Allowing on the reduce the current set up:

alldata = combine.rdf(
alldata, load.rdf("names.n3", format="N3")
)

to:

load.rdf("names.n3", format="N3", appendTo=alldata)

Hi , I eventually got an error, which makes sense - but I didn't get it until a subsequent call? Not sure what causes the errors to bubble up; I was able to write N-TRIPLES and thought it was the format vs what was not getting returned

Error in .jcall("com/github/egonw/rrdf/RJenaHelper", "V", "saveRdf", store, :
com.hp.hpl.jena.shared.BadURIException: Only well-formed absolute URIrefs can be included in RDF/XML output: http://semanticweb.com/xxx/example#abc1234#6#8 Code: 0/ILLEGAL_CHARACTER in FRAGMENT: The character violates the grammar rules for URIs/IRIs.

closing , but providing for awareness

A list of dependencies we need this info for, is to be created with issue #30.

Hi I tried to install the package using the instructions on github. The rrdflibs installed fine, but with the rrdf I get the following error message:

install_github("rrdf", "egonw", subdir="rrdf")
Installing github repo rrdf/master from egonw
Downloading master.zip from https://github.com/egonw/rrdf/archive/master.zip
Installing package from /var/folders/8w/60f85kqd1271y8bz6_k46pdr0000gn/T//RtmpH7nQjK/master.zip
arguments 'minimized' and 'invisible' are for Windows only
Installing rrdf
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD build
'/private/var/folders/8w/60f85kqd1271y8bz6_k46pdr0000gn/T/RtmpH7nQjK/devtools1735799aad53/rrdf-master/rrdf'
--no-manual --no-resave-data

• checking for file '/private/var/folders/8w/60f85kqd1271y8bz6_k46pdr0000gn/T/RtmpH7nQjK/devtools1735799aad53/rrdf-master/rrdf/DESCRIPTION' ... OK
• preparing 'rrdf':
• checking DESCRIPTION meta-information ... OK
• installing the package to build vignettes
• creating vignettes ... ERROR
  Loading required package: rJava
  Loading required package: rrdflibs

Error: processing vignette 'tutorial.Rnw' failed with diagnostics:
chunk 2
Error in .jcall("com/github/egonw/rrdf/RJenaHelper", "Lcom/hp/hpl/jena/rdf/model/Model;", :
RcallMethod: cannot determine object class
Execution halted
Error: Command failed (1)

Any idea here what could be causing this? Here's my sessionInfo():

sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] devtools_1.5 rJava_0.9-6

loaded via a namespace (and not attached):
[1] digest_0.6.3 evaluate_0.4.3 httr_0.2 memoise_0.1 parallel_3.0.2
[6] RCurl_1.95-4.1 stringr_0.6.2 tools_3.0.2 whisker_0.3-2

Best wishes,

Richard

Error:

> test_check("rrdf")
log4j:WARN No appenders could be found for logger (org.apache.jena.riot.RDFLanguages).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
1. Error: a triple can be added with as a xsd:string ---------------------------
no method for coercing this S4 class to a vector
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls, message =     function(c) invokeRestart("muffleMessage"), 
       warning = function(c) invokeRestart("muffleWarning"))
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: add.data.triple(store, subject = "http://example.org/Subject", predicate =     "http://example.org/Predicate", 
       data = "someName", type = "http://www.w3.org/2001/XMLSchema#string") at test-localStore.R:60
5: stop(exception)
6: .makeMessage(..., domain = domain)
7: lapply(list(...), as.character)
8: FUN(X[[1L]], ...)
9: as.character.default(X[[1L]], ...)
10: .handleSimpleError(function (e) 
   {
       e$calls <- head(sys.calls()[-seq_len(frame + 7)], -2)
       signalCondition(e)
   }, "no method for coercing this S4 class to a vector", quote(as.character.default(X[[1L]], 
       ...)))

[1] "Number of triples: 0"
[1] "Number of triples: 1"
testthat results ================================================================
OK: 34 SKIPPED: 0 FAILED: 1

Code that triggers this:

  add.data.triple(store,
    subject="http://example.org/Subject",
    predicate="http://example.org/Predicate",
    data="someName",
    type="http://www.w3.org/2001/XMLSchema#string")

... by exposing Jena functionality to link to stores, like Virtuoso.

Hi,

I understand this has nothing to do with the package but I'm trying to read a 500MB RDF file and I get an out of memory error. I've tried to increase the java memory to 8 GB:

options(java.parameters = "-Xmx8000m")`

But, that had no effect. Any ideas of how to get around this issue.

Thanks.

Carlos

This now gives

Name: construct.remote

Title: Run a SPARQL CONSTRUCT query on a SPARQL end point and

construct

a new model with the results.

