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Jamie Munro

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Aug 11, 2012, 5:39:18 AM8/11/12
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I'm just working through the manual installation instructions for StructWSF - I had problems with the automated installer failing and am not familiar enough with Linux to go digging around for errors and I figured I'd probably learn something by going through the manaul instructions which are very comprehensive and useful. Thanks! 

I've got to the installing Solr step and the instructions refer to version 1.4.0 which doesn't seem to available on any mirrors. Does it matter which version I install or does it have to be 1.4.0? And if so could you provide a link?

Thanks

Jamie

Jamie Munro

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Aug 12, 2012, 5:35:19 AM8/12/12
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Apologies! Please ignore my question! I found version 3.3 in the components listing. I've been staring at this for so long I think I'm going blind...

Frederick Giasson

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Aug 13, 2012, 1:10:17 PM8/13/12
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Hi Jamie!

I'm just working through the manual installation instructions for StructWSF - I had problems with the automated installer failing and am not familiar enough with Linux to go digging around for errors and I figured I'd probably learn something by going through the manaul instructions which are very comprehensive and useful. Thanks!

What are the errors that got reported? Take care about the manual instructions, 95% of them should still be right, but there has been some modifications in the automatic installer that may not yet be reflected into the manual instructions.




I've got to the installing Solr step and the instructions refer to version 1.4.0 which doesn't seem to available on any mirrors. Does it matter which version I install or does it have to be 1.4.0? And if so could you provide a link?


We started the process of upgrading OSF with Solr 3.6. Everything works fine, out of the box, if you are not using the Geo-location features of structWSF. If you are not, then you can use Solr 3.6 without any issues. If you are, then you will have to install structWSF by hands from the Dev branch of the structWSF Git project.

In the coming month or so, we should release a new version of structWSF which will includes all the modifications. This new version will be a big one with a new Solr index that includes new features (such as supporting different datatypes, using the Solr 3.6's core geo features and multiple languages handling).


But for now, knowing what chocked with the installer may be helpful to improve it.

[1] https://github.com/structureddynamics/structWSF-Open-Semantic-Framework/tree/dev


Thanks!

Take care,

Fred

Jamie Munro

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Aug 13, 2012, 3:53:05 PM8/13/12
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Fred

Thanks for the reply. I was using the automatic installer on Ubuntu 10.04 running on a local VMware player. I didn't manage to make a note of any error messages as it was running. I know that I couldn't get virtuoso, drupal or phpmyadmin to load once it had completed. I didn't try the solr admin page. I realised that the phpmyadmin install failed because I hadn't correctly selected Apache2 as the webserver (I pressed Enter without pressing space on the selection menu) and I may have fallen foul of this later on in the process. I also suspect that drupal wasn't accessible for two reasons - firstly I mistyped the mysql root password and the script noted the permission denied error and then moved on, and secondly, possibly because I didn't have a domain other than localhost on the VMware player configured. There was also a mention somewhere - sorry I can't remember where - of a log file in a 'tests' directory which didn't exist when I went looking for more detail about what may have gone wrong. 

I've abandoned the VMware on my local PC and I've since set up two micro instances on AWS and I am running the installer again on one (still waiting for it to finish) while I work through the manual process on the other one. So far I've managed to work my way around the different versions mentioned in the manual install file. Mostly this has just been a case of getting the updated links for wget and figuring out that the apache user and group are www-data:www-data in step 8. 

I've gone with structWSF-v1.0a94.zip as it matched the folder structure in the manual instructions. The folder structure in a95.zip seems to be completely different with additional nested levels and I couldn't find WebServices.php 

At the moment I am a bit confused with the order of when to create the ontology folder structure and if I just create this from the root or within the structwsf folder. Should I create these folders, download the .srz and .owl files before initiating the web services framework?

Hopefully the automated installer will work as expected this time but in any event I'm certainly learning a lot by going through the manual process! 

Thanks for your help

Jamie


On Saturday, 11 August 2012 10:39:18 UTC+1, Jamie Munro wrote:

Frederick Giasson

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Aug 14, 2012, 9:38:46 AM8/14/12
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Hi Jamie,


Thanks for the reply. I was using the automatic installer on Ubuntu 10.04 running on a local VMware player. I didn't manage to make a note of any error messages as it was running. I know that I couldn't get virtuoso, drupal or phpmyadmin to load once it had completed. I didn't try the solr admin page. I realised that the phpmyadmin install failed because I hadn't correctly selected Apache2 as the webserver (I pressed Enter without pressing space on the selection menu) and I may have fallen foul of this later on in the process. I also suspect that drupal wasn't accessible for two reasons - firstly I mistyped the mysql root password and the script noted the permission denied error and then moved on,

Yes, the installer has to be upgraded to enter the password twice, and to check if there is an error or not before continuing the process. I just created an issue about that [1]

and secondly, possibly because I didn't have a domain other than localhost on the VMware player configured.

That shouldn't be an issue. By default, "localhost" is used in the installer.


There was also a mention somewhere - sorry I can't remember where - of a log file in a 'tests' directory which didn't exist when I went looking for more detail about what may have gone wrong.

This is related to the tests suite used to see if structWSF is properly installed. Apparently that something did go wrong when creating that folder.


I've abandoned the VMware on my local PC and I've since set up two micro instances on AWS and I am running the installer again on one (still waiting for it to finish) while I work through the manual process on the other one. So far I've managed to work my way around the different versions mentioned in the manual install file. Mostly this has just been a case of getting the updated links for wget and figuring out that the apache user and group are www-data:www-data in step 8.

Good


I've gone with structWSF-v1.0a94.zip as it matched the folder structure in the manual instructions. The folder structure in a95.zip seems to be completely different with additional nested levels and I couldn't find WebServices.php

Yes it is. We refactored the code's folder structure to enable automatic classes loading in PHP. The installer for the version v1.095 should be working properly. This is the reason why I said that the installation manual was a bit out of sync with the latest version.


At the moment I am a bit confused with the order of when to create the ontology folder structure and if I just create this from the root or within the structwsf folder. Should I create these folders, download the .srz and .owl files before initiating the web services framework?

Take a look around line 594 in the osf-install.sh file. The procedure is there:

(1) create folders
(2) get ontologies into these folders
(3) upload the SRZ files
(4) change rights



Hopefully the automated installer will work as expected this time but in any event I'm certainly learning a lot by going through the manual process!

Yes, no doubts that you learned a lot in this process :)

We should have a new version of structWSF within 1 or 2 months (the one currently into the DEV branch of the structWSF repository). This will lead to a major release, but there won't be an upgrader script (since the supported ubuntu server will change, the solr version will change, the solr schema will change (so data will need to be re-indexed) and that the Drupal version will change as well).


[1] https://github.com/structureddynamics/Open-Semantic-Framework-Installer/issues/1

Thanks,

Fred

Frederick Giasson

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Aug 14, 2012, 2:07:03 PM8/14/12
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Hi Jamie,

Do use the installer version 1.0a94 for now. I think I will have to
re-create the one for the version 1.0a95 that doesn't use the same
codebase. I am thinking about that in prevision of the next major
version of OSF. I may have gone one step too far with the release of 1.0a95.

Thanks,

Fred

Jamie Munro

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Aug 15, 2012, 5:00:05 AM8/15/12
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Hi Fred

Just to clarify:

The automatic installation script "osf-installer-v1.0a5.zip" will install StructWSF version 1.0a95 correctly but if I want to complete my manual installation I should use StructWSF version 1.0a94?

Thanks again for all your help. 

