Engine Java Problem
>
> Running it anyway I got:
> Aug 2, 2009 6:48:26 PM  
> com.google.apphosting.utils.config.AppEngineWebXmlReader  
> readAppEngineWebXml
> SEVERE: Received exception processing /Users/Brad/Rividium/work/web- 
> protege-trunk/war/WEB-INF/appengine-web.xml
> com.google.apphosting.utils.config.AppEngineConfigException: Could  
> not locate /Users/Brad/Rividium/work/web-protege-trunk/war/WEB-INF/ 
> appengine-web.xml
> 	at  
> com 
> .google 
> .apphosting 
> .utils 
> .config 
> .AppEngineWebXmlReader.getInputStream(AppEngineWebXmlReader.java:102)
> 	at  
> com 
> .google 
> .apphosting 
> .utils 
> .config 
> .AppEngineWebXmlReader 
> .readAppEngineWebXml(AppEngineWebXmlReader.java:60)
> 	at  
> com 
> .google 
> .appengine 
> .tools 
> .development 
> .AbstractContainerService 
> .loadAppEngineWebXml(AbstractContainerService.java:201)
> 	at  
> com 
> .google 
> .appengine 
> .tools 
> .development 
> .AbstractContainerService.startup(AbstractContainerService.java:114)
> 	at  
> com 
> .google 
> .appengine 
> .tools.development.DevAppServerImpl.start(DevAppServerImpl.java:218)
> 	at  
> com 
> .google 
> .appengine 
> .tools 
> .development.gwt.AppEngineLauncher.start(AppEngineLauncher.java:86)
> 	at com.google.gwt.dev.HostedMode.doStartUpServer(HostedMode.java:365)
> 	at com.google.gwt.dev.HostedModeBase.startUp(HostedModeBase.java:590)
> 	at com.google.gwt.dev.HostedModeBase.run(HostedModeBase.java:397)
> 	at com.google.gwt.dev.HostedMode.main(HostedMode.java:232)
> Caused by: java.io.FileNotFoundException: /Users/Brad/Rividium/work/ 
> web-protege-trunk/war/WEB-INF/appengine-web.xml (No such file or  
> directory)
> 	at java.io.FileInputStream.open(Native Method)
> 	at java.io.FileInputStream.<init>(FileInputStream.java:106)
> 	at java.io.FileInputStream.<init>(FileInputStream.java:66)
> 	at  
> com 
> .google 
> .apphosting 
> .utils 
> .config 
> .AppEngineWebXmlReader.getInputStream(AppEngineWebXmlReader.java:99)
> 	... 9 more
> Unable to start embedded HTTP server
> com.google.gwt.core.ext.UnableToCompleteException: (see previous log  
> entries)
> 	at  
> com 
> .google 
> .appengine 
> .tools 
> .development.gwt.AppEngineLauncher.start(AppEngineLauncher.java:91)
> 	at com.google.gwt.dev.HostedMode.doStartUpServer(HostedMode.java:365)
> 	at com.google.gwt.dev.HostedModeBase.startUp(HostedModeBase.java:590)
> 	at com.google.gwt.dev.HostedModeBase.run(HostedModeBase.java:397)
> 	at com.google.gwt.dev.HostedMode.main(HostedMode.java:232)
>
> Indeed, WEB-INF/appengine-web.xml doesn't exist.
>
> This is on MacOSX Leopard.
>
> On Aug 1, 2009, at 3:01 AM, Tania Tudorache wrote:
>
>> I reproduced the problem. I refactored recently the metaproject  
>> manager, and the problem was caused by an unimplemented method.
>>
>> If you update from SVN:
>>
>> edu.stanford.bmir.protege.web.server.RemoteMetaProjectManager
>>
>> you should get the fix and you should be able to login also in  
>> client-server mode.
>>
>> If you update everything from SVN, you will find out that you are  
>> missing a jar. The missing jar is in this archive:
>>
>> http://smi-protege.stanford.edu/collab-protege/tmp/bioPortalReferencePlugin.zip
>>
>> All this will be explained in the developers guide for the next  
>> release.
>>
>> Tania
>>
>>
>> Tania Tudorache wrote:
>>> This is strange. The only thing that I can suggest in this case is  
>>> to debug it (MetaProjectManager.hasValidCredentials).
>>>
>>> We have made in the last days some significant changes to  
>>> webprotege to make it work with GWT 1.7 (structure of directories  
>>> have changed, etc.).
