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From: Ruben V. <rub...@ug...> - 2014-07-10 19:05:10
|
> Usual apologies for the usual delayed response — there have been a ton of changes to the sparql11 branch since your report and the reorganization should have fixed this bug. Thanks Eric, it compiles. Here's a fork that directly compiles on OSX Mavericks: https://github.com/RubenVerborgh/SWObjects > We're in the process of switching over to CMake so that may make it more fun to compile. Great! Note that I found one other bug (at least on OSX): a positive isomorphism check works (i.e., if graphs are equal, I get the right message). a negative isomorphism check (i.e., non-equal) results in a segmentation fault. Best, Ruben |
|
From: Eric Prud'h. <er...@w3...> - 2014-07-08 19:16:40
|
* Ruben Verborgh <rub...@ug...> [2014-06-16 16:33+0200] > > SWObjects is (finally) updated to the latest boost-log. It should > > compile with boost >= 1.54 > > Thanks, Eric. > > Tried to build an OSX version but failed. > > OSX diff: https://github.com/RubenVerborgh/SWObjects/commit/e07c954cf6d > build log: http://pastebin.com/gRFdvAat > > I have several errors of this type: > > lib/SWSexParser/location.hh:133:20: error: redefinition of 'operator+=' > inline location& operator+= (location& res, unsigned int width) > > What would be the issue? Usual apologies for the usual delayed response -- there have been a ton of changes to the sparql11 branch since your report and the reorganization should have fixed this bug. We're in the process of switching over to CMake so that may make it more fun to compile. > Best, > > Ruben -- -ericP office: +1.617.599.3509 mobile: +33.6.80.80.35.59 (er...@w3...) Feel free to forward this message to any list for any purpose other than email address distribution. There are subtle nuances encoded in font variation and clever layout which can only be seen by printing this message on high-clay paper. |
|
From: Ruben V. <rub...@ug...> - 2014-06-16 14:33:39
|
> SWObjects is (finally) updated to the latest boost-log. It should > compile with boost >= 1.54 Thanks, Eric. Tried to build an OSX version but failed. OSX diff: https://github.com/RubenVerborgh/SWObjects/commit/e07c954cf6d build log: http://pastebin.com/gRFdvAat I have several errors of this type: lib/SWSexParser/location.hh:133:20: error: redefinition of 'operator+=' inline location& operator+= (location& res, unsigned int width) What would be the issue? Best, Ruben |
|
From: Eric Prud'h. <er...@w3...> - 2014-06-14 13:48:26
|
* Ruben Verborgh <rub...@ug...> [2013-08-13 14:34+0200] > > (can you remind me how to compile cause I'm sure Ubuntu doesn't have updates for it?)), > > I’m probably not the right guy to ask :-) > I got it working with 1.42, because that’s what was on the machine I used. > > Compiling with the latest boost gave errors because of duplicate boost-log, > so you might want to settle for something less recent. SWObjects is (finally) updated to the latest boost-log. It should compile with boost >= 1.54 > > but what your seeing is a comparison of two result sets, one of which is a graph and the other is a table. > > But it’s the same file, should just indicate that it matches (as it does on OSX). > > > I'll have a 64 bit Ubuntu 12.10 when I next connect my laptop. Is that helpful? > > Yeah, probably, thanks! > > Ruben > -- -ericP office: +1.617.599.3509 mobile: +33.6.80.80.35.59 (er...@w3...) Feel free to forward this message to any list for any purpose other than email address distribution. There are subtle nuances encoded in font variation and clever layout which can only be seen by printing this message on high-clay paper. |
|
From: Ruben V. <rub...@ug...> - 2013-08-13 13:56:06
|
> I wasn't surprised that there was some pathological behavior related to the heuristics for guessing what to compare, buy I tried to replicate this and it actually worked fine on my build. Could you run again with --debug 3?
Sure. Here you go:
$ sparql -d IRI_subject.ttl --compare IRI_subject.ttl --debug 3
[- 2 +] log level "Default" set to 3.
[- 2 +] log level "Rewrite" set to 3.
[- 2 +] log level "IO" set to 3.
[- 2 +] log level "GraphMatch" set to 3.
[- 2 +] log level "SQL" set to 3.
[- 2 +] log level "Service" set to 3.
[- 2 +] log level "Process" set to 3.
I/O [- 2 +] Stream constructed to read file IRI_subject.ttl.
I/O [- 1 +] Reading IRI_subject.ttl with media type text/turtle into Default Graph.
I/O [- 2 +] <loadedData>
{
<http://a.example/s> <http://a.example/p> <http://a.example/o> .
}
</loadedData>
I/O [- 2 +] Stream constructed to read file IRI_subject.ttl.
I/O [- 1 +] Reading IRI_subject.ttl with media type text/turtle.
GraphMatch [- 3+] matching {
?t <http://www.w3.org/2001/sw/DataAccess/tests/result-set#boolean> ?bool .
}
GraphMatch [- 3+] produced
+-+
| |
+-+
GraphMatch [- 3+] vars and exprs tracked during project:
GraphMatch [- 3+] matching {
?set <http://www.w3.org/2001/sw/DataAccess/tests/result-set#resultVariable> ?var .
}
GraphMatch [- 3+] produced
+-+
| |
+-+
GraphMatch [- 3+] vars and exprs tracked during project:
GraphMatch [- 3+] matching {
_:b0x3270860 <http://www.w3.org/2001/sw/DataAccess/tests/result-set#variable> ?var .
_:b0x3270860 <http://www.w3.org/2001/sw/DataAccess/tests/result-set#value> ?val .
?soln <http://www.w3.org/2001/sw/DataAccess/tests/result-set#binding> _:b0x3270860 .
}
GraphMatch [- 3+] produced
+-+
| |
+-+
{
<http://a.example/s> <http://a.example/p> <http://a.example/o> .
}
!=
+-+
| |
+-+
Best,
Ruben
|
|
From: Eric Prud'h. <er...@w3...> - 2013-08-13 13:52:45
|
On Aug 13, 2013 2:34 PM, "Ruben Verborgh" <rub...@ug...> wrote: > > > (can you remind me how to compile cause I'm sure Ubuntu doesn't have updates for it?)), > > I’m probably not the right guy to ask :-) > I got it working with 1.42, because that’s what was on the machine I used. > Compiling with the latest boost gave errors because of duplicate boost-log, > so you might want to settle for something less recent. Yeah, my goal is to synch up with whatever has changed since the 1.46-compatible boost-log and ideally stop maintaining a branch of that code. People with distros that don't have the latest boost (probably all distros) will have to compile boost or use one of my older versions of log. > > but what your seeing is a comparison of two result sets, one of which is a graph and the other is a table. > > But it’s the same file, should just indicate that it matches (as it does on OSX). I wasn't surprised that there was some pathological behavior related to the heuristics for guessing what to compare, buy I tried to replicate this and it actually worked fine on my build. Could you run again with --debug 3? > > I'll have a 64 bit Ubuntu 12.10 when I next connect my laptop. Is that helpful? > > Yeah, probably, thanks! > > Ruben > |
|
From: Ruben V. <rub...@ug...> - 2013-08-13 12:34:18
|
> (can you remind me how to compile cause I'm sure Ubuntu doesn't have updates for it?)), I’m probably not the right guy to ask :-) I got it working with 1.42, because that’s what was on the machine I used. Compiling with the latest boost gave errors because of duplicate boost-log, so you might want to settle for something less recent. > but what your seeing is a comparison of two result sets, one of which is a graph and the other is a table. But it’s the same file, should just indicate that it matches (as it does on OSX). > I'll have a 64 bit Ubuntu 12.10 when I next connect my laptop. Is that helpful? Yeah, probably, thanks! Ruben |
|
From: Eric Prud'h. <er...@w3...> - 2013-08-13 12:28:20
|
On Aug 13, 2013 2:01 PM, "Ruben Verborgh" <rub...@ug...> wrote:
>
> Hi Eric,
>
> Thanks for the patch!