Jamie

Frederick Giasson

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Aug 15, 2012, 8:13:15 AM8/15/12
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Hi Jamie,

>
> The automatic installation script "osf-installer-v1.0a5.zip" will
> install StructWSF version 1.0a95 correctly but if I want to complete
> my manual installation I should use StructWSF version 1.0a94?
Yes, exactly


Thanks,

Fred

Jamie Munro

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Aug 17, 2012, 11:02:34 AM8/17/12
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Hi Fred

An update on my experiences so far with a few queries for good measure... 

The automated installer osf-installer-v1.0a5.zip completed without incident or reporting any errors and most things seem to work but I am still having a few problems. I created an ami image of the instance immediately afterwards so if you would like me to go back to check anything or provide more information that won't be a problem.

I can login to the Drupal installation on www.mydomain.com
I can login to the Virtuoso installation on www.mydomain.com:8890/conductor
I can see the Solr admin page on www.mydomain.com:8983/solr/admin

I had to enable the following drupal modules manually:

CCK
  • Content Permissions 
  • User Reference
Organic Groups
  • OG Access Control
Views
  • ViewsUI
The settings in the OG User Roles were blank so I selected admin, contributor and owner/curator and set the default roles for admin users to admin and new group users to contributors.

I also had to enable all the permissions to all modules for the admin user manually. When I tried to copy this command from the install script (sudo drush perm-grant 'admin' all) it failed with 

You must specify roles to grant permissions to, using the --roles    [error]
option.
Drush command terminated abnormally due to an unrecoverable error.   [error]

Both classHierarchySerialized.srz and classPropertyHierarchy.srz were empty and I needed to download them again from http://techwiki.openstructs.org/files

When I ran the test SPARQL query I was initially just getting the table headings s | p | o and a blank page but after renaming the wsf_indexer.php and playing with the domain names and ip addresses I managed to get this give me a listing of ontologies. I renamed it once I was finished.

These are the commands I used:

http://www.mydomain.com/ws/auth/wsf_indexer.php?action=create_wsf&server_address=http://localhost

http://www.mydomain.com/ws/auth/wsf_indexer.php?action=create_user_full_access&user_address=127.0.0.1&server_address=http://localhost

http://www.mydomain.com/ws/auth/wsf_indexer.php?action=create_user_full_access&user_address=[EC2_INTERNAL_IP]&server_address=http://localhost

http://www.mydomain.com/ws/auth/wsf_indexer.php?action=create_world_readable_dataset_read&server_address=http://localhost


Should I be using my external, (in this case elastic) IP address instead of the EC2 Internal IP address?

Once I had done this importing structwsf_test.xml from the conStruct import page worked (with several warnings about missing attributes) and I can browse the test dataset.

I am having a problem viewing any ontologies in Drupal and the www.mydomain.com/conStruct/ontology/ page simply shows a box with "error ::". I tried changing the ontologies location in settings to /data/ontologies/files/ but no luck.
The menu is visible on the right but clicking 'reload' gives me a series of errors:
Web service error: (status: 400) Bad Request - WS-ONTOLOGY-CREATE-302 /ws/ontology/create/ Ontology already existing Can't create the ontology because an ontology with that URI is already existing in the system. Error 

Is there a setting or permission setting that I have missed in order to view and edit ontologies?


Thanks again and sorry if some of this is basic stuff I just don't understand yet!


Jamie

Frederick Giasson

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Aug 20, 2012, 7:41:20 AM8/20/12
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Hi!


An update on my experiences so far with a few queries for good measure... 

The automated installer osf-installer-v1.0a5.zip completed without incident or reporting any errors and most things seem to work but I am still having a few problems. I created an ami image of the instance immediately afterwards so if you would like me to go back to check anything or provide more information that won't be a problem.

Good


I can login to the Drupal installation on www.mydomain.com
I can login to the Virtuoso installation on www.mydomain.com:8890/conductor
I can see the Solr admin page on www.mydomain.com:8983/solr/admin

I had to enable the following drupal modules manually:

CCK
  • Content Permissions 
  • User Reference
Organic Groups
  • OG Access Control
Views
  • ViewsUI
The settings in the OG User Roles were blank so I selected admin, contributor and owner/curator and set the default roles for admin users to admin and new group users to contributors.

Good, I will review the permissions currently setuped by Drush and see if some are missing on that regard.


I also had to enable all the permissions to all modules for the admin user manually. When I tried to copy this command from the install script (sudo drush perm-grant 'admin' all) it failed with 

You must specify roles to grant permissions to, using the --roles    [error]
option.
Drush command terminated abnormally due to an unrecoverable error.   [error]

Yes. This is what got fixed here, and that will make it to the next version of the installer:

  https://github.com/fgiasson/Open-Semantic-Framework-Installer/commit/1233a9266aff5b178b0d54958a46be5c0be61785


Both classHierarchySerialized.srz and classPropertyHierarchy.srz were empty and I needed to download them again from http://techwiki.openstructs.org/files

They should be used from here: https://github.com/structureddynamics/Open-Semantic-Framework-Installer/tree/master/owlapi

Maybe something else re-wrote them in your process



When I ran the test SPARQL query I was initially just getting the table headings s | p | o and a blank page but after renaming the wsf_indexer.php and playing with the domain names and ip addresses I managed to get this give me a listing of ontologies. I renamed it once I was finished.

These are the commands I used:

http://www.mydomain.com/ws/auth/wsf_indexer.php?action=create_wsf&server_address=http://localhost

http://www.mydomain.com/ws/auth/wsf_indexer.php?action=create_user_full_access&user_address=127.0.0.1&server_address=http://localhost

http://www.mydomain.com/ws/auth/wsf_indexer.php?action=create_user_full_access&user_address=[EC2_INTERNAL_IP]&server_address=http://localhost

http://www.mydomain.com/ws/auth/wsf_indexer.php?action=create_world_readable_dataset_read&server_address=http://localhost


Should I be using my external, (in this case elastic) IP address instead of the EC2 Internal IP address?

You should do both, along with "localhost" and maybe the IP of your development workstation. So, depending where the queries will be sent, they will be authenticated . Particularly when you are starting to develop on an instance.



Once I had done this importing structwsf_test.xml from the conStruct import page worked (with several warnings about missing attributes) and I can browse the test dataset.

Yes, attributes are normal. You will have to import the ontology you use, and click the "Generate All" button in structOntology. Next time you will re-import that dataset, they shouldn't appear anymore.



I am having a problem viewing any ontologies in Drupal and the www.mydomain.com/conStruct/ontology/ page simply shows a box with "error ::". I tried changing the ontologies location in settings to /data/ontologies/files/ but no luck.
The menu is visible on the right but clicking 'reload' gives me a series of errors:
Web service error: (status: 400) Bad Request - WS-ONTOLOGY-CREATE-302 /ws/ontology/create/ Ontology already existing Can't create the ontology because an ontology with that URI is already existing in the system. Error 

Is there a setting or permission setting that I have missed in order to view and edit ontologies?

Try this:

(1) reload tomcat6
(2) go to structOntology and press "reload all"

It should appear. Reload All will read all the ontologies files in /data/ontologies/files/ and reload them into the tomcat6 (owlapi) instance. Then you should see them into structOntology.



Thanks again and sorry if some of this is basic stuff I just don't understand yet!

Thanks to you! Well, a OSF instance is somewhat daunting at first, but once you will figure out the main pieces and how they interact together, it should become much more intuitive and easy to use!

Thanks,

Fred

Jamie Munro

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Aug 20, 2012, 9:25:57 AM8/20/12
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Hi again Fred

 

Thanks for the reply and I'm encouraged that I seem to be on the right path! You’re right that it is quite daunting for someone just starting out but I am slowly starting to see how things fit together and the articles on the Techwiki site are helpful so I am slowly wading through them.  I also appreciate your support!

