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[protege-dev] Building webprotege 3 from source

Marin Pranjic mpranjic at fastmail.com
Wed Mar 28 13:51:06 PDT 2018


Hi Matthew, 


For some reason I assumed the structure remained unchanged :) my bad. I
think I'll be ok if I stick with the v3.0.0 tag.I can successfully run the official release from GitHub (v3.0.0). Seems
to work when I build it myself.
Anyway, since I've already spent a few days debugging this, I'll write
what I found out. I'm not a java developer so don't bet on my
conclusions :)


=> Made a build with commit hash "b6abb4f9". It fails during runtime,
=> when I try to open a project in browser, with the error I reported
=> previously.
I think (?) that the problem is because now dependant modules are
packaged as .jar files inside of WEB-INF/lib/... , for example webprotege-server-
core(...).jar. Based on my research (google + SO) it seems it can't
access the files ("default-perspective-data") because now it's "hidden"
inside of .jar file.


=> Made a build with the most recent commit hash "f620c499". It fails
=> during initialization of the project (error on bottom).


=> It seems that with the new structure, maven is downloading snapshots
=> from the repository, instead of using local builds. I think this
=> might be a cause of the new error (on bottom).

Overall, there are some inconviniences in trying to make your own builds
from a specific git checksum.

Here's the error with the latest commit:

> Encountered an error during initialization: edu.stanford.bmir.protege-
> .web.server.persistence.MorphiaProvider_Factory.create(Ljavax/inject/-
> Provider;Ljavax/inject/Provider;Ljavax/inject/Provider;Ljavax/inject/-
> Provider;Ljavax/inject/Provider;Ljavax/inject/Provider;Ljavax/inject/-
> Provider;)Ldagger/internal/Factory;> java.lang.NoSuchMethodError: edu.stanford.bmir.protege.web.server.per-
> sistence.MorphiaProvider_Factory.create(Ljavax/inject/Provider;Ljavax-
> /inject/Provider;Ljavax/inject/Provider;Ljavax/inject/Provider;Ljavax-
> /inject/Provider;Ljavax/inject/Provider;Ljavax/inject/Provider;)Ldagg-
> er/internal/Factory;
I can see 7 parameters here, while in "f620c499" there are 9 in
constructor. This might be because of a different version from the
maven repo.
-- 
  Marin Pranjic
  mpranjic at fastmail.com