>
> > I poked around with perl's URI::URL lib and it produces the results
> > expected by Ruben. Attached is a patch which considers …://…#… an
> > absolute based on the "://" and the '#'. I haven't rolled that back
> > into the sparql11 branch yet. Other opinions?
>
> Isn’t it simply: relative if it doesn’t start with a protocol?
>
>
>
> On a different but related note:
> I’m using SWObjects to test graph equality in the EYE reasoner’s Turtle
spec EARL report generator.
> This hash issue was one of the things gave false negatives.
> While the patch solves this, SWObjects only works property on OSX for me.
> If we compile on Linux, we get strange errors like
>
> $ sparql -d IRI_subject.ttl --compare IRI_subject.ttl
> {
> <http://a.example/s> <http://a.example/p> <http://a.example/o> .
> }
> !=
> +-+
> | |
> +-+
I'll futz with this when I get a chance (ideally this evening when I'll be
near a power plug and downloading the latest boost (can you remind me how
to compile cause I'm sure Ubuntu doesn't have updates for it?)), but what
your seeing is a comparison of two result sets, one of which is a graph and
the other is a table.
> While comparing a file against itself works perfectly on OSX.
> Any clue on what we’re doing wrong with the compilation?
> Or do you perhaps have a compiled Linux version at hand?
I'll have a 64 bit Ubuntu 12.10 when I next connect my laptop. Is that
helpful?
> Best,
>
> Ruben
|
|
From: Ruben V. <rub...@ug...> - 2013-08-13 12:00:50
|
Hi Eric,
Thanks for the patch!
> I poked around with perl's URI::URL lib and it produces the results
> expected by Ruben. Attached is a patch which considers …://…#… an
> absolute based on the "://" and the '#'. I haven't rolled that back
> into the sparql11 branch yet. Other opinions?
Isn’t it simply: relative if it doesn’t start with a protocol?
On a different but related note:
I’m using SWObjects to test graph equality in the EYE reasoner’s Turtle spec EARL report generator.
This hash issue was one of the things gave false negatives.
While the patch solves this, SWObjects only works property on OSX for me.
If we compile on Linux, we get strange errors like
$ sparql -d IRI_subject.ttl --compare IRI_subject.ttl
{
<http://a.example/s> <http://a.example/p> <http://a.example/o> .
}
!=
+-+
| |
+-+
While comparing a file against itself works perfectly on OSX.
Any clue on what we’re doing wrong with the compilation?
Or do you perhaps have a compiled Linux version at hand?
Best,
Ruben
|
|
From: Eric Prud'h. <er...@w3...> - 2013-08-13 10:55:00
|
* Ruben Verborgh <rub...@ug...> [2013-08-10 20:06+0200] > Dear all, > > SWObjects [1] incorrectly interprets hashes. > It prepends the current filename before them, while it shouldn’t. > > $ echo "<http://ex.org#a> <http://ex.org#b> <http://ex.org#c>." > hash.ttl > $ sparql -d hash.ttl > { > <http://ex.orghash.ttl#a> <http://ex.orghash.ttl#b> <http://ex.orghash.ttl#c> . > } > > The expected output is instead > { > <http://ex.org#a> <http://ex.org#b> <http://ex.org#c>. > } > > Something similar happens when we use a prefix that doesn’t end in a slash: > $ echo "@prefix ex: <http://ex.org>. ex:a ex:b ex:c." > hash2.ttl > $ sparql -d hash2.ttl > { > <http://ex.orghash2.ttlahash2.ttl> <http://ex.orghash2.ttlbhash2.ttl> <http://ex.orghash2.ttlchash2.ttl> . > } I haven't done sufficient research to figure out what are the specified requirements for deciding that something is an absolute URI. libwww, from which I stole the URL parsing library, doesn't consider something absolute if it doesn't have a '/' after the hostname. I poked around with perl's URI::URL lib and it produces the results expected by Ruben. Attached is a patch which considers …://…#… an absolute based on the "://" and the '#'. I haven't rolled that back into the sparql11 branch yet. Other opinions? > Best, > > Ruben > > [1] commit 4283bf306 from sparql11 branch https://github.com/ericprud/SWObjects/commit/4283bf306 > compiled on OSX with https://github.com/RubenVerborgh/SWObjects/commit/1a3a9a02f > ------------------------------------------------------------------------------ > Get 100% visibility into Java/.NET code with AppDynamics Lite! > It's a free troubleshooting tool designed for production. > Get down to code-level detail for bottlenecks, with <2% overhead. > Download for free and get started troubleshooting in minutes. > http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk > _______________________________________________ > SWObjects-devel mailing list > SWO...@li... > https://lists.sourceforge.net/lists/listinfo/swobjects-devel -- -ericP |
|
From: Ruben V. <rub...@ug...> - 2013-08-10 18:06:38
|
Dear all, SWObjects [1] incorrectly interprets hashes. It prepends the current filename before them, while it shouldn’t. $ echo "<http://ex.org#a> <http://ex.org#b> <http://ex.org#c>." > hash.ttl $ sparql -d hash.ttl { <http://ex.orghash.ttl#a> <http://ex.orghash.ttl#b> <http://ex.orghash.ttl#c> . } The expected output is instead { <http://ex.org#a> <http://ex.org#b> <http://ex.org#c>. } Something similar happens when we use a prefix that doesn’t end in a slash: $ echo "@prefix ex: <http://ex.org>. ex:a ex:b ex:c." > hash2.ttl $ sparql -d hash2.ttl { <http://ex.orghash2.ttlahash2.ttl> <http://ex.orghash2.ttlbhash2.ttl> <http://ex.orghash2.ttlchash2.ttl> . } Best, Ruben [1] commit 4283bf306 from sparql11 branch https://github.com/ericprud/SWObjects/commit/4283bf306 compiled on OSX with https://github.com/RubenVerborgh/SWObjects/commit/1a3a9a02f |
|
From: Eric Prud'h. <er...@w3...> - 2013-08-10 17:45:40
|
* Ruben Verborgh <rub...@ug...> [2013-08-10 18:12+0200] > Dear all, > > Boost now seems to have the log library built-in [1], > which results in compilation errors of SWObjects. YAY!!! Major burden relieved. > What version of Boost should we use for compilation / > will SWObjects be made compatible with the built-in log? I'll update the sparql11 branch to use the latest boost (assuming I survive the migration). Might be a couple days 'cause I'll be vacation without electricity or network (but don't have to ship in my own oxygen). > Best, > > Ruben > > [1] http://www.boost.org/users/history/version_1_54_0.html > > ------------------------------------------------------------------------------ > Get 100% visibility into Java/.NET code with AppDynamics Lite! > It's a free troubleshooting tool designed for production. > Get down to code-level detail for bottlenecks, with <2% overhead. > Download for free and get started troubleshooting in minutes. > http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk > _______________________________________________ > SWObjects-devel mailing list > SWO...@li... > https://lists.sourceforge.net/lists/listinfo/swobjects-devel -- -ericP |
|
From: Ruben V. <rub...@ug...> - 2013-08-10 16:13:05
|
Dear all, Boost now seems to have the log library built-in [1], which results in compilation errors of SWObjects. What version of Boost should we use for compilation / will SWObjects be made compatible with the built-in log? Best, Ruben [1] http://www.boost.org/users/history/version_1_54_0.html |
|
From: venkates <ven...@nt...> - 2012-03-08 09:44:19
|
Hello,
I have installed all the necessary packages for SWObjects compilation.