 

I downloaded the .srz files and the new.owl file from the location you suggested then did sudo /etc/init.d/tomcat6 restart before trying to reload the ontologies from the Drupal page. The ontologies say they have loaded but then I get the java errors below and no ontologies appear in the list.

 

·         rdfs.xml reloaded

·         aggr.owl reloaded

·         wsf.owl reloaded

·         wgs84.owl reloaded

·         iron.owl reloaded

·         rdf.xml reloaded

·         owl.rdf reloaded

·         sco.owl reloaded

·         Web service error: (status: 500) Internal Server Error - HTTP-500 /ws/ontology/create/ Error Uncaught [[o:Exception]:"java.lang.Exception: Invoke failed: [[o:Request$PhpNull]]->toString. Cause: java.lang.NullPointerException: cannot call "toString()" on a Java null object. A previous Java call has returned a null value, use java_is_null($jvalue) to check. VM: 1.6.0_24@http://java.sun.com/" at:#-5 php.java.bridge.JavaBridge.Invoke(JavaBridge.java:999)#-4 php.java.bridge.Request.handleRequest(Request.java:417)#-3 php.java.bridge.Request.handleRequests(Request.java:500)#-2 php.java.bridge.http.ContextRunner.run(ContextRunner.java:145)#-1 php.java.bridge.ThreadPool$Delegate.run(ThreadPool.java:60)#0 http://localhost:8080/OWLAPI/java/Java.inc(232): java_ThrowExceptionProxyFactory->getProxy(20, 'php.java.bridge...', 'T', true)#1 http://localhost:8080/OWLAPI/java/Java.inc(360): java_Arg->getResult(true)#2 http://localhost:8080/OWLAPI/java/Java.inc(366): java_Client->getWrappedResult(true)#3 http://localhost:8080/OWLAPI/java/Java.inc(560): java_Client->getResult()#4 http://localhost:8080/OWLAPI/jav [file]: http://localhost:8080/OWLAPI/java/Java.inc[line]:195 Fatal

·         Web service error: (status: 500) Internal Server Error - HTTP-500 /ws/ontology/create/ Error Uncaught [[o:Exception]:"java.lang.Exception: Invoke failed: [[o:Request$PhpNull]]->toString. Cause: java.lang.NullPointerException: cannot call "toString()" on a Java null object. A previous Java call has returned a null value, use java_is_null($jvalue) to check. VM: 1.6.0_24@http://java.sun.com/" at:#-5 php.java.bridge.JavaBridge.Invoke(JavaBridge.java:999)#-4 php.java.bridge.Request.handleRequest(Request.java:417)#-3 php.java.bridge.Request.handleRequests(Request.java:500)#-2 php.java.bridge.http.ContextRunner.run(ContextRunner.java:145)#-1 php.java.bridge.ThreadPool$Delegate.run(ThreadPool.java:60)#0 http://localhost:8080/OWLAPI/java/Java.inc(232): java_ThrowExceptionProxyFactory->getProxy(20, 'php.java.bridge...', 'T', true)#1 http://localhost:8080/OWLAPI/java/Java.inc(360): java_Arg->getResult(true)#2 http://localhost:8080/OWLAPI/java/Java.inc(366): java_Client->getWrappedResult(true)#3 http://localhost:8080/OWLAPI/java/Java.inc(560): java_Client->getResult()#4 http://localhost:8080/OWLAPI/jav [file]: http://localhost:8080/OWLAPI/java/Java.inc[line]:195 Fatal

 

Not sure if it is relevant but I’ve had a look at the Apache2 error.log and can see several errors related to undefined indexes (HTTP_ACCEPT_CHARSET)  in /structwsf/ws/ontology/create/OntologyCreate.php (lines 488 and 487) and undefined variables (ontology) in /usr/share/structwsf/StructuredDynamics/structwsf/ws/ontology/create/index.php (lines 188 and 189)


Thanks

Jamie


On Saturday, 11 August 2012 10:39:18 UTC+1, Jamie Munro wrote:
I'm just working through the manual installation instructions for StructWSF - I had problems with the automated installer failing and am not familiar enough with Linux to go digging around for errors and I figured I'd probably learn something by going through the manaul instructions which are very comprehensive and useful. Thanks! 

I've got to the installing Solr step and the instructions refer to version 1.4.0 which doesn't seem to available on any mirrors. Does it matter which version I install or does it have to be 1.4.0? And if so could you provide a link?

Thanks

Jamie

Frederick Giasson

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Aug 20, 2012, 9:33:58 AM8/20/12
to open-semant...@googlegroups.com
Hi


Thanks for the reply and I'm encouraged that I seem to be on the right path! You’re right that it is quite daunting for someone just starting out but I am slowly starting to see how things fit together and the articles on the Techwiki site are helpful so I am slowly wading through them.  I also appreciate your support!


Good!


I downloaded the .srz files and the new.owl file from the location you suggested then did sudo /etc/init.d/tomcat6 restart before trying to reload the ontologies from the Drupal page. The ontologies say they have loaded but then I get the java errors below and no ontologies appear in the list.

 

·         rdfs.xml reloaded

·         aggr.owl reloaded

·         wsf.owl reloaded

·         wgs84.owl reloaded

·         iron.owl reloaded

·         rdf.xml reloaded

·         owl.rdf reloaded

·         sco.owl reloaded

·         Web service error: (status: 500) Internal Server Error - HTTP-500 /ws/ontology/create/ Error Uncaught [[o:Exception]:"java.lang.Exception: Invoke failed: [[o:Request$PhpNull]]->toString. Cause: java.lang.NullPointerException: cannot call "toString()" on a Java null object. A previous Java call has returned a null value, use java_is_null($jvalue) to check. VM: 1.6.0_24@http://java.sun.com/" at:#-5 php.java.bridge.JavaBridge.Invoke(JavaBridge.java:999)#-4 php.java.bridge.Request.handleRequest(Request.java:417)#-3 php.java.bridge.Request.handleRequests(Request.java:500)#-2 php.java.bridge.http.ContextRunner.run(ContextRunner.java:145)#-1 php.java.bridge.ThreadPool$Delegate.run(ThreadPool.java:60)#0 http://localhost:8080/OWLAPI/java/Java.inc(232): java_ThrowExceptionProxyFactory->getProxy(20, 'php.java.bridge...', 'T', true)#1 http://localhost:8080/OWLAPI/java/Java.inc(360): java_Arg->getResult(true)#2 http://localhost:8080/OWLAPI/java/Java.inc(366): java_Client->getWrappedResult(true)#3 http://localhost:8080/OWLAPI/java/Java.inc(560): java_Client->getResult()#4 http://localhost:8080/OWLAPI/jav [file]: http://localhost:8080/OWLAPI/java/Java.inc[line]:195 Fatal

