Re: Rya query time

[Fan Yang]

Hi Weiqi,

You can create your RyaAccumulo repository and upload data on it via 
openrdf-workbench (http://server/openrdf-workbench/), Instead of using Web JSP 
endpoint you can calculate the execution time by sending queries on your own 
java code. You can get the repository using HTTPRepository method, for example:

private static final String 
SESAME_SERVER="http://192.168.33.30:8080/openrdf-sesame”; //sesame server’s path
private static final String repositoryID="Federation1”; //same as your 
repository id on workbench

Repository repo1 = new HTTPRepository(SESAME_SERVER, repositoryID);

Then this repo1 could be initialized and get connected to be queried. Rest of 
the code is similar as the Direct Code you found on GitHub. You can find more 
example on openrdf sesame tutorial (http://archive.rdf4j.org/users/ch08.html).

Bests,

Fan

> On Feb 12, 2019, at 1:16 AM, 徐炜淇  wrote:
> 
> Hi
> I cannot get the execution time when I query data by Web JSP endpoint, if I 
> want to get the query time, do I need to change the method?
> When I use the Web REST endpoint, I cannot find 'The War sets up a Web REST 
> endpoint at http://server/web.rya/queryrdf' [0]
> Can you help me to get the Rya query time?
> Please!
> 
> 
> 
> 
> [0] 
> https://github.com/apache/incubator-rya/blob/rel/rya-incubating-3.2.10/extras/rya.manual/src/site/markdown/querydata.md#web-rest-endpoint
> 
> 
> 
> 

Compile error in ProspectorExample

[Fan Yang]

Hi,

I tried to modified the codes of ProspectorExample.java under the package of 
rya.indexing.example to use a real accumulo instance instead of using a mock 
instance. After compiling the codes, I got the error message like this:

Exception in thread "main" java.io.IOException: 
org.apache.accumulo.core.client.AccumuloSecurityException: Error 
TABLE_DOESNT_EXIST for user rya_spo - Unknown security exception
at 
org.apache.accumulo.core.client.mapreduce.lib.impl.InputConfigurator.validateOptions(InputConfigurator.java:663)
at 
org.apache.accumulo.core.client.mapreduce.AbstractInputFormat.validateOptions(AbstractInputFormat.java:343)
at 
org.apache.accumulo.core.client.mapreduce.AbstractInputFormat.getSplits(AbstractInputFormat.java:538)
at 
org.apache.hadoop.mapreduce.JobSubmitter.writeNewSplits(JobSubmitter.java:493)
at 
org.apache.hadoop.mapreduce.JobSubmitter.writeSplits(JobSubmitter.java:510)
at 
org.apache.hadoop.mapreduce.JobSubmitter.submitJobInternal(JobSubmitter.java:394)
at org.apache.hadoop.mapreduce.Job$10.run(Job.java:1285)
at org.apache.hadoop.mapreduce.Job$10.run(Job.java:1282)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at 
org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1614)
at org.apache.hadoop.mapreduce.Job.submit(Job.java:1282)
at org.apache.hadoop.mapreduce.Job.waitForCompletion(Job.java:1303)
at org.apache.rya.prospector.mr.Prospector.run(Prospector.java:101)
at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:70)
at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:84)
at ProspectorExample.main(ProspectorExample.java:108)
Caused by: org.apache.accumulo.core.client.AccumuloSecurityException: Error 
TABLE_DOESNT_EXIST for user rya_spo - Unknown security exception
at 
org.apache.accumulo.core.client.mock.MockSecurityOperationsImpl.hasTablePermission(MockSecurityOperationsImpl.java:124)
at 
org.apache.accumulo.core.client.mapreduce.lib.impl.InputConfigurator.validateOptions(InputConfigurator.java:646)
... 16 more

When I looked up the list of accumulo tables, “rya_spo" did exist and the 
“rya_perspects" was also created but empty. What I did is to modify the 
configuration part of the codes. The modified Java file is attached via email. 
Thank you so much!