While I issue the following command according to
the instructions provided, I get the following error:
venkates@Aravind:~/swobjects$ make bin/SWtransformer
(echo -e -n tests/test_SPARUL.dep tests/\\; g++ -DYYTEXT_POINTER=1 -fPIC
-g -O0 -W -Wall -Wextra -Wnon-virtual-dtor -ansi -std=c++98
-I/home/venkates/swobjects -I/home/venkates/swobjects/lib
-I/home/venkates/swobjects/MapSetParser
-I/home/venkates/swobjects/SPARQLfedParser
-I/home/venkates/swobjects/SQLParser
-I/home/venkates/swobjects/TrigSParser
-I/home/venkates/swobjects/TurtleSParser -I/home/venkates/swobjects/lib
-pipe -MM tests/test_SPARUL.cpp) > tests/test_SPARUL.dep || (rm
tests/test_SPARUL.dep; false)
In file included from tests/../tests/SPARQLTest.hpp:29,
from tests/test_SPARUL.cpp:9:
tests/../tests/../interface/SAXparser_expat.hpp:14:21: error: expat.h:
No such file or directory
I would be glad if you could help me out with this.
Regards,
|
|
From: Andrea S. <and...@bb...> - 2011-01-19 12:59:32
|
Hi,
Yes, a real logger would be nice.
I have to restart my laptop to use WireShark... I usually restart it every 2-3 months. So... give me a couple of days! (I do long term ultra multi-tasking...)
ciao,
Andrea
Il giorno 18/gen/2011, alle ore 15.35, Eric Prud'hommeaux ha scritto:
> * Andrea Splendiani <and...@bb...> [2011-01-18 01:15+0000]
>> Hi,
>>
>> I have some problem with SWObjects.
>>
>> first: with debug on it prints a lot of information, but not all so
>> informative. It prints a lot of html (possibly the one that is served) but I
>> don't easily find the query translation (which is pretty useful).
>> Also, I think it prints the binary png all the time the browser request
>> it... which is a bit annoying.
>
> It looks like it's time to put in a real logger with debug levels and that sort of thing. There's a package proposed for the boost libraries; I've been hoping it would be incorporated into the mainstream before I needed it, but I can get around this by incorporating the source directly into the package. Due to lots of demands, this will take me a couple days.
>
> You can reduce the noise but invoking the query you want to investigate from the command line, à la: /Applications/Sparql.app/Contents/MacOS/Sparql --debug 1 -m YourMapFile -npe 'SomeQuery'
>
>
>> I'm trying to put SWObjects in the middle of RelFinder on one side and
>> Joseki on the other. SWObjects starts with a mapping rule which has a
>> Service clause which match to the Joseki endpoint.
>>
>> So far I had mixed experiences.
>>
>> Re: RelFinder.
>> I've used reverse proxy to get around the crosdmain.xml issue.
>> I didn't manage to have RelFinder working on the SWObjects endpoint yet
>> (still have to play a bit with configurations). However SWObjects easily
>> gets to consume all CPU for hours without any debug message. Maybe it gets
>> in some loop ?
>
> Yeah, sounds like an issue with the HTTP server (which needs a lot of hardening). I'm guessing we'll see better reliability if I just do the Apache module hack (as writing a real HTTP 1.1 server is a sizable project). There's also the possibility of using JNI (I've never compiled it on a mac, but is hopefully not too hard) or calling the sparql executable as a CGI script.
>
>
>> Re: Joseki.
>>
>> I had mixed results.
>>
>> Sometimes it works.
>>
>> For a query like:
>>
>> select ?x ?y
>> where {?x <http://www.test.org/causativeOf> ?y }
>>
>> (the predicate is constructed in a mapping file, and that's the only rule).
>>
>>
>>
>> With this query:
>>
>> select ?x ?xl ?y
>> where {?x <http://www.test.org/causativeOf> ?y .
>> ?x ?p1 ?xl }
>>
>> JOSEKI gives this:
>>
>> 01:10:43 INFO SPARQL :: OK/select: SELECT DISTINCT
>> ?_0x10100e800_0_specGene ?x ?_0x10100e800_0_pert ?_0x10100e800_0_interaction
>> ?_0x10100e800_0_phenotype ?y WHERE { ?_0x10100e800_0_specGene
>> <http://localhost:8180/phibase/hasReferenceGene> ?x . ?_0x10100e800_0_pert
>> <http://localhost:8180/phibase/relativeToExperimentSpecificEntity>
>> ?_0x10100e800_0_specGene . ?_0x10100e800_0_interaction
>> <http://localhost:8180/phibase/Perturbation2Interaction>
>> ?_0x10100e800_0_pert . ?_0x10100e800_0_phenotype
>> <http://localhost:8180/phibase/GenericPhenotype_interactionID>
>> ?_0x10100e800_0_interaction . ?_0x10100e800_0_phenotype
>> <http://localhost:8180/phibase/GenericPhenotype_CV-ProcessPhenotype> ?y . }
>> 01:10:47 WARN log :: handle failed
>> java.io.IOException: FULL head
>> at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:276)
>> at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:205)
>> at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:380)
>> at
>> org.mortbay.jetty.nio.BlockingChannelConnector$Connection.run(BlockingChannelConnector.java:163)
>> at
>> org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:488)
>
> Let's see if I understand this failure; JOSEKI is crashing when reading the query, presumably 'cause Sparql is sending a broken HTTP packet? Can you run a packet sniffer like http://www.wireshark.org/download.html ? That should help us see exactly what's going wrong.
>
>
>> Note that the translated query works directly on JOSEKI. It is possibly
>> something that has to do with the http messanging.
>>
>>
>> Sometimes (not easily reproducible) SWOBjects yield nothing but the query
>> doesn't even go to JOSEKI (but this is a bit vague)
>>
>>
>> Any hint ?
>>
>> Regarding deployment. In the long run, it would be nice to have one (or
>> more) SPARQL module(s) in apache conf. But that's not something so urgent.
>
> ... unless it's the shortest path to satisfaction on the above HTTP issues...
>
>
>> ciao,
>> Andrea
>>
>>
>> Il giorno 16/gen/2011, alle ore 17.59, Eric Prud'hommeaux ha scritto:
>>
>>> * Andrea Splendiani <and...@bb...> [2011-01-16
>> 14:45+0000]
>>>> Hi,
>>>>
>>>> now it works, though at times I had some strange error where in the logs
>> you see some binary blurp (like an image). But that's not so common and
>> reproducible, may be something else around the system.
>>>
>>> Is that only when you have --debug enabled?
>>> If so, it's probably your web browser asking for the favicon and the
>>> server responding with a silly "mr yuck" face.
>>>
>>>
>>>> a question: is there a way to serve some file through the same http
>> server which serves sparql ?
>>>> I would need a crossdomain.xml file for flash!
>>>
>>> It would be pretty trivial to hack the source to do that (I could help
>> there).
>>> I'd like to add this functionality in general, but I haven't worked out
>> the packaging issues. Specifically, I'd like to take the favicon and the
>> generated HTML at the root out and put them into the filesystem somewhere.
>> Issues:
>>> where's that somewhere and how does the executable find it? (it should
>> have a convenient zero-config behavior)
>>> what's the interaction between named graphs and the filesystem? GET and
>> PUT of some named graph has nice behaviors now; should they be shadowed in
>> the filesystem?
>>>
>>> TimBL's leaning on me for the filesystem shadow. I have to write some
>> serializers to make it work.