·         Web service error: (status: 500) Internal Server Error - HTTP-500 /ws/ontology/create/ Error Uncaught [[o:Exception]:"java.lang.Exception: Invoke failed: [[o:Request$PhpNull]]->toString. Cause: java.lang.NullPointerException: cannot call "toString()" on a Java null object. A previous Java call has returned a null value, use java_is_null($jvalue) to check. VM: 1.6.0_24@http://java.sun.com/" at:#-5 php.java.bridge.JavaBridge.Invoke(JavaBridge.java:999)#-4 php.java.bridge.Request.handleRequest(Request.java:417)#-3 php.java.bridge.Request.handleRequests(Request.java:500)#-2 php.java.bridge.http.ContextRunner.run(ContextRunner.java:145)#-1 php.java.bridge.ThreadPool$Delegate.run(ThreadPool.java:60)#0 http://localhost:8080/OWLAPI/java/Java.inc(232): java_ThrowExceptionProxyFactory->getProxy(20, 'php.java.bridge...', 'T', true)#1 http://localhost:8080/OWLAPI/java/Java.inc(360): java_Arg->getResult(true)#2 http://localhost:8080/OWLAPI/java/Java.inc(366): java_Client->getWrappedResult(true)#3 http://localhost:8080/OWLAPI/java/Java.inc(560): java_Client->getResult()#4 http://localhost:8080/OWLAPI/jav [file]: http://localhost:8080/OWLAPI/java/Java.inc[line]:195 Fatal

 

Not sure if it is relevant but I’ve had a look at the Apache2 error.log and can see several errors related to undefined indexes (HTTP_ACCEPT_CHARSET)  in /structwsf/ws/ontology/create/OntologyCreate.php (lines 488 and 487) and undefined variables (ontology) in /usr/share/structwsf/StructuredDynamics/structwsf/ws/ontology/create/index.php (lines 188 and 189)


I already saw that issues on other instances, but this seems to be an occasional bug reported at that stage. Next time I will create a OSF install from the installation script (sometime this week) I will make sure I am not getting this error, and if I do, I will track down the little bugger.

However, there is no real impacts with this issue, as long as everything got loaded.

For the undefined indexes: there is no impact with them. There are just notices returned by PHP. However, I will have to clean them out eventually. For now, you can disable the notices reported in the log file by properly configuring your php.ini file to just return errors and warnings.

Thanks,

Fred
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Jamie Munro

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Aug 20, 2012, 9:55:04 AM8/20/12
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Hi Fred

I think I may still be missing something because even though pressing 'reload' reported that the ontologies had been loaded, when I click on the Ontology link I just get 'error::' under active ontology. Screenshot attached. 

Thanks again!

Jamie



On Monday, 20 August 2012 14:33:58 UTC+1, Frederick Giasson wrote:
Hi

Thanks for the reply and I'm encouraged that I seem to be on the right path! You’re right that it is quite daunting for someone just starting out but I am slowly starting to see how things fit together and the articles on the Techwiki site are helpful so I am slowly wading through them.  I also appreciate your support!


Good!

I downloaded the .srz files and the new.owl file from the location you suggested then did sudo /etc/init.d/tomcat6 restart before trying to reload the ontologies from the Drupal page. The ontologies say they have loaded but then I get the java errors below and no ontologies appear in the list.

 

·         rdfs.xml reloaded

·         aggr.owl reloaded

·         wsf.owl reloaded

·         wgs84.owl reloaded

·         iron.owl reloaded

·         rdf.xml reloaded

·         owl.rdf reloaded

·         sco.owl reloaded

·         Web service error: (status: 500) Internal Server Error - HTTP-500 /ws/ontology/create/ Error Uncaught [[o:Exception]:"java.lang.Exception: Invoke failed: [[o:Request$PhpNull]]->toString. Cause: java.lang.NullPointerException: cannot call "toString()" on a Java null object. A previous Java call has returned a null value, use java_is_null($jvalue) to check. VM: 1.6....@http://java.sun.com/" at:#-5 php.java.bridge.JavaBridge.Invoke(JavaBridge.java:999)#-4 php.java.bridge.Request.handleRequest(Request.java:417)#-3 php.java.bridge.Request.handleRequests(Request.java:500)#-2 php.java.bridge.http.ContextRunner.run(ContextRunner.java:145)#-1 php.java.bridge.ThreadPool$Delegate.run(ThreadPool.java:60)#0 http://localhost:8080/OWLAPI/java/Java.inc(232): java_ThrowExceptionProxyFactory->getProxy(20, 'php.java.bridge...', 'T', true)#1 http://localhost:8080/OWLAPI/java/Java.inc(360): java_Arg->getResult(true)#2 http://localhost:8080/OWLAPI/java/Java.inc(366): java_Client->getWrappedResult(true)#3 http://localhost:8080/OWLAPI/java/Java.inc(560): java_Client->getResult()#4 http://localhost:8080/OWLAPI/jav [file]: http://localhost:8080/OWLAPI/java/Java.inc[line]:195 Fatal

·         Web service error: (status: 500) Internal Server Error - HTTP-500 /ws/ontology/create/ Error Uncaught [[o:Exception]:"java.lang.Exception: Invoke failed: [[o:Request$PhpNull]]->toString. Cause: java.lang.NullPointerException: cannot call "toString()" on a Java null object. A previous Java call has returned a null value, use java_is_null($jvalue) to check. VM: 1.6....@http://java.sun.com/" at:#-5 php.java.bridge.JavaBridge.Invoke(JavaBridge.java:999)#-4 php.java.bridge.Request.handleRequest(Request.java:417)#-3 php.java.bridge.Request.handleRequests(Request.java:500)#-2 php.java.bridge.http.ContextRunner.run(ContextRunner.java:145)#-1 php.java.bridge.ThreadPool$Delegate.run(ThreadPool.java:60)#0 http://localhost:8080/OWLAPI/java/Java.inc(232): java_ThrowExceptionProxyFactory->getProxy(20, 'php.java.bridge...', 'T', true)#1 http://localhost:8080/OWLAPI/java/Java.inc(360): java_Arg->getResult(true)#2 http://localhost:8080/OWLAPI/java/Java.inc(366): java_Client->getWrappedResult(true)#3 http://localhost:8080/OWLAPI/java/Java.inc(560): java_Client->getResult()#4 http://localhost:8080/OWLAPI/jav [file]: http://localhost:8080/OWLAPI/java/Java.inc[line]:195 Fatal

 

Not sure if it is relevant but I’ve had a look at the Apache2 error.log and can see several errors related to undefined indexes (HTTP_ACCEPT_CHARSET)  in /structwsf/ws/ontology/create/OntologyCreate.php (lines 488 and 487) and undefined variables (ontology) in /usr/share/structwsf/StructuredDynamics/structwsf/ws/ontology/create/index.php (lines 188 and 189)

Ontology Error.png

Frederick Giasson

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Aug 20, 2012, 9:57:32 AM8/20/12
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Hi Jamie,


>
> I think I may still be missing something because even though pressing
> 'reload' reported that the ontologies had been loaded, when I click on
> the Ontology link I just get 'error::' under active ontology.
> Screenshot attached.
>


Normally, if no ontologies are loaded, you get a blank list. This
current error usually appear when we can't reach the OWLAPI instance.

So, first thing to check is: is tomcat6 currently running with the
OWLAPI webapp?

Thanks,

Fred

Jamie Munro

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Aug 20, 2012, 10:52:48 AM8/20/12
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Hi Fred

I can see the OWLAPI folder in /var/lib/tomcat6/webapps/OWLAPI (which is not empty). 
After opening up port 8080 I can browse to http://www.mydomain.com:8080/OWLAPI/java/Java.inc which simply shows the text of Java.inc 

I had a look at the tomcat6 policy file and added the line from the manual install file then restarted tomcat6
grant codeBase "file:/var/lib/tomcat6/webapps/OWLAPI/WEB-INF/-" { permission java.security.AllPermission; }; 

Still no luck and the ontologies page is still showing an error. 

I also saw the two notes about PHP/Java bridge in the manual install file and have been trying to go through the FAQs file to debug it but must confess to getting lost...

Thanks

Jamie

Frederick Giasson

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Aug 20, 2012, 4:48:09 PM8/20/12
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Hi!