Bests,

Fan

Re: GSoC - community bonding period

[Fan Yang]

Hi Amila,

I’m nor sure if you download and unzip the distribution package correctly. For 
me, I have 226 jar packages under “lib” folder. You could try to manually 
download the distribution package from 
"https://www.dropbox.com/s/7e74yiuq4jmu0od/rya.indexing.example-3.2.10-distribution.zip”
 and redo the steps on vagrant file to see if it works. 

Bests,

Fan
> On May 14, 2016, at 7:53 AM, Amila Wijayarathna  
> wrote:
> 
> Hi Adina,
> I went through the vagrant file. And there is a line,
> 
> 
> *# soft linking the files doesn't seem to work in tomcat, so we copy them
> instead :(*
> 
> *sudo cp
> rya.indexing.example-${RYA_EXAMPLE_VERSION}-distribution/dist/lib/*
> /var/lib/tomcat7/webapps/openrdf-workbench/WEB-INF/lib/*
> 
> *sudo cp
> rya.indexing.example-${RYA_EXAMPLE_VERSION}-distribution/dist/lib/*
> /var/lib/tomcat7/webapps/openrdf-sesame/WEB-INF/lib/*
> 
> But I was unable to do so because I cannot find */dist/lib/* .*
> Any guidelines about this is thoroughly appreciated.
> 
> Thank you!
> 
> On Mon, May 9, 2016 at 7:45 PM, Amila Wijayarathna > wrote:
> 
>> Hi Adina,
>> 
>> The files you mentioned are not existing in the directory.
>> I will go through your guidelines and vagrant file.
>> 
>> Thank you!
>> 
>> On Mon, May 9, 2016 at 7:29 PM, Adina Crainiceanu  wrote:
>> 
>>> Based on your error and the vagrant readme file, I think the OpenRDF
>>> Workbench transformations are not installed.
>>> 
>>> Try this - adapted for your computer instead of the vagrant VM:
>>> "OpenRDF Workbench requires a set of "transformations" for listing Rya in
>>> the OpenRDF Workbench Repository list. The transforms are in this
>>> directory: /var/lib/tomcat7/webapps/openrdf-workbench/transformations/
>>> 
>>>   1. Verify that this file exists: create-RyaAccumuloSail.xsl
>>>   2. Verify that create.xsl has been updated for rya. (run: "cat
>>>   create.xsl | grep Rya" and make sure there's some stuff there.)
>>> 
>>> If these files do note exists, open the vagrant file and look for the
>>> line echo "Downloading Rya". Try working through those commands manually
>>> on your Vagrant VM."
>>> 
>>> In particular, the lines for "# Download and install new templates for
>>> OpenRdf WorkBench" in the vagrant file might be the ones that you are
>>> missing.
>>> 
>>> Please make detailed notes of what you are doing, so we can reproduce the
>>> process on a new machine - I'm tryiong to get an Amazon EC2 instance so  we
>>> can all have access to it.
>>> 
>>> 
>>> Adina
>>> 
>>> 
>>> 
>>> 
>>> On Mon, May 9, 2016 at 9:09 AM, Amila Wijayarathna <
>>> amwijayarat...@gmail.com> wrote:
>>> 
 Hi Adina,
 As in the vagrant file i tried to connect Rya via  OpenRDF workbench to
 insert data. When i create new repository in workbench  i have chose the
 type. But there is no "Rya Accumulo Store"  type to chose as in the
 vagrant file.
 Any idea about this is thoroughly appriciated.
 
 Thank you!
 