>>>
>>>
>>>> ciao,
>>>> Andrea
>>>>
>>>> Il giorno 16/gen/2011, alle ore 04.42, Eric Prud'hommeaux ha scritto:
>>>>
>>>>> * Andrea Splendiani <and...@bb...> [2011-01-15
>> 17:30+0000]
>>>>>> Hi,
>>>>>>
>>>>>> I was trying to use the SWObjects that you (tele)presented at the
>> SWAT4LS tutorial in December.
>>>>>>
>>>>>> I have a few problems, perhaps I'm getting something wrong:
>>>>>>
>>>>>> So, I'm starting a Sparql server with the following command:
>>>>>>
>>>>>> ./Sparql --debug 2 -npm
>> /Users/andreasplendiani/Dropbox/WorkingProjects/PhiBase2/phibaseRDFMap.mp
>> --serve http://localhost:8200/SPARQL -i
>> /Users/andreasplendiani/Dropbox/WorkingProjects/PhiBase2/d2r-server-0.7/PhiBaseRDFv003.n3
>>
>>>>>>
>>>>>> The maps is something as:
>>>>>>
>>>>>> CONSTRUCT
>>>>>> {
>>>>>> ?gene <http://www.test.org/causativeOf> ?specGene
>>>>>> }
>>>>>> WHERE {
>>>>>> ?specGene <http://localhost:8180/phibase/hasReferenceGene> ?gene
>>>>>> }
>>>>>>
>>>>>> When I query the endpoint, I get:
>>>>>>
>>>>>> (endpoint result):
>>>>>>
>>>>>> Q&D SPARQL Server Error
>>>>>>
>>>>>> SELECT ?x ?y ?z
>>>>>> where {?x ?y ?z}
>>>>>>
>>>>>> yeilded
>>>>>>
>>>>>> failed to match triples prefixed by "!" in
>>>>>> SELECT ?x ?y ?z
>>>>>> WHERE
>>>>>> {
>>>>>> ! ?x ?y ?z .
>>>>>> }
>>>>>
>>>>> that version didn't support wildcard predicates over mapped rules. could
>> you try the latest?
>>>>>
>>>>>> (log):
>>>>>>
>>>>>> 127.0.0.1 - - [2011-00-15T17:23:00]"GET /favicon.ico 1.1" 200 620
>>>>>> GET /favicon.ico HTTP/1.1
>>>>>> Host: 127.0.0.1:8200
>>>>>> User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US;
>> rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13
>>>>>> Accept:
>> text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
>>>>>> Accept-Language: en-us,en;q=0.5
>>>>>> Accept-Encoding: gzip,deflate
>>>>>> Accept-Charset: ISO-8859-1,utf-8;q=0.7,*;q=0.7
>>>>>> Keep-Alive: 115
>>>>>> Connection: keep-alive
>>>>>> Cookie:
>> __utma=96992031.761815913.1280272954.1288624527.1291566200.4;
>> __utmz=96992031.1280272954.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none)
>>>>>>
>>>>>>
>>>>>> HTTP/1.0 200 OK
>>>>>> Content-Type: image/x-icon
>>>>>>
>>>>>> ?PNG
>>>>>>
>>>>>> (then binary blurp).
>>>>>>
>>>>>> Not sure what's going on, any idea ?
>>>>>> Same things if I try via SERVICE (instead of actually pointing to a
>> local dataset, which I suspect is not read)
>>>>>>
>>>>>> Is there a mailing list for SWObjects ?
>>>>>>
>>>>>> ciao,
>>>>>> Andrea
>>>>>>
>>>>>>
>>>>>>
>>>>>> Andrea Splendiani
>>>>>> Senior Bioinformatics Scientist
>>>>>> Centre for Mathematical and Computational Biology
>>>>>> +44(0)1582 763133 ext 2004
>>>>>> and...@bb...
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> -ericP
>>>>
>>>> Andrea Splendiani
>>>> Senior Bioinformatics Scientist
>>>> Centre for Mathematical and Computational Biology
>>>> +44(0)1582 763133 ext 2004
>>>> and...@bb...
>>>>
>>>>
>>>>
>>>
>>> --
>>> -ericP
>>
>> Andrea Splendiani
>> Senior Bioinformatics Scientist
>> Centre for Mathematical and Computational Biology
>> +44(0)1582 763133 ext 2004
>> and...@bb...
>>
>>
>>
>>
>
> --
> -ericP
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004
and...@bb...
|
|
From: Eric Prud'h. <er...@w3...> - 2011-01-18 15:36:05
|
* Andrea Splendiani <and...@bb...> [2011-01-18 01:15+0000]
> Hi,
>
> I have some problem with SWObjects.
>
> first: with debug on it prints a lot of information, but not all so
> informative. It prints a lot of html (possibly the one that is served) but I
> don't easily find the query translation (which is pretty useful).
> Also, I think it prints the binary png all the time the browser request
> it... which is a bit annoying.
It looks like it's time to put in a real logger with debug levels and that sort of thing. There's a package proposed for the boost libraries; I've been hoping it would be incorporated into the mainstream before I needed it, but I can get around this by incorporating the source directly into the package. Due to lots of demands, this will take me a couple days.
You can reduce the noise but invoking the query you want to investigate from the command line, à la: /Applications/Sparql.app/Contents/MacOS/Sparql --debug 1 -m YourMapFile -npe 'SomeQuery'
> I'm trying to put SWObjects in the middle of RelFinder on one side and
> Joseki on the other. SWObjects starts with a mapping rule which has a
> Service clause which match to the Joseki endpoint.
>
> So far I had mixed experiences.
>
> Re: RelFinder.
> I've used reverse proxy to get around the crosdmain.xml issue.
> I didn't manage to have RelFinder working on the SWObjects endpoint yet
> (still have to play a bit with configurations). However SWObjects easily
> gets to consume all CPU for hours without any debug message. Maybe it gets
> in some loop ?
Yeah, sounds like an issue with the HTTP server (which needs a lot of hardening). I'm guessing we'll see better reliability if I just do the Apache module hack (as writing a real HTTP 1.1 server is a sizable project). There's also the possibility of using JNI (I've never compiled it on a mac, but is hopefully not too hard) or calling the sparql executable as a CGI script.
> Re: Joseki.
>
> I had mixed results.
>
> Sometimes it works.
>
> For a query like:
>
> select ?x ?y
> where {?x <http://www.test.org/causativeOf> ?y }
>
> (the predicate is constructed in a mapping file, and that's the only rule).
>
>
>
> With this query:
>
> select ?x ?xl ?y
> where {?x <http://www.test.org/causativeOf> ?y .
> ?x ?p1 ?xl }
>
> JOSEKI gives this:
>
> 01:10:43 INFO SPARQL :: OK/select: SELECT DISTINCT
> ?_0x10100e800_0_specGene ?x ?_0x10100e800_0_pert ?_0x10100e800_0_interaction
> ?_0x10100e800_0_phenotype ?y WHERE { ?_0x10100e800_0_specGene
> <http://localhost:8180/phibase/hasReferenceGene> ?x . ?_0x10100e800_0_pert
> <http://localhost:8180/phibase/relativeToExperimentSpecificEntity>
> ?_0x10100e800_0_specGene . ?_0x10100e800_0_interaction
> <http://localhost:8180/phibase/Perturbation2Interaction>
> ?_0x10100e800_0_pert . ?_0x10100e800_0_phenotype
> <http://localhost:8180/phibase/GenericPhenotype_interactionID>
> ?_0x10100e800_0_interaction . ?_0x10100e800_0_phenotype
> <http://localhost:8180/phibase/GenericPhenotype_CV-ProcessPhenotype> ?y . }
> 01:10:47 WARN log :: handle failed
> java.io.IOException: FULL head
> at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:276)
> at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:205)
> at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:380)
> at
> org.mortbay.jetty.nio.BlockingChannelConnector$Connection.run(BlockingChannelConnector.java:163)
> at
> org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:488)
Let's see if I understand this failure; JOSEKI is crashing when reading the query, presumably 'cause Sparql is sending a broken HTTP packet? Can you run a packet sniffer like http://www.wireshark.org/download.html ? That should help us see exactly what's going wrong.