>>>
>>> Jennifer started to document the developers' guide for the new  
>>> version here:
>>>
>>> http://protegewiki.stanford.edu/index.php/WebProtegeDevelopersGuide
>>>
>>> The new version is more robust and configurable, and it will run  
>>> by default in local mode (not client-server mode) to make the life  
>>> of developers easier (no more metaproject copying around). We will  
>>> make a release for the new version next week.
>>>
>>> If you can wait, I suggest to update to the new version once it is  
>>> released, and this problem might go away.
>>>
>>> Tania
>>>
>>>
>>> Peter Ward wrote:
>>>> Hello Tania
>>>>
>>>> I can log into the Protege server from the Protege thick client.
>>>> I can browse ontologies in WebProtege without logging in.
>>>> Any attempt to log in from WebProtege fails. There is no message  
>>>> in the Protege server window. The protege log contains:
>>>>
>>>> 2009.07.30 11:47:17.213 BST INFO: *** SYSTEM START ***
>>>> 2009.07.30 11:47:17.244 BST INFO: In AdminServiceImpl -- init --  
>>>> AdminServiceImpl.init()
>>>> 2009.07.30 11:47:27.200 BST INFO: WebProtege server running with  
>>>> remote projects loaded from the Protege server: localhost --  
>>>> ProjectManager.<init>()
>>>> 2009.07.30 11:47:55.521 BST INFO: In init of OntologyServiceImp  
>>>> -- OntologyServiceImpl.init()
>>>> 2009.07.30 11:47:56.521 BST INFO: Loading project Collaborative  
>>>> Pizza from Protege server localhost --  
>>>> ProjectManager.openProjectRemote()
>>>> 2009.07.30 11:48:03.288 BST WARNING: [Local Folder Repository]  
>>>> The specified file must be a directory. (D:\workspace\web-protege 
>>>> \plugins\edu.stanford.smi.protegex.owl) --  
>>>> LocalFolderRepository.update()
>>>> 2009.07.30 11:48:03.351 BST CONFIG: Preloading frame values:  
>>>> JenaOWLModel(KB_323587) -- RemoteClientFrameStore.preload()
>>>> 2009.07.30 11:48:03.570 BST CONFIG: Preloading frame values:  
>>>> DefaultKnowledgeBase(KB_895231) -- RemoteClientFrameStore.preload()
>>>> 2009.07.30 11:48:09.243 BST CONFIG: Preloading frame values:  
>>>> RDFKnowledgeBase(KB_861771) -- RemoteClientFrameStore.preload()
>>>> 2009.07.30 11:48:09.275 BST CONFIG: Preloading frame values:  
>>>> DefaultKnowledgeBase(KB_392397) -- RemoteClientFrameStore.preload()
>>>> 2009.07.30 11:48:10.837 BST INFO: In init of  
>>>> ProjectConfigurationImpl -- ProjectConfigurationServiceImpl.init()
>>>> 2009.07.30 11:48:11.963 BST INFO: Path to project configuration  
>>>> file: D:\workspace\web-protege\tomcat\webapps\ROOT 
>>>> \projectConfigurations\configuration.xml --  
>>>> ProjectConfigurationServiceImpl.getConfigurationFile()
>>>>
>>>> The server console ends with:
>>>>
>>>> Protege server ready to accept connections...
>>>> Server: Adding Session(id=100, user=webprotege) on Thu Jul 30  
>>>> 11:47:59 BST 2009
>>>> Server: Opened project Collaborative Pizza for Session(id=100,  
>>>> user=webprotege)
>>>> on Thu Jul 30 11:47:59 BST 2009
>>>> Server: Adding Session(id=101, user=webprotege) on Thu Jul 30  
>>>> 11:48:09 BST 2009
>>>> Server: Opened project Collaborative Pizza Annotations for  
>>>> Session(id=101, user=
>>>> webprotege) on Thu Jul 30 11:48:09 BST 2009
>>>>
>>>> I can't see anyother relevant logs (this is running hosted mode  
>>>> in Eclipse). It's odd, as the data is clearly coming from the  
>>>> Protege server using the webprotege login, but any other attempt  
>>>> fails. I am convinced I have the right metaproject and have  
>>>> verified this by changing passwords and observing password error  
>>>> from Protege client. Can I turn on more debugging info on the  
>>>> client and server side??
>>>>
>>>> Peter
>>>>
>>>> ------------------------------------------------------------------------
>>>>
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>>>
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>>
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