 On Sat, May 7, 2016 at 9:36 PM, Adina Crainiceanu 
 wrote:
 
> Hi,
> 
> The screen shot for the web.rya/sparqlQuery.jsp looks correct. You
> should try to insert some data and see if you can query it back. You might
> be able to do an insert and select through the web.rya interface, but I'm
> not sure about the insert.
> 
> 
> The easiest way to do insert is through the openRDF Workbench interface.
> Look in the vagrant file to see how to set it up.
> Look in the Readme file for the vagrant example to see how to load some
> data
> https://github.com/apache/incubator-rya/tree/develop/extras/vagrantExample/src/main/vagrant
> 
> Once you have data, you should be able to use either the we.rya
> interface or the openRDf workbench interface to query the data using a
> sparql select query.
> 
> Adina
> 
> On Sat, May 7, 2016 at 8:37 AM, Amila Wijayarathna <
> amwijayarat...@gmail.com> wrote:
> 
>> Hi Adina,
>> 
>> I changed some settings and restart tomcat server. And when I browse
>> in to http://localhost:8080/web.rya/sparqlQuery.jsp , I got the
>> following window.
>> 
>> Am I doing it correctly? If it is, I would like to know how to proceed
>> further.
>> ​
>> 
>> Thank you!
>> 
>> On Sat, May 7, 2016 at 12:43 PM, Amila Wijayarathna <
>> amwijayarat...@gmail.com> wrote:
>> 
>>> Hi Adina,
>>> 
>>> When I changed the Accumulo instance volume in accumulo site.xml , I
>>> can successfully start accumulo and I think it will not a problem for
>>> instance name, it is remaining the same. So after a restart my laptop I
>>> started the hadoop, zookeeper and accumulo and got the following,
>>> 
>>> amila@amila-X550LD:~$ ~/Installs/hadoop-2.7.2/sbin/start-dfs.sh
>>> Starting namenodes on [localhost]
>>> localhost: starting namenode, 

Re: Maven Build Error

[Fan Yang]

Hi Aaron,

There is no such files in these two directories. Actually I cannot access rya 
at the beginning, there is no "web.rya” folder under webapps. So I just 
download the rya project zip file and use maven to build it.