Aliases: construct.remote

Keywords: RDF triple

** Examples

store = construct.remote("http://rdf.farmbio.uu.se/chembl/sparql",

• paste(

• "CONSTRUCT { ?instance a http://example.org/Article } ",
  

• "WHERE { ?instance a http://purl.org/ontology/bibo/Article }",
  

• "LIMIT 5"
  

• ))
  Error in .jcall("com/github/egonw/rrdf/RJenaHelper", "Lcom/hp/hpl/jena/rdf/model/Model;", :
  HttpException: HttpException: 503 Service Temporarily Unavailable: HttpException: 503 Service Temporarily Unavailable

but 'temporary' has been going on for a week now, so that server is misconfigured at best.

Your code needs to be more robust: any example which needs an outside resource should be able to 'work' without error if it is unavailable.

Can we please have a working update ASAP.

"""
It has been brought to our attention that a number of CRAN packages contain jar files which appear not to be written by the author of the package, and without the corresponding Java sources. Let us remind you of the policies:

'The ownership of copyright and intellectual property rights of all components of the package must be clear and unambiguous (including from the authors specification in the DESCRIPTION file). Where code is copied (or derived) from the work of others (including from R itself), care must be taken that any copyright/license statements are preserved and authorship is not misrepresented.'

If the code compiled into a .jar was written by anyone else or you are not the copyright holder, this needs to be declared. [And 'see the documentation for the authors' does not suffice: an AUTHORS file may need to be used.]

'Source packages under an Open Source license must provide source or something which can easily be converted back to source (e.g., .rda files) for all components of the package (including for example PDF documentation, configure files produced by autoconf). For Java .class and .jar files, the sources should be in a top-level java directory in the source package (or that directory should explain how they can be obtained).'

Please check that packages
"""

The usual recommendation would be to split the jars into a separate
package (e.g., rrdfjars) so that updating the package to change a few
lines of code would not consume another 10MB of CRAN disk space.

E.g.:

WARN main - An error occurred while attempting to read from http://purl.obolibrary.org/obo/clo/UBERON_import.owl. Msg was 'http://purl.obolibrary.org/obo/clo/UBERON_import.owl'.
com.hp.hpl.jena.shared.DoesNotExistException: http://purl.obolibrary.org/obo/clo/UBERON_import.owl
at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:89)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.read(ModelCom.java:187)
at com.hp.hpl.jena.util.FileManager.readModelWorker(FileManager.java:367)

It currently only reports one:

load.rdf package:rrdf R Documentation

Load RDF content

Description:

 Loads triples from a RDF serialization.

Usage:

 load.rdf(filename, format = "RDF/XML", appendTo=NULL)

Arguments:

filename: Name of the file to read the triples from.

format: Format of the RDF file, e.g. RDF/XML.

appendTo: Optional Java Model object to which read statements are
added.

Value:

 A Java Model object containing the triples loaded from the file.

Author(s):

 Egon Willighagen

Examples:

 ## Not run: model = load.rdf("someFile.xml", "RDF/XML")
 ## Not run: model = new.rdf(ontology=FALSE)
 ## Not run: load.rdf("someFile.xml", "RDF/XML", model)

Orginally reported by Maarten-Jan Kallen on rOpenSci for one method (that one actually is applied, but there is more such use):

No, you should just do

add.prefix <- function(store, prefix, namespace) {
      if (missing(store)) stop("A store must be given.")
      if (missing(prefix)) stop("A prefix must be given.")
      if (missing(namespace)) stop("A namespace must be given.")
# ...
}

Unfortunately, the original bug report is lost.

Reported in a private email:

"I am trying use the sparql.remote function in the rrdf package to retrieve a count of patients in my triple store (an OWLIM-SE repository).
My query looks like this:

patient_count <-
"PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema#
SELECT (count(distinct ?patientid) as ?count)
WHERE {
?patienttype rdfs:subClassOf http://purl.obolibrary.org/obo/OHD_0000012 .
?patienti http://purl.obolibrary.org/obo/OHD_0000092 ?patienttype .
?patienti rdfs:label ?patientid .
} "