> Note that the translated query works directly on JOSEKI. It is possibly
> something that has to do with the http messanging.
>
>
> Sometimes (not easily reproducible) SWOBjects yield nothing but the query
> doesn't even go to JOSEKI (but this is a bit vague)
>
>
> Any hint ?
>
> Regarding deployment. In the long run, it would be nice to have one (or
> more) SPARQL module(s) in apache conf. But that's not something so urgent.
... unless it's the shortest path to satisfaction on the above HTTP issues...
> ciao,
> Andrea
>
>
> Il giorno 16/gen/2011, alle ore 17.59, Eric Prud'hommeaux ha scritto:
>
> > * Andrea Splendiani <and...@bb...> [2011-01-16
> 14:45+0000]
> >> Hi,
> >>
> >> now it works, though at times I had some strange error where in the logs
> you see some binary blurp (like an image). But that's not so common and
> reproducible, may be something else around the system.
> >
> > Is that only when you have --debug enabled?
> > If so, it's probably your web browser asking for the favicon and the
> > server responding with a silly "mr yuck" face.
> >
> >
> >> a question: is there a way to serve some file through the same http
> server which serves sparql ?
> >> I would need a crossdomain.xml file for flash!
> >
> > It would be pretty trivial to hack the source to do that (I could help
> there).
> > I'd like to add this functionality in general, but I haven't worked out
> the packaging issues. Specifically, I'd like to take the favicon and the
> generated HTML at the root out and put them into the filesystem somewhere.
> Issues:
> > where's that somewhere and how does the executable find it? (it should
> have a convenient zero-config behavior)
> > what's the interaction between named graphs and the filesystem? GET and
> PUT of some named graph has nice behaviors now; should they be shadowed in
> the filesystem?
> >
> > TimBL's leaning on me for the filesystem shadow. I have to write some
> serializers to make it work.
> >
> >
> >> ciao,
> >> Andrea
> >>
> >> Il giorno 16/gen/2011, alle ore 04.42, Eric Prud'hommeaux ha scritto:
> >>
> >>> * Andrea Splendiani <and...@bb...> [2011-01-15
> 17:30+0000]
> >>>> Hi,
> >>>>
> >>>> I was trying to use the SWObjects that you (tele)presented at the
> SWAT4LS tutorial in December.
> >>>>
> >>>> I have a few problems, perhaps I'm getting something wrong:
> >>>>
> >>>> So, I'm starting a Sparql server with the following command:
> >>>>
> >>>> ./Sparql --debug 2 -npm
> /Users/andreasplendiani/Dropbox/WorkingProjects/PhiBase2/phibaseRDFMap.mp
> --serve http://localhost:8200/SPARQL -i
> /Users/andreasplendiani/Dropbox/WorkingProjects/PhiBase2/d2r-server-0.7/PhiBaseRDFv003.n3
>
> >>>>
> >>>> The maps is something as:
> >>>>
> >>>> CONSTRUCT
> >>>> {
> >>>> ?gene <http://www.test.org/causativeOf> ?specGene
> >>>> }
> >>>> WHERE {
> >>>> ?specGene <http://localhost:8180/phibase/hasReferenceGene> ?gene
> >>>> }
> >>>>
> >>>> When I query the endpoint, I get:
> >>>>
> >>>> (endpoint result):
> >>>>
> >>>> Q&D SPARQL Server Error
> >>>>
> >>>> SELECT ?x ?y ?z
> >>>> where {?x ?y ?z}
> >>>>
> >>>> yeilded
> >>>>
> >>>> failed to match triples prefixed by "!" in
> >>>> SELECT ?x ?y ?z
> >>>> WHERE
> >>>> {
> >>>> ! ?x ?y ?z .
> >>>> }
> >>>
> >>> that version didn't support wildcard predicates over mapped rules. could
> you try the latest?
> >>>
> >>>> (log):
> >>>>
> >>>> 127.0.0.1 - - [2011-00-15T17:23:00]"GET /favicon.ico 1.1" 200 620
> >>>> GET /favicon.ico HTTP/1.1
> >>>> Host: 127.0.0.1:8200
> >>>> User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US;
> rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13
> >>>> Accept:
> text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
> >>>> Accept-Language: en-us,en;q=0.5
> >>>> Accept-Encoding: gzip,deflate
> >>>> Accept-Charset: ISO-8859-1,utf-8;q=0.7,*;q=0.7
> >>>> Keep-Alive: 115
> >>>> Connection: keep-alive
> >>>> Cookie:
> __utma=96992031.761815913.1280272954.1288624527.1291566200.4;
> __utmz=96992031.1280272954.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none)
> >>>>
> >>>>
> >>>> HTTP/1.0 200 OK
> >>>> Content-Type: image/x-icon
> >>>>
> >>>> ?PNG
> >>>>
> >>>> (then binary blurp).
> >>>>
> >>>> Not sure what's going on, any idea ?
> >>>> Same things if I try via SERVICE (instead of actually pointing to a
> local dataset, which I suspect is not read)
> >>>>
> >>>> Is there a mailing list for SWObjects ?
> >>>>
> >>>> ciao,
> >>>> Andrea
> >>>>
> >>>>
> >>>>
> >>>> Andrea Splendiani
> >>>> Senior Bioinformatics Scientist
> >>>> Centre for Mathematical and Computational Biology
> >>>> +44(0)1582 763133 ext 2004
> >>>> and...@bb...
> >>>>
> >>>>
> >>>>
> >>>
> >>> --
> >>> -ericP
> >>
> >> Andrea Splendiani
> >> Senior Bioinformatics Scientist
> >> Centre for Mathematical and Computational Biology
> >> +44(0)1582 763133 ext 2004
> >> and...@bb...
> >>
> >>
> >>
> >
> > --
> > -ericP
>
> Andrea Splendiani
> Senior Bioinformatics Scientist
> Centre for Mathematical and Computational Biology
> +44(0)1582 763133 ext 2004
> and...@bb...
>
>
>
>
--
-ericP
|
|
From: Andrea S. <and...@bb...> - 2011-01-18 02:01:13
|
Hi,
I have some problem with SWObjects.
first: with debug on it prints a lot of information, but not all so
informative. It prints a lot of html (possibly the one that is served) but I
don't easily find the query translation (which is pretty useful).
Also, I think it prints the binary png all the time the browser request
it... which is a bit annoying.
I'm trying to put SWObjects in the middle of RelFinder on one side and
Joseki on the other. SWObjects starts with a mapping rule which has a
Service clause which match to the Joseki endpoint.
So far I had mixed experiences.
Re: RelFinder.
I've used reverse proxy to get around the crosdmain.xml issue.
I didn't manage to have RelFinder working on the SWObjects endpoint yet
(still have to play a bit with configurations). However SWObjects easily
gets to consume all CPU for hours without any debug message. Maybe it gets
in some loop ?
Re: Joseki.
I had mixed results.
Sometimes it works.
For a query like:
select ?x ?y
where {?x <http://www.test.org/causativeOf> ?y }
(the predicate is constructed in a mapping file, and that's the only rule).
With this query:
select ?x ?xl ?y
where {?x <http://www.test.org/causativeOf> ?y .