Bests,

Fan
> On Jan 12, 2016, at 11:00 PM, Aaron D. Mihalik <aaron.miha...@gmail.com> 
> wrote:
> 
> I'm kinda worried that there is no create-RyaAccumuloSail.xsl.
> 
> Can you check to see if rya libs are installed in the OpenRDF Web apps?
> 
> run these two commands and see if you have any rya files in the two lib 
> directories:
> 
> ls /var/lib/tomcat7/webapps/openrdf-sesame/WEB-INF/lib/rya*
> 
> ls /var/lib/tomcat7/webapps/openrdf-workbench/WEB-INF/lib/rya* 
> 
> Also, are you able to access the Rya web page at: 
> http://rya-example-box:8080/web.rya/sparqlQuery.jsp 
> <http://rya-example-box:8080/web.rya/sparqlQuery.jsp>
> 
> --Aaron
> 
> On Tue, Jan 12, 2016 at 10:23 PM Fan Yang <fya...@umbc.edu 
> <mailto:fya...@umbc.edu>> wrote:
> Hi Aaron,
> 
> I followed the steps you suggest and checked the folder “transformations”, 
> there is still no such file named “create-RyaAccumuloSail.xsl”. I attach my 
> screenshot of openrdf-workbench, those types listed are the ones I have in 
> that folder. Thanks!
> 
> Bests,
> 
> Fan
> 
> 
>> On Jan 12, 2016, at 2:33 PM, Aaron D. Mihalik <aaron.miha...@gmail.com 
>> <mailto:aaron.miha...@gmail.com>> wrote:
>> 
> 
>> You shouldn't have to make any changes... I've attache a screen shot of what 
>> you should see.
>> 
>> If you don't see "Rya Accumulo Store" try these steps:
>> 
>> Restart Tomcat
>> -- 1. Log into the vm (run: "ssh vagrant@rya-example-box" with pass: vagrant)
>> -- 2. switch to root (run: "su" with pass: vagrant)
>> -- 3. restart tomcat (run: "service tomcat7 restart")
>> -- 4. open the "new repository" page again and see if rya was added (new 
>> repo page: 
>> http://rya-example-box:8080/openrdf-workbench/repositories/NONE/create 
>> <http://rya-example-box:8080/openrdf-workbench/repositories/NONE/create>)
>> 
>> If that doesn't work, make sure that the openrdf-workbench transforms are 
>> correct:
>> The transforms are in this directory: 
>> /var/lib/tomcat7/webapps/openrdf-workbench/transformations/
>> 
>> -- 1. Verify that this file exists: create-RyaAccumuloSail.xsl
>> --- 2. Verify that create.xsl has been updated for rya.  (run: "cat 
>> create.xsl | grep Rya" and make sure there's some stuff there.)
>> 
>> Thanks for testing this out.  Let me know if this resolves your issues.
>> 
>> --Aaron
>> 
>> 
>> 
>> 
>> On Tue, Jan 12, 2016 at 1:04 PM Fan Yang <fya...@umbc.edu 
>> <mailto:fya...@umbc.edu>> wrote:
>> Hi Aaron,
>> 
>> Thank you so much for your help! I followed the instructions and created the 
>> VM. Everything works fine except one thing I am not very clear: in 
>> “connecting to Rya via OpenRDF Workbench” step, I cannot find “Rya Accumulo 
>> Store” in “Type” option. I am wondering if I should make some configurations 
>> in Rya and Accumulo. 
>> 
>> Bests,
>> 
>> Fan
>> 
>>> On Jan 1, 2016, at 10:54 PM, Aaron D. Mihalik <aaron.miha...@gmail.com 
>>> <mailto:aaron.miha...@gmail.com>> wrote:
>>> 
>>> Fan,
>>> 
>>> I'm sorry about the delay, but I finally got the Rya/Vagrant/OpenRDF 
>>> Workbench VM into a good spot.  Can you test out the instructions at:
>>> 
>>> https://github.com/amihalik/incubator-rya/blob/RYA-4/extras/vagrantExample/src/main/vagrant/readme.md
>>>  
>>> <https://github.com/amihalik/incubator-rya/blob/RYA-4/extras/vagrantExample/src/main/vagrant/readme.md>
>>> 
>>> Once you run this VM, it should be straightforward to upload and query your 
>>> data through OpenRDF Workbench.
>>> 
>>> For instance, once you connect Rya and OpenRDF Workbench, you can open the 
>>> Workbench, click on "Add", and cut-and-paste your ntriples into the "RDF 
>>> Content" field.
>>> 
>>> Then you can click on "Query" and run this SPARQL query:  
>>> 
>>> select * where { <http://mynamespace/ProductType1 
>>> <http://mynamespace/ProductType1>> ?p ?o. }
>>> 
>>> --Aaron
>>> 
>>> On Thu, Dec 17, 2015 at 1:00 PM Fan Yang <fya...@umbc.edu 
>>> <mailto:fya...@umbc.edu>> wrote:
>>> Hi Dr. Adina,
&

Re: Maven Build Error

[Fan Yang]

Hi Dr. Adina,I named my $RDF_DATA file as ntriplesFile and put it under the folder same as Java code’s. I tried to delete the empty loadrdf file and re-run the code, the same error message was showed up. The error log containing the command I’m using, loadrdf java code and ntripleFile are attached in this email. Thanks!Bests,Fan

ntriplesFile
Description: Binary data


LoadDataServletRun.java
Description: Binary data


error log
Description: Binary data
 On Dec 16, 2015, at 2:55 PM, Fan Yang <fya...@umbc.edu> wrote:Hi Dr. Adina,The one I’m using is an empty file. Cause when the war package is deployed, there is no such file named loadrdf under the certain folder. The n-Triples file I’m using is the one listed on the tutorial, the content is :<http://mynamespace/ProductType1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://mynamespace/ProductType> .
<http://mynamespace/ProductType1> <http://www.w3.org/2000/01/rdf-schema#label> "Thing" .
<http://mynamespace/ProductType1> <http://purl.org/dc/elements/1.1/publisher> <http://mynamespace/Publisher1> .Bests,FanOn Dec 16, 2015, at 2:23 PM, Adina Crainiceanu <ad...@usna.edu> wrote:Fan,Can you please send the rdf file you are trying to load? Maybe that is the problem.AdinaOn Thu, Dec 3, 2015 at 12:44 PM, Fan Yang <fya...@umbc.edu> wrote:Hi Aaron,