When run the query, I get the following error:

sparql.remote(owlim_se_r21, patient_count)

error-message
[1,] "Encountered "" at line 9, column 10.\nWas expecting one of:\n "(" ...\n "exists" ...\n "not exists" ...\n "str" ...\n "lang" ...\n "langmatches" ...\n "datatype" ...\n "bound" ...\n "sameTerm" ...\n <IS_IRI> ...\n "isBlank" ...\n "isLiteral" ...\n "isNumeric" ...\n "coalesce" ...\n "bnode" ...\n "strdt" ...\n "strlang" ...\n ...\n "if" ...\n "regex" ...\n "strlen" ...\n "substr" ...\n "strStarts" ...\n "strEnds" ...\n "strBefore" ...\n "strAfter" ...\n "replace" ...\n "ucase" ...\n "lcase" ...\n "concat" ...\n "contains" ...\n "encode_for_URI" ...\n "rand" ...\n "abs" ...\n "ceil" ...\n "floor" ...\n "round" ...\n "now" ...\n "year" ...\n "month" ...\n "day" ...\n "hours" ...\n "minutes" ...\n "seconds" ...\n "timezone" ...\n "tz" ...\n "md5" ...\n "sha1" ...\n "sha224" ...\n "sha256" ...\n "sha384" ...\n "sha512" ...\n <Q_IRI_REF> ...\n <PNAME_NS> ...\n <PNAME_LN> ...\n ...\n ..."

This query string works with other sparql packages (e.g., SPARQL). Am I doing something wrong?"

It would be nice if there was support for Sparql Construct statements in the library, so that graphs could be extracted, fiddled with, and merged together.

Reported in a private email:

"Is it possible to have sparql.remote return empty column names with an "" in the column?

Currently if the query doesn't find a value, the column is not return."

... for huge data results...

Dear Egon,

thanks a lot for the package rrdf.

As I am really new to the package and the concept of RDF in general I am facing some issues in loading RDF-data into R.
After installing the package in R (which was a little bit of a hastle, but in the end I got it working) I have problems loading RDF-data into R.
I use following commands:
library("rrdf")
endpoint = "http://www.bcn.cat/tercerlloc/educacio.rdf"
query <- "SELECT * {};"
data <- sparql.remote(endpoint, query)

Unfortunately the result was following warning:
Warning message: In .jcall("com/github/egonw/rrdf/RJenaHelper", "Lcom/github/egonw/rrdf/StringMatrix;", : com.hp.hpl.jena.sparql.resultset.ResultSetException: Failed when initializing the StAX parsing engine

Do you have any idea what is the reason for that?
Would be great if you could provide some further assistance. I feel I got stuck a few steps before the finish line and I would be very grateful, if you could push me over the line.

Thanks,
Magnus

R version 2.11.1 (2010-05-31)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

....

install.packages(pkgs=c("rrdflibs", "rrdf"))
Warning in install.packages(pkgs = c("rrdflibs", "rrdf")) :
argument 'lib' is missing: using '/Users/arademaker/Library/R/2.11/library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
CRAN mirror

...

Selection: 79
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
packages ‘rrdflibs’, ‘rrdf’ are not available

Let me know my mistake and congratulations. I was planning to develop something similar.

See:

http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/rrdf-00check.html

checking examples ... ERROR
Running examples in 'rrdf-Ex.R' failed
The error most likely occurred in:

Name: add.data.triple

Title: Add an data property to the model.

Aliases: add.data.triple

Keywords: data predicate triple

** Examples

store = new.rdf()
Error in .jcall("com/github/egonw/rrdf/RJenaHelper", "Lcom/hp/hpl/jena/rdf/model/Model;", :
RcallMethod: cannot determine object class
Calls: new.rdf -> .jcall -> .External
Execution halted

Also, you may find it more convenient to use inst/java for the jars.

@sandsfish wrote: "I'm trying to use the excellent 'rrdf' package, but get "package ‘rrdf’ is not available (for R version 2.15.2)" Thoughts?"

That is asking too much. I think I have seen comments on how to disable vignette creation and will look at that asap. Traveling at the moment, so it may take a week or two...

The issue is that in convertIntoTable, the varNames are taken from the QuerySolution. But suppose you have selected from a variable that has no bindings for the query. Then it will not be included in the results that are provided because it is in no solution. Also, the ordering of variables is not guaranteed in the QuerySolution instances. Instead use the varnames parsed from the XML head element.

    List<String> varnames = results.getResultVars();

private static StringMatrix convertIntoTable(
PrefixMapping prefixMap, ResultSet results) {
StringMatrix table = new StringMatrix();
int rowCount = 0;
--> List resultVarNames = results.getResultVars()
while (results.hasNext()) {
rowCount++;
QuerySolution soln = results.nextSolution();

not this:
Iterator varNames = soln.varNames();
instead:
Iterator varNames = resultVarNames.iterator();

Fix this sparql.remote() output:

data
min
[1,] "10^^http://www.w3.org/2001/XMLSchema#double"
[2,] "2^^http://www.w3.org/2001/XMLSchema#double"

In rrdf/R/add.data.triple.R - add double. Maybe also also QName and NOTATION to have all the primitive datatypes in XML Schema Part 2: Datatypes Second Edition, section 3.2 Primitive datatypes in (http://www.w3.org/TR/xmlschema-2/#built-in-primitive-datatypes). The following are not stated in the types list.

