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[protege-discussion] WebProtege and 3.4.1 login issue

Jennifer Vendetti vendetti at stanford.edu
Sun Aug 2 12:09:27 PDT 2009


When you created a new Web Application Project, did you uncheck the "Use 
Google App Engine" checkbox on the New Web Application Project dialog?  
(This part of the process is described on the wiki [1] - there is also a 
screenshot of the dialog as it should look [2]).  From your error 
message, its seems that you may have left this checked.  It's not 
necessary to use the Google App Engine to run WebProtege, and in fact we 
haven't done any kind of testing with this.

Jennifer

[1] 
http://protegewiki.stanford.edu/index.php/WebProtegeDevelopersGuide#Checkout_WebProtege_source_code
[2] 
http://protegewiki.stanford.edu/index.php/File:Webprotege-new-webapp-prj-dialog.jpg


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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