On Wed, 28 Mar 2018, at 19:23, Matthew Horridge wrote:
> Hi Marin, 
> 
> The project structure and set of build artefacts has changed since the
> 3.0.0 release of WebProtege.  GitHub provides the latest “official”
> version.> 
> With regards to the error below, do you get this with the released
> .war file or with the build from GitHub?> 
> Cheers,
> 
> Matthew
> 
> 
>> On 28 Mar 2018, at 05:13, Marin Pranjic
>> <mpranjic at fastmail.com> wrote:>> 
>> I have noticed that contents of my webprotege-server-VERSION.war is
>> much different than the war file downloaded via github.>> 
>> So I'm interested in steps needed to produce the  .war file as the
>> official one.>> 
>> --
>>   Marin Pranjic
>>   mpranjic at fastmail.com
>> 
>> 
>> 
>> On Tue, 27 Mar 2018, at 16:55, Marin Pranjic wrote:
>>> Hey Matthew,
>>> 
>>> the instructions were clear and simple :)
>>> 
>>> However, I made a fresh install with the .war file, bootstrapped
>>> admin, and am getting  the following error when I enter a project
>>> page (blank project I just created):>>> 
>>>> 27-Mar-2018 14:39:40.189 SEVERE [http-nio-8080-exec-2] edu.stanfor-
>>>> d.bmir.protege.web.server.dispatch.impl.DispatchServiceExecutorImp-
>>>> l.execute An error occurred whilst executing an action>>>> java.lang.IllegalArgumentException: URI is not hierarchical>>>>         at java.io.File.<init>(File.java:418)>>>>         at edu.stanford.bmir.protege.web.server.perspective.Perspe-
>>>>         ctiveDataCopier.copyDefaultPerspectiveData(PerspectiveData-
>>>>         Copier.java:38)>>>>         at edu.stanford.bmir.protege.web.server.perspective.Perspe-
>>>>         ctiveFileManager.copyDefaultPerspectiveDataIfNecessary(Per-
>>>>         spectiveFileManager.java:54)>>>>         at edu.stanford.bmir.protege.web.server.perspective.Perspe-
>>>>         ctiveFileManager.getDefaultPerspectiveLayout(PerspectiveFi-
>>>>         leManager.java:46)>>>>         at edu.stanford.bmir.protege.web.server.perspective.Perspe-
>>>>         ctiveLayoutStoreImpl.getPerspectiveFile(PerspectiveLayoutS-
>>>>         toreImpl.java:80)>>>>         at edu.stanford.bmir.protege.web.server.perspective.Perspe-
>>>>         ctiveLayoutStoreImpl.getPerspectiveFile(PerspectiveLayoutS-
>>>>         toreImpl.java:72)>>>>         at edu.stanford.bmir.protege.web.server.perspective.Perspe-
>>>>         ctiveLayoutStoreImpl.getPerspectiveLayout(PerspectiveLayou-
>>>>         tStoreImpl.java:40)>>>>         at edu.stanford.bmir.protege.web.server.perspective.GetPer-
>>>>         spectiveLayoutActionHandler.execute(GetPerspectiveLayoutAc-
>>>>         tionHandler.java:50)>>>>         at edu.stanford.bmir.protege.web.server.perspective.GetPer-
>>>>         spectiveLayoutActionHandler.execute(GetPerspectiveLayoutAc-
>>>>         tionHandler.java:23)>>>>         at edu.stanford.bmir.protege.web.server.dispatch.impl.Disp-
>>>>         atchServiceExecutorImpl.execute(DispatchServiceExecutorImp-
>>>>         l.java:67)>>>>         at edu.stanford.bmir.protege.web.server.dispatch.DispatchS-
>>>>         ervlet.executeAction(DispatchServlet.java:49)>>>> 
>>> 
>>> 
>>> Does that sound familiar? Did I forget something?
>>> 
>>> 
>>> --
>>>   Marin Pranjic
>>>   mpranjic at fastmail.com
>>> 
>>> 
>>> 
>>> On Mon, 12 Mar 2018, at 03:24, Matthew Horridge wrote:
>>>> Hi Marin, 
>>>> 
>>>> Make sure your working directory is the project root.  To build,
>>>> you can type>>>> 
>>>> *mvn clean package*
>>>> 
>>>> The .war file will be in the webprotege-server/target directory.
>>>> 
>>>> You can run dev mode by opening a fresh terminal and typing
>>>> 
>>>> *mvn gwt:codeserver *
>>>> 
>>>> This will run the GWT code server.  In another fresh terminal
>>>> window you can start the WebProtege server by tying>>>> 
>>>> *mvn jetty:run -Denv=dev*
>>>> 
>>>> Browse to http://localhost:8080/ in a web browser of you choice.
>>>> 
>>>> Cheers,
>>>> 
>>>> Matthew
>>>> 
>>>> p.s. I’ll update the build instructions.
>>>> 
>>>> 
>>>>> On 11 Mar 2018, at 16:28, Marin Pranjic <mpranjic at fastmail.com>
>>>>> wrote:>>>>> 
>>>>> Hello,
>>>>> 
>>>>> it seems that webprotege 3.0 build instructions are missing from
>>>>> the project repo and wiki.>>>>> 
>>>>> Which steps are needed to produce webprotege.war?
>>>>> 
>>>>> I managed to build webprotege-client.war and webprotege-
>>>>> server.war, but honestly, no idea how to build a combined one.>>>>> 
>>>>> I tried executing "mvn gwt:compile" in the project root, but the
>>>>> task failed.>>>>> 
>>>>> Any help is appreciated.
>>>>> 
>>>>> Regards,
>>>>> 
>>>>> -- 
>>>>>  Marin Pranjic
>>>>>  mpranjic at fastmail.com
>>>>> _______________________________________________
>>>>> protege-dev mailing list
>>>>> protege-dev at lists.stanford.edu
>>>>> https://mailman.stanford.edu/mailman/listinfo/protege-dev
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