• 3.2.5 double
• 3.2.18 QName
• 3.2.19 NOTATION

BTW: Thanks for the rrdf package!

@mj_kallen wrote on Twitter:

"""@egonwillighagen you already have the Jena helper class so you would just need to replace the .jcall calls."""

This options the possibility to update rrdf to support both GNU R and Renjin.

So that we can use default summary(model) stuff on it?

Hi,

I'm trying to run the examples from the sparql.remote help page, but in both cases I am treated to a warning and get no output:
"In .jcall("com/github/egonw/rrdf/RJenaHelper", "Lcom/github/egonw/rrdf/StringMatrix;", :
java.lang.UnsupportedClassVersionError: com/github/egonw/rrdf/RJenaHelper : Unsupported major.minor version 51.0"

I'm not sure what that means. Any ideas how I can resolve it?

Best,

Richard

data = load.rdf("citograph.ttl", format="N/TRIPLES")
Error in load.rdf("citograph.ttl", format = "N/TRIPLES") :
Formats must be one in: RDF/XMLTURTLEN-TRIPLESN3

Not just Jena, but also the dependencies of Jena itself.

Hey Egon,
I've been trying to build rrdf with a newer version of Jena (to get better SPARQL support), but I've been running into problems with the build. rrdflibs builds just fine, but when I run
R CMD check rrdf
I get back a NoClassDefFoundError: org/w3c/dom/ElementTraversal
and I haven't found a way around it. The only change I made was to rrdflibs.R, where the jenaJars array was changed to
"commons-codec-1.5.jar", "jena-tdb-0.9.4.jar",
"httpclient-4.1.2.jar", "log4j-1.2.16.jar",
"httpcore-4.1.3.jar", "slf4j-api-1.6.4.jar",
"jcl-over-slf4j-1.6.4.jar", "slf4j-log4j12-1.6.4.jar",
"jena-arq-2.9.4.jar", "xercesImpl-2.10.0.jar",
"jena-core-2.7.4.jar", "xml-apis.1.4.01.jar",
"jena-iri-0.9.4.jar"
(using the apache jena 2.7.4 build from last Fall at http://archive.apache.org/dist/jena/binaries/apache-jena-2.7.4.tar.gz)

Any ideas why the dependency isn't being picked up? I assume it's got something to do with the xercesImpl and xml-apis jars, but I've hit a wall. I also unsuccessfully tried the latest 2.10.1 release.

For example, to use rdf:label as row names...

a construct.remote() method.

As reported by "R CMD check":

As from R 2.14.0 all packages need a namespace.
One will be generated on installation, but it is better to handcraft a
NAMESPACE file: R CMD build will produce a suitable starting point.

Sorry for the late reply. I got round to playing with the rrdf package. But I see an error from the code you provided in test.R:

m3 = summarize.rdf(m1, m2)
Error in summarize.rdf(m1, m2) : unused argument(s) (m2)

Having an issue loading rrdf, as the .jinit() call fails as follows:

library(rrdf)
Loading required package: rrdflibs
Error in .jinit(classpath = c(paste(lib, pkg, "java", "arq-2.8.7.jar", : cannot obtain Class.getSimpleName method ID
Error: package 'rrdflibs' could not be loaded

I suspected this to be an issue with rJava and posted the issue on their Bugzilla tracker.

(Kindly refer to this rJava Bugzilla thread: https://www.rforge.net/bugzilla/show_bug.cgi?id=223)

But the developer quotes: "Finally, packages should NOT call .jinit so that is a bug in rrdf - please use .jpackage instead. I would uggest discussing it on the mailing list as this doesn't look like rJava bug so far."

Passing along this issue to you, as I'm not 100% sure where the actual issue lies based on this conversation.

Any thoughts would be much appreciated.

Thanks!

See comment here:

http://chem-bla-ics.blogspot.nl/2009/10/sparql-end-points-jena-and-bifcontains.html?google_comment_id=z130jnl4gkzdilouo22pcruamxqfgdohi04

From email:

endpoint <- "http://rdf.farmbio.uu.se/chembl/sparql"

test_query <- "

• SELECT ?organism ?instance
• WHERE {
• ?instance a http://rdf.farmbio.uu.se/chembl/onto/#Target ;

• http://rdf.farmbio.uu.se/chembl/onto/#organism ?organism .
  

• }
• ";

data = sparql.remote(endpoint, test_query)
Warning message:
In .jcall("com/github/egonw/rrdf/RJenaHelper", "Lcom/github/egonw/rrdf/StringMatrix;", :
com.hp.hpl.jena.sparql.resultset.ResultSetException: Not an ResultSet result

The SPARQL end point was down at the time.