I can see the OWLAPI folder in /var/lib/tomcat6/webapps/OWLAPI (which is not empty). 
After opening up port 8080 I can browse to http://www.mydomain.com:8080/OWLAPI/java/Java.inc which simply shows the text of Java.inc 


Good, this would mean that it is up and running


I had a look at the tomcat6 policy file and added the line from the manual install file then restarted tomcat6
grant codeBase "file:/var/lib/tomcat6/webapps/OWLAPI/WEB-INF/-" { permission java.security.AllPermission; }; 

Still no luck and the ontologies page is still showing an error. 

I also saw the two notes about PHP/Java bridge in the manual install file and have been trying to go through the FAQs file to debug it but must confess to getting lost...

Would it be possible for you to install FireBug, and check the "Console" and/or the "Net" tab and give me what is returned by the structWSF server at loading time. This will helps us investigating the current issue.

Thanks,

Fred

Jamie Munro

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Aug 21, 2012, 5:16:43 AM8/21/12
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Hi Fred

This is what I get Firebug's Net tab when I try to browse to ../conStruct/ontology/ 
I just copied it straight from the tab:

Thanks 

Jamie

GET /conStruct/ontology/
200 OK
3 KB
 
203ms
GET jquery.contextMenu.css
404 Not Found
1022 B
 
174ms
GET node.css?G
304 Not Modified
325 B
 
32ms
GET defaults.css?G
304 Not Modified
378 B
 
33ms
GET system.css?G
304 Not Modified
2.7 KB
 
36ms
GET system-menus.css?G
304 Not Modified
323 B
 
34ms
GET user.css?G
304 Not Modified
433 B
 
34ms
GET content-module.css?G
304 Not Modified
871 B
 
49ms
GET og.css?G
304 Not Modified
471 B
 
48ms
GET views.css?G
304 Not Modified
636 B
 
51ms
GET style.css?G
304 Not Modified
4.4 KB
 
51ms
GET print.css?G
304 Not Modified
497 B
 
51ms
GET jquery.js?G
304 Not Modified
15.3 KB
 
64ms
GET drupal.js?G
304 Not Modified
3.4 KB
 
65ms
GET og.js?G
304 Not Modified
554 B
 
66ms
GET jquery.min.js?G
304 Not Modified
29.2 KB
 
67ms
GET ontology.js?G
304 Not Modified
1.8 KB
 
67ms
GET resultset.js?G
304 Not Modified
3.9 KB
 
81ms
GET ontologySearch.js?G
304 Not Modified
5.1 KB
 
82ms
POST /ws/ontology/read/
Aborted
localhost
0
 
1.01s
 
20 requests
74.3 KB
(70.2 KB from cache)

Frederick Giasson

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Aug 21, 2012, 7:46:51 AM8/21/12
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Hi Jamie,

>
> 82ms
> POST /ws/ontology/read/
> Aborted
> localhost
> 0

This is what interest us. Please, extend that item, and click the
"response" tab and copy/paste its content here. This should gives us the
error and so the reason why it aborted there.

Thanks,


Fred

Jamie Munro

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Aug 21, 2012, 8:24:08 AM8/21/12
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Hi Fred

Unfortunately there is nothing to expand. I noticed that that entry in Firebug is the only one that has localhost listed under domain so I tried running the wsf_indexer commands again with all my possible IP addresses for the user address but still no luck.

Thanks

Jamie

Frederick Giasson

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Aug 21, 2012, 8:37:57 AM8/21/12
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Hi Jamie,


> Unfortunately there is nothing to expand. I noticed that that entry in
> Firebug is the only one that has localhost listed under domain so I
> tried running the wsf_indexer commands again with all my possible IP
> addresses for the user address but still no luck.

Ok, this means that structOntology tells your browser that the WSF
network to reach is located on the localhost. But if your browser
doesn't share the same local host, it won't get it.

This means that you have to properly configure it as well:

(1) Make sure you see your "www.mydomain.com/ws" structWSF instance
registered in structNetwork (http://www.mydomain.com/construct/networks/)
(2) Make sure to select your registered network in the Ontology
Settings: http://www.mydomain.com/admin/settings/conStruct/structOntology/


Then refresh that page.

Thanks,

Fred

Jamie Munro

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Aug 21, 2012, 9:01:43 AM8/21/12
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Hi Fred

That's given me a new variation! It's now coming up with "parsererror::" and then the whole page loads within the ontology box as though it was an iframe. Screenshot attached.

The Response tab for the line that aborted previously in firebug is below.

Thanks!

Jamie

POST http://www.saears.eu/conStruct/ontology/www.saears.eu/ws/ontology/read/
   
200 OK

   
saears.eu
   
1.8 KB
   
54.247.101.169:80
   
 
203ms
HeadersPostResponseHTMLCookies

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en" dir="ltr">
  <head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link type="text/css" rel="stylesheet" media="all" href="http://www.saears.eu/sites/all/modules/conStruct/modules/structOntology/css/style.css" />
<link type="text/css" rel="stylesheet" media="all" href="http://www.saears.eu/sites/all/modules/conStruct/modules/structOntology/css/jquery.contextMenu.css" />
<link rel="shortcut icon" href="/misc/favicon.ico" type="image/x-icon" />
    <title>SAEARS Ontology | A SAEARS Ontology</title>
    <link type="text/css" rel="stylesheet" media="all" href="/modules/node/node.css?G" />
<link type="text/css" rel="stylesheet" media="all" href="/modules/system/defaults.css?G" />
<link type="text/css" rel="stylesheet" media="all" href="/modules/system/system.css?G" />
<link type="text/css" rel="stylesheet" media="all" href="/modules/system/system-menus.css?G" />
<link type="text/css" rel="stylesheet" media="all" href="/modules/user/user.css?G" />
<link type="text/css" rel="stylesheet" media="all" href="/sites/all/modules/cck/theme/content-module.css?G" />
<link type="text/css" rel="stylesheet" media="all" href="/sites/all/modules/og/theme/og.css?G" />
<link type="text/css" rel="stylesheet" media="all" href="/sites/all/modules/views/css/views.css?G" />
<link type="text/css" rel="stylesheet" media="all" href="/themes/garland/style.css?G" />
<link type="text/css" rel="stylesheet" media="print" href="/themes/garland/print.css?G" />
    <script type="text/javascript" src="/misc/jquery.js?G"></script>
<script type="text/javascript" src="/misc/drupal.js?G"></script>
<script type="text/javascript" src="/sites/all/modules/og/og.js?G"></script>
<script type="text/javascript" src="/sites/all/modules/conStruct/modules/structOntology/js/jquery.min.js?G"></script>
<script type="text/javascript" src="/sites/all/modules/conStruct/modules/structOntology/js/ontology.js?G"></script>
<script type="text/javascript" src="/sites/all/modules/conStruct/modules/structOntology/js/resultset.js?G"></script>
<script type="text/javascript">
<!--//--><![CDATA[//><!--
jQuery.extend(Drupal.settings, { "basePath": "/" });
//--><!]]>
</script>
    <!--[if lt IE 7]>
      <link type="text/css" rel="stylesheet" media="all" href="/themes/garland/fix-ie.css" />    <![endif]-->
  </head>
  <body class="sidebars">

<!-- Layout -->
  <div id="header-region" class="clear-block"></div>

    <div id="wrapper">
    <div id="container" class="clear-block">

      <div id="header">
        <div id="logo-floater">
        <h1><a href="/" title="SAEARS Ontology"><img src="/themes/garland/logo.png" alt="SAEARS Ontology" id="logo" /><span>SAEARS Ontology</span></a></h1>        </div>

                                                   
      </div> <!-- /header -->

              <div id="sidebar-left" class="sidebar">
                    <div id="block-user-1" class="clear-block block block-user">

  <h2>admin</h2>

  <div class="content"><ul class="menu"><li class="collapsed first"><a href="/og">Groups</a></li>
<li class="leaf"><a href="/group">My Unread</a></li>
<li class="leaf"><a href="/user/1">My account</a></li>
<li class="collapsed"><a href="/node/add">Create content</a></li>
<li class="collapsed"><a href="/admin">Administer</a></li>
<li class="leaf last"><a href="/logout">Log out</a></li>
</ul></div>
</div>
        </div>
     
      <div id="center"><div id="squeeze"><div class="right-corner"><div class="left-corner">
          <div class="breadcrumb"><a href="/">Home</a></div>                                                                                <div class="clear-block">
                      </div>
                    <div id="footer"><div id="block-system-0" class="clear-block block block-system">


  <div class="content"><a href="http://drupal.org"><img src="/misc/powered-blue-80x15.png" alt="Powered by Drupal, an open source content management system" title="Powered by Drupal, an open source content management system" width="80" height="15" /></a></div>
</div>
</div>
      </div></div></div></div> <!-- /.left-corner, /.right-corner, /#squeeze, /#center -->

              <div id="sidebar-right" class="sidebar">
                    <div id="block-structUpdate-0" class="clear-block block block-structUpdate">

  <h2>conStruct Update Tool</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/modules/structUpdate/imgs/overlays.png" style="padding-right:5px;" /><a href="http://www.saears.eu/conStruct/update/">Update Record</a><br /></div>
</div>
<div id="block-conStruct-0" class="clear-block block block-conStruct">

  <h2>conStruct Tools</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/imgs/kcontrol.png" style="padding-right:5px;" alt="" /><a href="http://www.saears.eu/admin/settings/conStruct/">Settings</a><br /><img src="http://www.saears.eu/sites/all/modules/conStruct/imgs/kcontrol.png" style="padding-right:5px;" alt="" /><a href="http://www.saears.eu/admin/settings/conStruct/access/">Access Settings</a><br /><img src="http://www.saears.eu/sites/all/modules/conStruct/imgs/kcontrol.png" style="padding-right:5px;" alt="" /><a href="http://www.saears.eu/admin/settings/conStruct/structOntology/">Ontology Settings</a><br /><img src="http://www.saears.eu/sites/all/modules/conStruct/imgs/kcontrol.png" style="padding-right:5px;" alt="" /><a href="http://www.saears.eu/admin/settings/conStruct/scones/">Scones Settings</a><br /></div>
</div>
<div id="block-structSearch-0" class="clear-block block block-structSearch">

  <h2>conStruct Search Tool</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/modules/structSearch/imgs/katomic.png" style="padding-right:5px;" alt="" /><a href="http://www.saears.eu/conStruct/search/">Search</a><br /></div>
</div>
<div id="block-structScones-0" class="clear-block block block-structScones">

  <h2>conStruct scones Tool</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/modules/structScones/imgs/tag_blue.png" style="padding-right:5px;" /><a href="http://www.saears.eu/conStruct/scones/">Scones</a><br /></div>
</div>
<div id="block-structOntology-0" class="clear-block block block-structOntology">

  <h2>conStruct Ontology Tool</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/modules/structOntology/imgs/cog.png" style="padding-right:5px;" /><a href="http://www.saears.eu/conStruct/ontology/">Ontology</a><br /></div>
</div>
<div id="block-structNetworks-0" class="clear-block block block-structNetworks">

  <h2>conStruct Networks Tool</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/modules/structNetworks/imgs/chart_organisation.png" style="padding-right:5px;" /><a href="http://www.saears.eu/conStruct/networks/">Networks</a><br /></div>
</div>
<div id="block-structImport-0" class="clear-block block block-structImport">

  <h2>conStruct Import Tool</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/modules/structImport/imgs/view_detailed.png" style="padding-right:5px;" alt="" /><a href="http://www.saears.eu/conStruct/import/">Import</a><br /></div>
</div>
<div id="block-structExport-0" class="clear-block block block-structExport">

  <h2>conStruct Export Tool</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/modules/structExport/imgs/export.png" style="padding-right:5px;" alt="" /><a href="http://www.saears.eu/conStruct/export/">Export</a><br /></div>
</div>
<div id="block-structDelete-0" class="clear-block block block-structDelete">

  <h2>conStruct Delete Tool</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/modules/structDelete/imgs/cancel.png" style="padding-right:5px;" /><a href="http://www.saears.eu/conStruct/delete/">Delete Record</a><br /></div>
</div>
<div id="block-structDataset-0" class="clear-block block block-structDataset">

  <h2>conStruct Dataset Tool</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/modules/structDataset/imgs/bricks.png" style="padding-right:5px;" alt="Dataset" /><a href="http://www.saears.eu/conStruct/dataset/">Dataset</a><br /></div>
</div>
<div id="block-structCreate-0" class="clear-block block block-structCreate">

  <h2>conStruct Create Tool</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/modules/structCreate/imgs/edit_add.png" style="padding-right:5px;" /><a href="http://www.saears.eu/conStruct/create/">Create Record</a><br /></div>
</div>
<div id="block-structBrowse-0" class="clear-block block block-structBrowse">

  <h2>conStruct Browse Tool</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/modules/structBrowse/imgs/view_detailed.png" style="padding-right:5px;" alt="" /><a href="http://www.saears.eu/conStruct/browse/">Browse</a><br /></div>
</div>
<div id="block-structAppend-0" class="clear-block block block-structAppend">

  <h2>conStruct Append Tool</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/modules/structAppend/imgs/arrow_join.png" style="padding-right:5px;" alt="" /><a href="http://www.saears.eu/conStruct/append/">Append</a><br /></div>
</div>
<div id="block-structView-0" class="clear-block block block-structView">

  <h2>conStruct View Tool</h2>

  <div class="content"><img src="http://www.saears.eu/sites/all/modules/conStruct/modules/structView/imgs/view_detailed.png" style="padding-right:5px;" alt="" /><a href="http://www.saears.eu/conStruct/view/">View</a><br /></div>
</div>
        </div>
     
    </div> <!-- /container -->
  </div>
<!-- /layout -->

    </body>
</html>
ParserError.png

Frederick Giasson

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Aug 21, 2012, 9:05:58 AM8/21/12
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Hi!

The endpoint is still not right. The browser tries to access:

> POST
> http://www.saears.eu/conStruct/ontology/www.saears.eu/ws/ontology/read/


But it should:

http://www.saears.eu/ws/ontology/read/

What it gets is a html page from that URL instead of reaching the
Ontology Read endpoint.

Do you have an idea of what could be the problem (some of your configs?)

Thanks,



Fred

Jamie Munro

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Aug 21, 2012, 9:51:55 AM8/21/12
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Fred,

You're a genius! I'd typed the domain in as www.domain.com instead of http://www.domain.com and it's working now.

Thanks for all your time and patient support!

Jamie

Frederick Giasson

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Aug 21, 2012, 10:01:43 AM8/21/12
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Hi!

> You're a genius! I'd typed the domain in as www.domain.com instead of
> http://www.domain.com and it's working now.

Good!

> Thanks for all your time and patient support!

So, next thing to do is to load and test your ontology :)

Thanks,

Fred

Jamie Munro

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Aug 21, 2012, 10:08:02 AM8/21/12
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Pausing only to finish building it... :)

Shan Wan

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Jul 8, 2017, 4:22:41 AM7/8/17
to Open Semantic Framework
Hi Fred, 

I searched the mailling list, then found this post similar but different with mine.
I got some issue during Loading core Ontologies when installing OSF not OSF for drupal, 
here is what I got:

Downloading the core OSF ontologies...
Installing the core OSF ontologies...
Loading the core OSF ontologies...

Loading: file://localhost/data//ontologies/files/aggr.owl
Can't create permissions for the loaded ontology: file://localhost/data//ontologies/files/aggr.owl. Bad Request<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>WS-AUTH-RE GISTRAR-ACCESS-309</id>                  <webservice>/ws/auth/registrar/access/</webservice>                                  <name>Invalid group URI</name>                  <description>The URI of the group is not valid.</description>                  <debugInformation></debugInformation>                  <level>Warning                </level>                </error>
Debug file: /tmp/4394ece664d19dd912aa9e1f4f76f08a.error
Can't load ontology file file://localhost/data//ontologies/files/aggr.owl. Internal Server Error<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>HTTP-500</id>                                  <webservice>/ws/ontology/create/</webservice>                  <name>Compile Error</name>                                  <description>require_once(): Failed opening required 'http://localhost:8080/OWLAPI/java/Java.inc' (include_path='.:/usr/share/php')</description>                  <debugInformation>[file]: /usr                /share/osf/StructuredDynamics/osf/ws/ontology/create/interfaces/DefaultSourceInterface.php[line]:189</                debugInformation>                  <level>Fatal</level>                </error>
Debug file: /tmp/d441b65a1f6e698e2cbc4c23fce6deb3.error
Loading: file://localhost/data//ontologies/files/iron.owl
Can't create permissions for the loaded ontology: file://localhost/data//ontologies/files/iron.owl. Bad Request<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>WS-AUTH-REGISTRAR-ACCESS-309</id>                  <webservice>/ws/auth/registrar/access/</webservice>                                  <name>Invalid group URI</name>                  <description>The URI of the group is not valid                .</description>                  <debugInformation></debugInformation>                  <level>Warning                </level>                </error>
Debug file: /tmp/0c3d59cbcab6d942f466819c70546fef.error
Can't load ontology file file://localhost/data//ontologies/files/iron.owl. Internal Server Error<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>HTTP-500</id>                                  <webservice>/ws/ontology/create/</webservice>                  <name>Compile Error</name>                                  <description>require_once(): Failed opening required 'http://localhost:8080/OWLAPI/java/Java.inc' (include_path='.:/usr/share/php')</description>                  <debugInformation>[file]: /usr /share/osf/StructuredDynamics/osf/ws/ontology/create/interfaces/DefaultSourceInterface.php[line]:189</                debugInformation>                  <level>Fatal</level>                </error>
Debug file: /tmp/0ae480bc7e6208cf34242ee35dc656c1.error
Loading: file://localhost/data//ontologies/files/owl.rdf
Can't create permissions for the loaded ontology: file://localhost/data//ontologies/files/owl.rdf. Bad Request<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>WS-AUTH-REGISTRAR-ACCESS-309</id>                  <webservice>/ws/auth/registrar/access/</webservice>                                  <name>Invalid group URI</name>                  <description>The URI of the group is not valid.                </description>                  <debugInformation></debugInformation>                  <level>Warning<                /level>                </error>
Debug file: /tmp/f3c85a00a3ab3a657d16f8e95bd032ae.error
Can't load ontology file file://localhost/data//ontologies/files/owl.rdf. Internal Server Error<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>HTTP-500</id>                                  <webservice>/ws/ontology/create/</webservice>                  <name>Compile Error</name>                                  <description>require_once(): Failed opening required 'http://localhost:8080/OWLAPI/java/Java.inc' (include_path='.:/usr/share/php')</description>                  <debugInformation>[file]: /usr/ share/osf/StructuredDynamics/osf/ws/ontology/create/interfaces/DefaultSourceInterface.php[line]:189</d                ebugInformation>                  <level>Fatal</level>                </error>
Debug file: /tmp/309f20f5e8b3b19d30a563894ced4e8d.error
Loading: file://localhost/data//ontologies/files/rdfs.xml
Can't create permissions for the loaded ontology: file://localhost/data//ontologies/files/rdfs.xml. Bad Request<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>WS-AUTH-REGISTRAR-ACCESS-309</id>                  <webservice>/ws/auth/registrar/access/</webservice>                                  <name>Invalid group URI</name>                  <description>The URI of the group is not valid                .</description>                  <debugInformation></debugInformation>                  <level>Warning                </level>                </error>
Debug file: /tmp/79fc17a29537894dfc598118baa31a07.error
Can't load ontology file file://localhost/data//ontologies/files/rdfs.xml. Internal Server Error<?xmlversion="1.0" encoding="utf-8"?>                <error>                  <id>HTTP-500</id>                                  <webservice>/ws/ontology/create/</webservice>                  <name>Compile Error</name>                                  <description>require_once(): Failed opening required 'http://localhost:8080/OWLAPI/java/Java.inc' (include_path='.:/usr/share/php')</description>                  <debugInformation>[file]: /usr                /share/osf/StructuredDynamics/osf/ws/ontology/create/interfaces/DefaultSourceInterface.php[line]:189</                debugInformation>                  <level>Fatal</level>                </error>
Debug file: /tmp/a8cc0c527f41e20485e7b5c0f834cd0c.error
Loading: file://localhost/data//ontologies/files/rdf.xml
Can't create permissions for the loaded ontology: file://localhost/data//ontologies/files/rdf.xml. Bad Request<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>WS-AUTH-REGISTRAR-ACCESS-309</id>                  <webservice>/ws/auth/registrar/access/</webservice>                                  <name>Invalid group URI</name>                  <description>The URI of the group is not valid. </description>                  <debugInformation></debugInformation>                  <level>Warning<                /level>                </error>
Debug file: /tmp/a05aa3b90170974c5584c77dbf8eec42.error
Can't load ontology file file://localhost/data//ontologies/files/rdf.xml. Internal Server Error<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>HTTP-500</id>                                  <webservice>/ws/ontology/create/</webservice>                  <name>Compile Error</name>                                  <description>require_once(): Failed opening required 'http://localhost:8080/OWLAPI/java/Java.inc' (include_path='.:/usr/share/php')</description>                  <debugInformation>[file]: /usr/                share/osf/StructuredDynamics/osf/ws/ontology/create/interfaces/DefaultSourceInterface.php[line]:189</d                ebugInformation>                  <level>Fatal</level>                </error>
Debug file: /tmp/5a3312f2d7e260ef38097c7bebcfd54a.error
Loading: file://localhost/data//ontologies/files/sco.owl
Can't create permissions for the loaded ontology: file://localhost/data//ontologies/files/sco.owl. BadRequest<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>WS-AUTH-REGISTRAR-ACCESS-309</id>                  <webservice>/ws/auth/registrar/access/</webservice>                                  <name>Invalid group URI</name>                  <description>The URI of the group is not valid.  </description>                  <debugInformation></debugInformation>                  <level>Warning<                /level>                </error>
Debug file: /tmp/a78885a2ae79120219e3f417df07001d.error
Can't load ontology file file://localhost/data//ontologies/files/sco.owl. Internal Server Error<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>HTTP-500</id>                                  <webservice>/ws/ontology/create/</webservice>                  <name>Compile Error</name>                                  <description>require_once(): Failed opening required 'http://localhost:8080/OWLAPI/java/Java.inc' (include_path='.:/usr/share/php')</description>                  <debugInformation>[file]: /usr/share/osf/StructuredDynamics/osf/ws/ontology/create/interfaces/DefaultSourceInterface.php[line]:189</d                ebugInformation>                  <level>Fatal</level>                </error>
Debug file: /tmp/e04fbc61ea94e4095f6c1abff4f5ad9c.error
Loading: file://localhost/data//ontologies/files/wgs84.owl
Can't create permissions for the loaded ontology: file://localhost/data//ontologies/files/wgs84.owl. Bad Request<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>WS-AUTH-REGISTRAR-ACCESS-309</id>                  <webservice>/ws/auth/registrar/access/</webservice>                                  <name>Invalid group URI</name>                  <description>The URI of the group is not valid.</description>                  <debugInformation></debugInformation>                  <level>Warning</level>                </error>
Debug file: /tmp/4d5aadc016e411c349389d2ffaf71136.error
Can't load ontology file file://localhost/data//ontologies/files/wgs84.owl. Internal Server Error<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>HTTP-500</id>                                  <webservice>/ws/ontology/create/</webservice>                  <name>Compile Error</name>                                  <description>require_once(): Failed opening required 'http://localhost:8080/OWLAPI/java/Java.inc' (include_path='.:/usr/share/php')</description>                  <debugInformation>[file]: /us r/share/osf/StructuredDynamics/osf/ws/ontology/create/interfaces/DefaultSourceInterface.php[line]:189< /debugInformation>                  <level>Fatal</level>                </error>
Debug file: /tmp/754cd21ff563b4006d7cac7288c4feef.error
Loading: file://localhost/data//ontologies/files/wsf.owl
Can't create permissions for the loaded ontology: file://localhost/data//ontologies/files/wsf.owl. Bad  Request<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>WS-AUTH-REGISTRAR-ACCESS-309</id>                  <webservice>/ws/auth/registrar/access/</webservice>                                  <name>Invalid group URI</name>                  <description>The URI of the group is not valid.</description>                  <debugInformation></debugInformation>                  <level>Warning<                /level>                </error>
Debug file: /tmp/58cd9e51abc9683c39eb4e8ad065983b.error
Can't load ontology file file://localhost/data//ontologies/files/wsf.owl. Internal Server Error<?xml v                ersion="1.0" encoding="utf-8"?>                <error>                  <id>HTTP-500</id>                                  <webservice>/ws/ontology/create/</webservice>                  <name>Compile Error</name>                                  <description>require_once(): Failed opening required 'http://localhost:8080/OWLAPI/java/Java .inc' (include_path='.:/usr/share/php')</description>                  <debugInformation>[file]: /usr/share/osf/StructuredDynamics/osf/ws/ontology/create/interfaces/DefaultSourceInterface.php[line]:189</d                ebugInformation>                  <level>Fatal</level>                </error>
Debug file: /tmp/b6409e8b0156dcb6a5de0c276fb2dffa.error
Loading: file://localhost/data//ontologies/files/drupal.owl
Can't create permissions for the loaded ontology: file://localhost/data//ontologies/files/drupal.owl.                 Bad Request<?xml version="1.0" encoding="utf-8"?>                <error>                  <id>WS-AUTH-REGISTRAR-ACCESS-309</id>                  <webservice>/ws/auth/registrar/access/</webservice>                                  <name>Invalid group URI</name>                  <description>The URI of the group is not valid.</description>                  <debugInformation></debugInformation>                  <level>Warni                ng</level>                </error>
Debug file: /tmp/a60b783771f815cd6b407b1941465c51.error
Can't load ontology file file://localhost/data//ontologies/files/drupal.owl. Internal Server Error<?xm                l version="1.0" encoding="utf-8"?>                <error>                  <id>HTTP-500</id>                                  <webservice>/ws/ontology/create/</webservice>                  <name>Compile Error</name>                                  <description>require_once(): Failed opening required 'http://localhost:8080/OWLAPI/java/Java.inc' (include_path='.:/usr/share/php')</description>                  <debugInformation>[file]: /usr/share/osf/StructuredDynamics/osf/ws/ontology/create/interfaces/DefaultSourceInterface.php[line]:189                </debugInformation>                  <level>Fatal</level>                </error>
Debug file: /tmp/d90cc2c6cb56f148599123ddfc2181b8.error