?x ?p1 ?xl }
JOSEKI gives this:
01:10:43 INFO SPARQL :: OK/select: SELECT DISTINCT
?_0x10100e800_0_specGene ?x ?_0x10100e800_0_pert ?_0x10100e800_0_interaction
?_0x10100e800_0_phenotype ?y WHERE { ?_0x10100e800_0_specGene
<http://localhost:8180/phibase/hasReferenceGene> ?x . ?_0x10100e800_0_pert
<http://localhost:8180/phibase/relativeToExperimentSpecificEntity>
?_0x10100e800_0_specGene . ?_0x10100e800_0_interaction
<http://localhost:8180/phibase/Perturbation2Interaction>
?_0x10100e800_0_pert . ?_0x10100e800_0_phenotype
<http://localhost:8180/phibase/GenericPhenotype_interactionID>
?_0x10100e800_0_interaction . ?_0x10100e800_0_phenotype
<http://localhost:8180/phibase/GenericPhenotype_CV-ProcessPhenotype> ?y . }
01:10:47 WARN log :: handle failed
java.io.IOException: FULL head
at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:276)
at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:205)
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:380)
at
org.mortbay.jetty.nio.BlockingChannelConnector$Connection.run(BlockingChannelConnector.java:163)
at
org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:488)
Note that the translated query works directly on JOSEKI. It is possibly
something that has to do with the http messanging.
Sometimes (not easily reproducible) SWOBjects yield nothing but the query
doesn't even go to JOSEKI (but this is a bit vague)
Any hint ?
Regarding deployment. In the long run, it would be nice to have one (or
more) SPARQL module(s) in apache conf. But that's not something so urgent.
ciao,
Andrea
Il giorno 16/gen/2011, alle ore 17.59, Eric Prud'hommeaux ha scritto:
> * Andrea Splendiani <and...@bb...> [2011-01-16
14:45+0000]
>> Hi,
>>
>> now it works, though at times I had some strange error where in the logs
you see some binary blurp (like an image). But that's not so common and
reproducible, may be something else around the system.
>
> Is that only when you have --debug enabled?
> If so, it's probably your web browser asking for the favicon and the
> server responding with a silly "mr yuck" face.
>
>
>> a question: is there a way to serve some file through the same http
server which serves sparql ?
>> I would need a crossdomain.xml file for flash!
>
> It would be pretty trivial to hack the source to do that (I could help
there).
> I'd like to add this functionality in general, but I haven't worked out
the packaging issues. Specifically, I'd like to take the favicon and the
generated HTML at the root out and put them into the filesystem somewhere.
Issues:
> where's that somewhere and how does the executable find it? (it should
have a convenient zero-config behavior)
> what's the interaction between named graphs and the filesystem? GET and
PUT of some named graph has nice behaviors now; should they be shadowed in
the filesystem?
>
> TimBL's leaning on me for the filesystem shadow. I have to write some
serializers to make it work.
>
>
>> ciao,
>> Andrea
>>
>> Il giorno 16/gen/2011, alle ore 04.42, Eric Prud'hommeaux ha scritto:
>>
>>> * Andrea Splendiani <and...@bb...> [2011-01-15
17:30+0000]
>>>> Hi,
>>>>
>>>> I was trying to use the SWObjects that you (tele)presented at the
SWAT4LS tutorial in December.
>>>>
>>>> I have a few problems, perhaps I'm getting something wrong:
>>>>
>>>> So, I'm starting a Sparql server with the following command:
>>>>
>>>> ./Sparql --debug 2 -npm
/Users/andreasplendiani/Dropbox/WorkingProjects/PhiBase2/phibaseRDFMap.mp
--serve http://localhost:8200/SPARQL -i
/Users/andreasplendiani/Dropbox/WorkingProjects/PhiBase2/d2r-server-0.7/PhiBaseRDFv003.n3
>>>>
>>>> The maps is something as:
>>>>
>>>> CONSTRUCT
>>>> {
>>>> ?gene <http://www.test.org/causativeOf> ?specGene
>>>> }
>>>> WHERE {
>>>> ?specGene <http://localhost:8180/phibase/hasReferenceGene> ?gene
>>>> }
>>>>
>>>> When I query the endpoint, I get:
>>>>
>>>> (endpoint result):
>>>>
>>>> Q&D SPARQL Server Error
>>>>
>>>> SELECT ?x ?y ?z
>>>> where {?x ?y ?z}
>>>>
>>>> yeilded
>>>>
>>>> failed to match triples prefixed by "!" in
>>>> SELECT ?x ?y ?z
>>>> WHERE
>>>> {
>>>> ! ?x ?y ?z .
>>>> }
>>>
>>> that version didn't support wildcard predicates over mapped rules. could
you try the latest?
>>>
>>>> (log):
>>>>
>>>> 127.0.0.1 - - [2011-00-15T17:23:00]"GET /favicon.ico 1.1" 200 620
>>>> GET /favicon.ico HTTP/1.1
>>>> Host: 127.0.0.1:8200
>>>> User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US;
rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13
>>>> Accept:
text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
>>>> Accept-Language: en-us,en;q=0.5
>>>> Accept-Encoding: gzip,deflate
>>>> Accept-Charset: ISO-8859-1,utf-8;q=0.7,*;q=0.7
>>>> Keep-Alive: 115
>>>> Connection: keep-alive
>>>> Cookie:
__utma=96992031.761815913.1280272954.1288624527.1291566200.4;
__utmz=96992031.1280272954.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none)
>>>>
>>>>
>>>> HTTP/1.0 200 OK
>>>> Content-Type: image/x-icon
>>>>
>>>> ?PNG
>>>>
>>>> (then binary blurp).
>>>>
>>>> Not sure what's going on, any idea ?
>>>> Same things if I try via SERVICE (instead of actually pointing to a
local dataset, which I suspect is not read)
>>>>
>>>> Is there a mailing list for SWObjects ?
>>>>
>>>> ciao,
>>>> Andrea
>>>>
>>>>
>>>>
>>>> Andrea Splendiani
>>>> Senior Bioinformatics Scientist
>>>> Centre for Mathematical and Computational Biology
>>>> +44(0)1582 763133 ext 2004
>>>> and...@bb...
>>>>
>>>>
>>>>
>>>
>>> --
>>> -ericP
>>
>> Andrea Splendiani
>> Senior Bioinformatics Scientist
>> Centre for Mathematical and Computational Biology
>> +44(0)1582 763133 ext 2004
>> and...@bb...
>>
>>
>>
>
> --
> -ericP
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004
and...@bb...
|
|
From: Eric Prud'h. <er...@w3...> - 2011-01-16 18:29:18
|
* Eric Prud'hommeaux <er...@w3...> [2011-01-16 12:59-0500]
> * Andrea Splendiani <and...@bb...> [2011-01-16 14:45+0000]
> > Hi,
> >
> > now it works, though at times I had some strange error where in the logs you see some binary blurp (like an image). But that's not so common and reproducible, may be something else around the system.
>
> Is that only when you have --debug enabled?
> If so, it's probably your web browser asking for the favicon and the
> server responding with a silly "mr yuck" face.
>
>
> > a question: is there a way to serve some file through the same http server which serves sparql ?
> > I would need a crossdomain.xml file for flash!
>
> It would be pretty trivial to hack the source to do that (I could help there).
> I'd like to add this functionality in general, but I haven't worked out the packaging issues. Specifically, I'd like to take the favicon and the generated HTML at the root out and put them into the filesystem somewhere. Issues:
> where's that somewhere and how does the executable find it? (it should have a convenient zero-config behavior)
> what's the interaction between named graphs and the filesystem? GET and PUT of some named graph has nice behaviors now; should they be shadowed in the filesystem?
>
> TimBL's leaning on me for the filesystem shadow. I have to write some serializers to make it work.
