Building webprotege 3 from source

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Building webprotege 3 from source

Marin Pranjic
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
  [hidden email]
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Re: Building webprotege 3 from source

Matthew Horridge-2
Administrator
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 <[hidden email]> 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
 [hidden email]
_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev


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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
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Re: Building webprotege 3 from source

Marin Pranjic
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.stanford.bmir.protege.web.server.dispatch.impl.DispatchServiceExecutorImpl.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.PerspectiveDataCopier.copyDefaultPerspectiveData(PerspectiveDataCopier.java:38)                                              
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveFileManager.copyDefaultPerspectiveDataIfNecessary(PerspectiveFileManager.java:54)                                 
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveFileManager.getDefaultPerspectiveLayout(PerspectiveFileManager.java:46)                                           
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveLayoutStoreImpl.getPerspectiveFile(PerspectiveLayoutStoreImpl.java:80)                                            
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveLayoutStoreImpl.getPerspectiveFile(PerspectiveLayoutStoreImpl.java:72)                                            
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveLayoutStoreImpl.getPerspectiveLayout(PerspectiveLayoutStoreImpl.java:40)
        at edu.stanford.bmir.protege.web.server.perspective.GetPerspectiveLayoutActionHandler.execute(GetPerspectiveLayoutActionHandler.java:50)
        at edu.stanford.bmir.protege.web.server.perspective.GetPerspectiveLayoutActionHandler.execute(GetPerspectiveLayoutActionHandler.java:23)
        at edu.stanford.bmir.protege.web.server.dispatch.impl.DispatchServiceExecutorImpl.execute(DispatchServiceExecutorImpl.java:67)
        at edu.stanford.bmir.protege.web.server.dispatch.DispatchServlet.executeAction(DispatchServlet.java:49)



Does that sound familiar? Did I forget something?


--
  Marin Pranjic



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 <[hidden email]> 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
_______________________________________________
protege-dev mailing list
https://mailman.stanford.edu/mailman/listinfo/protege-dev
_______________________________________________
protege-dev mailing list


_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
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Re: Building webprotege 3 from source

Marin Pranjic
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



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.stanford.bmir.protege.web.server.dispatch.impl.DispatchServiceExecutorImpl.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.PerspectiveDataCopier.copyDefaultPerspectiveData(PerspectiveDataCopier.java:38)                                              
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveFileManager.copyDefaultPerspectiveDataIfNecessary(PerspectiveFileManager.java:54)                                 
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveFileManager.getDefaultPerspectiveLayout(PerspectiveFileManager.java:46)                                           
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveLayoutStoreImpl.getPerspectiveFile(PerspectiveLayoutStoreImpl.java:80)                                            
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveLayoutStoreImpl.getPerspectiveFile(PerspectiveLayoutStoreImpl.java:72)                                            
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveLayoutStoreImpl.getPerspectiveLayout(PerspectiveLayoutStoreImpl.java:40)
        at edu.stanford.bmir.protege.web.server.perspective.GetPerspectiveLayoutActionHandler.execute(GetPerspectiveLayoutActionHandler.java:50)
        at edu.stanford.bmir.protege.web.server.perspective.GetPerspectiveLayoutActionHandler.execute(GetPerspectiveLayoutActionHandler.java:23)
        at edu.stanford.bmir.protege.web.server.dispatch.impl.DispatchServiceExecutorImpl.execute(DispatchServiceExecutorImpl.java:67)
        at edu.stanford.bmir.protege.web.server.dispatch.DispatchServlet.executeAction(DispatchServlet.java:49)



Does that sound familiar? Did I forget something?


--
  Marin Pranjic



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 <[hidden email]> 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
_______________________________________________
protege-dev mailing list
https://mailman.stanford.edu/mailman/listinfo/protege-dev
_______________________________________________
protege-dev mailing list

_______________________________________________
protege-dev mailing list


_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
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Re: Building webprotege 3 from source

Matthew Horridge-2
Administrator
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 <[hidden email]> 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



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.stanford.bmir.protege.web.server.dispatch.impl.DispatchServiceExecutorImpl.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.PerspectiveDataCopier.copyDefaultPerspectiveData(PerspectiveDataCopier.java:38)                                              
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveFileManager.copyDefaultPerspectiveDataIfNecessary(PerspectiveFileManager.java:54)                                 
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveFileManager.getDefaultPerspectiveLayout(PerspectiveFileManager.java:46)                                           
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveLayoutStoreImpl.getPerspectiveFile(PerspectiveLayoutStoreImpl.java:80)                                            
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveLayoutStoreImpl.getPerspectiveFile(PerspectiveLayoutStoreImpl.java:72)                                            
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveLayoutStoreImpl.getPerspectiveLayout(PerspectiveLayoutStoreImpl.java:40)
        at edu.stanford.bmir.protege.web.server.perspective.GetPerspectiveLayoutActionHandler.execute(GetPerspectiveLayoutActionHandler.java:50)
        at edu.stanford.bmir.protege.web.server.perspective.GetPerspectiveLayoutActionHandler.execute(GetPerspectiveLayoutActionHandler.java:23)
        at edu.stanford.bmir.protege.web.server.dispatch.impl.DispatchServiceExecutorImpl.execute(DispatchServiceExecutorImpl.java:67)
        at edu.stanford.bmir.protege.web.server.dispatch.DispatchServlet.executeAction(DispatchServlet.java:49)



Does that sound familiar? Did I forget something?


--
  Marin Pranjic



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 <[hidden email]> 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
_______________________________________________
protege-dev mailing list
_______________________________________________
protege-dev mailing list

_______________________________________________
protege-dev mailing list

_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev


_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
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Re: Building webprotege 3 from source

Marin Pranjic
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.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;                                                                                                         

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



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 <[hidden email]> 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



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.stanford.bmir.protege.web.server.dispatch.impl.DispatchServiceExecutorImpl.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.PerspectiveDataCopier.copyDefaultPerspectiveData(PerspectiveDataCopier.java:38)                                              
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveFileManager.copyDefaultPerspectiveDataIfNecessary(PerspectiveFileManager.java:54)                                 
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveFileManager.getDefaultPerspectiveLayout(PerspectiveFileManager.java:46)                                           
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveLayoutStoreImpl.getPerspectiveFile(PerspectiveLayoutStoreImpl.java:80)                                            
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveLayoutStoreImpl.getPerspectiveFile(PerspectiveLayoutStoreImpl.java:72)                                            
        at edu.stanford.bmir.protege.web.server.perspective.PerspectiveLayoutStoreImpl.getPerspectiveLayout(PerspectiveLayoutStoreImpl.java:40)
        at edu.stanford.bmir.protege.web.server.perspective.GetPerspectiveLayoutActionHandler.execute(GetPerspectiveLayoutActionHandler.java:50)
        at edu.stanford.bmir.protege.web.server.perspective.GetPerspectiveLayoutActionHandler.execute(GetPerspectiveLayoutActionHandler.java:23)
        at edu.stanford.bmir.protege.web.server.dispatch.impl.DispatchServiceExecutorImpl.execute(DispatchServiceExecutorImpl.java:67)
        at edu.stanford.bmir.protege.web.server.dispatch.DispatchServlet.executeAction(DispatchServlet.java:49)



Does that sound familiar? Did I forget something?


--
  Marin Pranjic



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 <[hidden email]> 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
_______________________________________________
protege-dev mailing list
_______________________________________________
protege-dev mailing list

_______________________________________________
protege-dev mailing list

_______________________________________________
protege-dev mailing list
_______________________________________________
protege-dev mailing list


_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev