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 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!
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/conductorI 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_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
curl -H "Accept: text/xml" "http://localhost/ws/dataset/create/" -d "uri=http://localhost/test/&title=Test&description=test&creator=http://localhost/drupal/user/1/"
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!
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)
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?ThanksJamie
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)
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)
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 tomcat6grant 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...