I forgot to add, there's another possible strategy here, which is to make the sparql executable also be an apache module, leaning on apache for the generic file serving and registering a handler which takes a partition of the web space for named graphs with relative names (e.g. "tree/and/leaf" vs. "/root/tree/and/leaf" or "http://server/root/tree/and/leaf"). I have no idea how easy it is to compile a .so (or .dynlib) for one version of apache and run it on another.
> > ciao,
> > Andrea
> >
> > Il giorno 16/gen/2011, alle ore 04.42, Eric Prud'hommeaux ha scritto:
> >
> > > * Andrea Splendiani <and...@bb...> [2011-01-15 17:30+0000]
> > >> Hi,
> > >>
> > >> I was trying to use the SWObjects that you (tele)presented at the SWAT4LS tutorial in December.
> > >>
> > >> I have a few problems, perhaps I'm getting something wrong:
> > >>
> > >> So, I'm starting a Sparql server with the following command:
> > >>
> > >> ./Sparql --debug 2 -npm /Users/andreasplendiani/Dropbox/WorkingProjects/PhiBase2/phibaseRDFMap.mp --serve http://localhost:8200/SPARQL -i /Users/andreasplendiani/Dropbox/WorkingProjects/PhiBase2/d2r-server-0.7/PhiBaseRDFv003.n3
> > >>
> > >> The maps is something as:
> > >>
> > >> CONSTRUCT
> > >> {
> > >> ?gene <http://www.test.org/causativeOf> ?specGene
> > >> }
> > >> WHERE {
> > >> ?specGene <http://localhost:8180/phibase/hasReferenceGene> ?gene
> > >> }
> > >>
> > >> When I query the endpoint, I get:
> > >>
> > >> (endpoint result):
> > >>
> > >> Q&D SPARQL Server Error
> > >>
> > >> SELECT ?x ?y ?z
> > >> where {?x ?y ?z}
> > >>
> > >> yeilded
> > >>
> > >> failed to match triples prefixed by "!" in
> > >> SELECT ?x ?y ?z
> > >> WHERE
> > >> {
> > >> ! ?x ?y ?z .
> > >> }
> > >
> > > that version didn't support wildcard predicates over mapped rules. could you try the latest?
> > >
> > >> (log):
> > >>
> > >> 127.0.0.1 - - [2011-00-15T17:23:00]"GET /favicon.ico 1.1" 200 620
> > >> GET /favicon.ico HTTP/1.1
> > >> Host: 127.0.0.1:8200
> > >> User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13
> > >> Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
> > >> Accept-Language: en-us,en;q=0.5
> > >> Accept-Encoding: gzip,deflate
> > >> Accept-Charset: ISO-8859-1,utf-8;q=0.7,*;q=0.7
> > >> Keep-Alive: 115
> > >> Connection: keep-alive
> > >> Cookie: __utma=96992031.761815913.1280272954.1288624527.1291566200.4; __utmz=96992031.1280272954.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none)
> > >>
> > >>
> > >> HTTP/1.0 200 OK
> > >> Content-Type: image/x-icon
> > >>
> > >> ?PNG
> > >>
> > >> (then binary blurp).
> > >>
> > >> Not sure what's going on, any idea ?
> > >> Same things if I try via SERVICE (instead of actually pointing to a local dataset, which I suspect is not read)
> > >>
> > >> Is there a mailing list for SWObjects ?
> > >>
> > >> ciao,
> > >> Andrea
> > >>
> > >>
> > >>
> > >> Andrea Splendiani
> > >> Senior Bioinformatics Scientist
> > >> Centre for Mathematical and Computational Biology
> > >> +44(0)1582 763133 ext 2004
> > >> and...@bb...
> > >>
> > >>
> > >>
> > >
> > > --
> > > -ericP
> >
> > Andrea Splendiani
> > Senior Bioinformatics Scientist
> > Centre for Mathematical and Computational Biology
> > +44(0)1582 763133 ext 2004
> > and...@bb...
> >
> >
> >
>
> --
> -ericP
--
-ericP
|
|
From: Eric Prud'h. <er...@w3...> - 2011-01-16 17:59:48
|
* Andrea Splendiani <and...@bb...> [2011-01-16 14:45+0000]
> Hi,
>
> now it works, though at times I had some strange error where in the logs you see some binary blurp (like an image). But that's not so common and reproducible, may be something else around the system.
Is that only when you have --debug enabled?
If so, it's probably your web browser asking for the favicon and the
server responding with a silly "mr yuck" face.
> a question: is there a way to serve some file through the same http server which serves sparql ?
> I would need a crossdomain.xml file for flash!
It would be pretty trivial to hack the source to do that (I could help there).
I'd like to add this functionality in general, but I haven't worked out the packaging issues. Specifically, I'd like to take the favicon and the generated HTML at the root out and put them into the filesystem somewhere. Issues:
where's that somewhere and how does the executable find it? (it should have a convenient zero-config behavior)
what's the interaction between named graphs and the filesystem? GET and PUT of some named graph has nice behaviors now; should they be shadowed in the filesystem?
TimBL's leaning on me for the filesystem shadow. I have to write some serializers to make it work.
> ciao,
> Andrea
>
> Il giorno 16/gen/2011, alle ore 04.42, Eric Prud'hommeaux ha scritto:
>
> > * Andrea Splendiani <and...@bb...> [2011-01-15 17:30+0000]
> >> Hi,
> >>
> >> I was trying to use the SWObjects that you (tele)presented at the SWAT4LS tutorial in December.
> >>
> >> I have a few problems, perhaps I'm getting something wrong:
> >>
> >> So, I'm starting a Sparql server with the following command:
> >>
> >> ./Sparql --debug 2 -npm /Users/andreasplendiani/Dropbox/WorkingProjects/PhiBase2/phibaseRDFMap.mp --serve http://localhost:8200/SPARQL -i /Users/andreasplendiani/Dropbox/WorkingProjects/PhiBase2/d2r-server-0.7/PhiBaseRDFv003.n3
> >>
> >> The maps is something as:
> >>
> >> CONSTRUCT
> >> {
> >> ?gene <http://www.test.org/causativeOf> ?specGene
> >> }
> >> WHERE {
> >> ?specGene <http://localhost:8180/phibase/hasReferenceGene> ?gene
> >> }
> >>
> >> When I query the endpoint, I get:
> >>
> >> (endpoint result):
> >>
> >> Q&D SPARQL Server Error
> >>
> >> SELECT ?x ?y ?z
> >> where {?x ?y ?z}
> >>
> >> yeilded
> >>
> >> failed to match triples prefixed by "!" in
> >> SELECT ?x ?y ?z
> >> WHERE
> >> {
> >> ! ?x ?y ?z .
> >> }
> >
> > that version didn't support wildcard predicates over mapped rules. could you try the latest?
> >
> >> (log):
> >>
> >> 127.0.0.1 - - [2011-00-15T17:23:00]"GET /favicon.ico 1.1" 200 620
> >> GET /favicon.ico HTTP/1.1
> >> Host: 127.0.0.1:8200
> >> User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13
> >> Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
> >> Accept-Language: en-us,en;q=0.5
> >> Accept-Encoding: gzip,deflate
> >> Accept-Charset: ISO-8859-1,utf-8;q=0.7,*;q=0.7
> >> Keep-Alive: 115
> >> Connection: keep-alive
> >> Cookie: __utma=96992031.761815913.1280272954.1288624527.1291566200.4; __utmz=96992031.1280272954.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none)
> >>
> >>
> >> HTTP/1.0 200 OK
> >> Content-Type: image/x-icon
> >>
> >> ?PNG
> >>
> >> (then binary blurp).
> >>
> >> Not sure what's going on, any idea ?