Creating underlying ontological structures...

Generating derivate ontological structures...
Can't get loaded ontologies. Internal Server Error<?xml version="1.0" encoding="utf-8"?>                                <error>                  <id>HTTP-500</id>                  <webservice>/ws/ontology/read/</webservice>                  <name>Compile Error</name>                  <description>require_once(): Failed o                pening required 'http://localhost:8080/OWLAPI/java/Java.inc' (include_path='.:/usr/share/php')</description>                  <debugInformation>[file]: /usr/share/osf/StructuredDynamics/osf/ws/ontology/read/interfaces/DefaultSourceInterface.php[line]:359</debugInformation>                  <level>Fatal</l                evel>                </error>
Debug file: /tmp/f4fea2cbc72c89f59aa01b87d6fba4a9.error

When I try to load ontologies myself using "sudo omt --load="file://localhost/data//ontologies/files/aggr.owl" --osf-web-services="https://localhost/ws"
it shows: 
Loading: file://localhost/data//ontologies/files/aggr.owl
Can't get the list of registered web services to create the permissions file://localhost/data//ontologies/files/aggr.owl. Service UnavailableCan't reach remote server (Failed to connect to localhost port 443: Connection refused)
Debug file: /tmp/a574dbbc274a2457bf2a4ceb01923f32.error

It seems like server can't be accessed. then I tried to put "http://localhost:8080/OWLAPI/java/Java.inc" I got "localhost reject the connection request", 
then I check the tomcat6 is running by 'sudo /etc/init.d/tomcat6 restart' and try the above link again, but same errors.

and also I checked the /var/lib/tomcat6/OWLAPI is not empty. 
and if I run 'pmt --list-groups', I got:
                  Application ID: administer
                      (1) http://localhost/wsf/groups/administrators

Do you have any idea about my situation?
Many thanks,

Shan


在 2012年8月21日星期二 UTC+8上午4:48:09,Frederick Giasson写道:

Shan Wan

unread,
Jul 10, 2017, 10:32:27 AM7/10/17
to Open Semantic Framework
Hi Fred,

I think I need to clear some errors after fixing them by myself. 

Relating to the "HTTP-500"eror.
I checked "ws/ontology/create/interfaces/DefaultSourceInterface.php[line]:189", and "/ws/ontology/read/interfaces/DefaultSourceInterface.php[line]:359" and found nothing, while when I checked the installation file "/usr/share/osf-installer/inc/distros/OSF-installer_Ubuntu_14.04.php", I got some useful information on line 224 and 225 in function installOWLAPI() section (attached), it is setting php5.ini which is not the right .ini file of php5.6 that I am using (that's why the url can't be included), the one I am using is "/etc/php/5.6/cli/php.ini" and "/etc/php/5.6/apache2/php.ini". so I set "allow_url_include" as "on" manually, and re-ran the installer again, then the HTTP-500 error was gone.

So is it a bug here, the function didn't check which php version and php.ini the system is using? 

But I am still facing the "WS-AUTH-**" errors while loading ontologies.
The current error ids are: 
WS-AUTH-REGISTRAR-ACCESS-309,Invalid group URI
WS-DATASET-CREATE-203, Invalid dataset URI
while loading the ontologies list.

and WS-AUTH-VALIDATION-104,Unauthorized Request while Generating derivate ontological structures.

Thanks,

Shan




.

 

在 2012年8月21日星期二 UTC+8下午10:01:43,Frederick Giasson写道:
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