There is an additional information you may need: Once I checked the web.rya folder under the webapps directory, there is no such file named loadrdf or queryrdf, so I created empty ones. Maybe that causes the error. Could you check your webapps directory to see if those files contain some certain scripts? Thank you so much!

Bests,

Fan
> On Dec 3, 2015, at 3:15 AM, Fan Yang <fya...@umbc.edu> wrote:
>
> Hi Aaron,
>
> Thank you so much for your help! I reproduced the Vagrant VM successfully by following your instruction. Everything is working except loading data part. Even I fixed the “/“ error in the code I still face the same HTTP 500 error. I capture the error message when I load the link [4] http://localhost:8080/web.rya/loadrdf?format=N-Triples <http://localhost:8080/web.rya/loadrdf?format=N-Triples> on my browser and copy the tomcat log file to you.
>
> Bests,
>
> Fan
>
> 
> 
>
>> On Dec 2, 2015, at 4:34 AM, Aaron D. Mihalik <aaron.miha...@gmail.com <mailto:aaron.miha...@gmail.com>> wrote:
>>
>> Hi Fan,
>>
>> The tutorial is a bit dated, so it might be confusing/incorrect.
>>
>> You have a couple options:
>>
>> 1. You could start using the Vagrant vm that I'm putting together as a "Rya Quickstart VM".
>>
>> It's a bit rough right now, and it doesn't have Hadoop or MapReduce (so you can't do the bulk load), but it does have the script you mentioned for loading N-Triples.  An early copy of the Vagrantfile is here [1].
>>
>> It'll take about 30 minutes to build the VM, but once you do, you'll have the rya web endpoint up and running here [2] and you can ssh into the box to load data.  Once you ssh into the machine, you can run 'java LoadDataServletRun' to load n-triples files.  Infact, you that script will take a "batchSize" parameter to split a large ntriples into small loads.
>>
>> 2. We can help you debug your current vm.
>>
>> The first step would be to try to hit this webpage [3] and see if the sparql query page loads.  Also note that the URL you provided has an extra "/" in it and you should try [4].
>>
>> If those load properly, then the issue might be the LoadDataServletRun file itself (I haven't tried the one you mentioned), but you could try the new one located at the bottom of the Vagrant file.
>>
>> If those links do not load properly, please send us your tomcat logs and we'll take a look to see what's up with tomcat.
>>
>> --Aaron
>>
>> [1] https://raw.githubusercontent.com/amihalik/incubator-rya/RYA-4/extras/indexingSailExample/src/main/vagrant/Vagrantfile <https://raw.githubusercontent.com/amihalik/incubator-rya/RYA-4/extras/indexingSailExample/src/main/vagrant/Vagrantfile>
>> [2] http://192.168.33.10:8080/web.rya/sparqlQuery.jsp <http://192.168.33.10:8080/web.rya/sparqlQuery.jsp> or  http://accumulo-dev-box:8080/web.rya/sparqlQuery.jsp <http://accumulo-dev-box:8080/web.rya/sparqlQuery.jsp>
>> [3] http://localhost:8080/web.rya/sparqlQuery.jsp <http://localhost:8080/web.rya/sparqlQuery.jsp>
>> [4] http://localhost:8080/web.rya/loadrdf?format=N-Triples <http://localhost:8080/web.rya/loadrdf?format=N-Triples>
>> On Wed, Dec 2, 2015 at 2:25 AM Fan Yang <fya...@umbc.edu <mailto:fya...@umbc.edu>> wrote:
>> Hi Aaron,
>>
>> Sorry to bother you again. I faced a new problem in loading RDF data process. Followin

Maven Build Error

[Fan Yang]

Hi,

My name is Fan Yang, I am a phd student in Information Systems Department, 
UMBC. Currently I am working on Rya project under the supervision of Dr. Adina. 
I faced a problem when I tried to reproduce the development environment on my 
virtual machine.

When I built Rya project by Maven, it gave me some error report and same thing 
happened even I tried different versions of Maven. I am attaching the log files 
generated by Maven 3.3.3 (log333.txt) and Maven 2.2.1 (log221.txt) and looking 
for some help. Thank you so much!

My development environment is:

OS: Hortonworks Sandbox with HDP 2.2.4 (Cent OS 6 64bit)
Maven version: 3.3.3
Java version: OpenJDK Runtime Environment 1.7.0_79
Accumulo version: 1.6.1.2.2.4.2-2
Hadoop version:2.6.0.2.2.4.2-2

Bests,

Fan

[INFO] Scanning for projects...
[INFO] Reactor build order: 
[INFO]   mvm.rya.parent
[INFO]   mvm.rya.rya.common
[INFO]   mvm.rya.rya.api
[INFO]   mvm.rya.rya.provenance
[INFO]   mvm.rya.rya.iterators
[INFO]   mvm.rya.accumulo.iterators
[INFO]   mvm.rya.rya.dao
[INFO]   mvm.rya.accumulo.rya
[INFO]   mvm.rya.mongodb.rya
[INFO]   mvm.rya.rya.extras
[INFO]   mvm.rya.rya.prospector
[INFO]   RYA Manual
[INFO]   mvm.rya.rya.sail
[INFO]   mvm.rya.rya.sail.impl
[INFO]   mvm.rya.tinkerpop.rya
[INFO]   mvm.rya.rya.osgi
[INFO]   mvm.rya.alx.rya
[INFO]   mvm.rya.alx.rya.console
[INFO]   mvm.rya.camel.rya
[INFO]   mvm.rya.rya.pig
[INFO]   mvm.rya.accumulo.pig
[INFO]   mvm.rya.rya.utils
[INFO]   mvm.rya.rya.web
[INFO]   mvm.rya.web.rya
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from codehaus.org
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[INFO] artifact org.codehaus.groovy:groovy-eclipse-batch: checking for updates 
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[INFO] 
[INFO] Building mvm.rya.parent
[INFO]task-segment: [clean, install]
[INFO] 
[INFO] 
[ERROR] BUILD ERROR
[INFO] 
[INFO] 'jar-no-fork' was specified in an execution, but not found in the plugin
[INFO] 
[INFO] For more information, run Maven with the -e switch
[INFO] 
[INFO] Total time: 1 minute 1 second
[INFO] Finished at: Thu Nov 19 07:20:44 UTC 2015
[INFO] Final Memory: 18M/164M
[INFO] 
[INFO] Scanning for projects...
Downloading: 
http://repository.codehaus.org/org/codehaus/groovy/groovy-eclipse-batch/maven-metadata.xml
Downloading: 
http://nexus.codehaus.org/snapshots/org/codehaus/groovy/groovy-eclipse-batch/maven-metadata.xml


[WARNING] Could not transfer metadata 
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org.codehaus.groovy:groovy-eclipse-batch/maven-metadata.xml from/to 
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[WARNING] 
[WARNING] Some problems were encountered while building the effective model for 
mvm.rya:rya.api:jar:3.2.10-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-source-plugin is missing. @ 
mvm.rya:parent:3.2.10-SNAPSHOT, /root/Documents/incubator-rya-develop/pom.xml, 
line 414, column 20
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for 
mvm.rya:rya.provenance:jar:3.2.10-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for 
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[WARNING] 
[WARNING] Some problems were encountered while building the effective model for 
mvm.rya:rya.common:pom:3.2.10-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-source-plugin is missing. @ 
mvm.rya:parent:3.2.10-SNAPSHOT