> >> Same things if I try via SERVICE (instead of actually pointing to a local dataset, which I suspect is not read)
> >>
> >> Is there a mailing list for SWObjects ?
> >>
> >> ciao,
> >> Andrea
> >>
> >>
> >>
> >> Andrea Splendiani
> >> Senior Bioinformatics Scientist
> >> Centre for Mathematical and Computational Biology
> >> +44(0)1582 763133 ext 2004
> >> and...@bb...
> >>
> >>
> >>
> >
> > --
> > -ericP
>
> Andrea Splendiani
> Senior Bioinformatics Scientist
> Centre for Mathematical and Computational Biology
> +44(0)1582 763133 ext 2004
> and...@bb...
>
>
>
--
-ericP
|
|
From: Eric Prud'h. <er...@w3...> - 2011-01-08 20:32:55
|
Bill, as you're working on the automake for SWObjects, a teeny bit
about the parser rules in Makefile:
Bison generates five files from foo.ypp:
foo.cpp
foo.hpp
location.hh
stack.hh
postion.hh
These are currently sequestered into a directory called foo/ so that a
$(make -j) (which does parallel builds) doesn't tromp on a shared
{location,stack,position}.hh . They could all share the same directory
(e.g lib/) if it weren't for that collision.
--
-ericP
|
|
From: William S F. <ws...@fu...> - 2010-08-20 05:56:09
|
Eric Prud'hommeaux wrote:
> I have a project where
> swig -c++ -python swig/SWObjects.i
> works but
> swig -c++ -java swig/SWObjects.i
> fails with
> [[
> swig/SWObjects.i:3: Error: Unable to find 'std_set.i'
> /usr/local/share/swig/2.0.0/std/std_basic_string.i:2: Error: Unable to find 'std_container.i'
> /usr/local/share/swig/2.0.0/std/std_basic_string.i:3: Error: Unable to find 'std_alloc.i'
> /usr/local/share/swig/2.0.0/std/std_basic_string.i:4: Error: Unable to find 'std_char_traits.i'
>
> ]]. The -python codepath includes
> /usr/local/share/swig/2.0.0/std/std_set.i ; the -java codepath looks in
> [[
> open("std_set.i", O_RDONLY) = ENOENT
> open("./std_set.i", O_RDONLY) = ENOENT
> open("lib/std_set.i", O_RDONLY) = ENOENT
> open("interface/std_set.i", O_RDONLY) = ENOENT
> open("./swig_lib/java/std_set.i", O_RDONLY) = ENOENT
> open("/usr/local/share/swig/2.0.0/java/std_set.i", O_RDONLY) = ENOENT
> → open("./swig_lib/std_set.i", O_RDONLY) = ENOENT
> → open("/usr/local/share/swig/2.0.0/std_set.i", O_RDONLY) = ENOENT
> open("./std_set.i", O_RDONLY) = ENOENT
> open("swig/std_set.i", O_RDONLY) = ENOENT
> ]] while the python codepath looks for *std/*std_set.i . Attempting to
> cheat fate with
> cp ../std/{std_container.i,std_set.i,std_alloc.i,std_char_traits.i} /usr/local/share/swig/2.0.0/java
> I confuse swig
> /usr/local/share/swig/2.0.0/java/std_set.i:93: Error: Syntax error in input(3).
> with this line:
> [[
> %traits_swigtype(_Key);
> ]] — /usr/local/share/swig/2.0.0/java/std_set.i:93
> ^^^^^ well, std/ really
>
> http://prdownloads.sourceforge.net/swig/swig-2.0.0.tar.gz
> SWIG Version 2.0.0
> Compiled with g++ [i686-pc-linux-gnu]
>
> Minimal setup to reproduce the bug furnished upon request.
There is no std_set.i supplied for Java.
William
|
|
From: Eric Prud'h. <er...@w3...> - 2010-08-16 18:42:27
|
Someone who feels like enhancing this can record a nice tutorial in
the SWObjects wiki.
Suppose someone wants to ask a question which spans a bunch of query
services, but doesn't (care to) enumerate those resources. The
ChainingMapper takes rules (currently written as SPARQL CONSTRUCTs)
and maps a query over the consequents of those rules to a query over
the antecedents of those rules. This can be used to partition queries
into SERVICE graphs.
For a terse example, imagine service S12 includes triples with
predicates <p1> and <p2>, and S3 includes predicates <p3>. Voila a
SPARQL invocation and tranformed query:
Query and mapping rules:
SPARQL -npq \
-M 'CONSTRUCT { ?s <p1> ?o1 ; <p2> ?o2 } WHERE { SERVICE <S12> { ?s <p1> ?o1 ; <p2> ?o2 } }' \
-M 'CONSTRUCT { ?s <p3> ?o } WHERE { SERVICE <S3> { ?s <p3> ?o } }' \
-e 'SELECT * WHERE { ?x1 <p1> ?n1 ; <p2> ?n2 ; <p3> ?n3 }'
Transformed query:
SELECT * WHERE {
SERVICE <S12> { ?x1 <p1> ?n1 . ?x1 <p2> ?n2 }
SERVICE <S3> { ?x1 <p3> ?n3 }
}
If the system has a list of SERVICE graphs, then the user just has to
ask the base question and the systems handles query federation. What
if some predicates can be obtained from multiple endpoints?
SPARQL -npq \
-M 'CONSTRUCT { ?s <p1> ?o1 ; <p2> ?o2 } WHERE { SERVICE <S12> { ?s <p1> ?o1 ; <p2> ?o2 } }' \
-M 'CONSTRUCT { ?s <p2> ?o2 ; <p3> ?o3 } WHERE { SERVICE <S23> { ?s <p2> ?o2 ; <p3> ?o3 } }' \
-e 'SELECT * WHERE { ?x1 <p1> ?n1 ; <p2> ?n2 ; <p3> ?n3 }'
Now we expect <p2> to come from both S12 and S23:
SELECT * WHERE { {
SERVICE <S12> { ?x1 <p1> ?n1 . ?x1 <p2> ?n2 }
SERVICE <S23> { ?x1 <p2> ?_0x8752540_0_o2 . ?x1 <p3> ?n3 }
} UNION {
SERVICE <S12> { ?x1 <p1> ?n1 . ?x1 <p2> ?_0x874df10_1_o2 }
SERVICE <S23> { ?x1 <p2> ?n2 . ?x1 <p3> ?n3 }
} }
So our query for predicates <p1> <p2> <p3> could be answered by <S12>
providing <p1> <p2> and <S23> providing <p3>, or by <p2> coming from
<S23> (hence the UNION).
What are those odd variables like _0x8752540_0_o2 ? In order to be
sound with respect to the rules, the ChainingMapper has to ensure that
the complete antecedent of each query is satisfied. Looking at the
first side of the UNION, <S23> is expected to match { ?x <p2> ?o2;
<p3> ?o3 }, so the generated query must make sure that for any { ?x1
<p3> ?n3 }, ?x1 also has a property <p2> (though the value is
unimportant).
Since those rules are two course, we can write more, simpler rules:
SPARQL -npq \
-M 'CONSTRUCT { ?s <p1> ?o1 } WHERE { SERVICE <S12> { ?s <p1> ?o1 } }' \
-M 'CONSTRUCT { ?s <p2> ?o2 } WHERE { SERVICE <S12> { ?s <p2> ?o2 } }' \
-M 'CONSTRUCT { ?s <p2> ?o2 } WHERE { SERVICE <S23> { ?s <p2> ?o2 } }' \
-M 'CONSTRUCT { ?s <p3> ?o3 } WHERE { SERVICE <S23> { ?s <p3> ?o3 } }' \
-e 'SELECT * WHERE { ?x1 <p1> ?n1 ; <p2> ?n2 ; <p3> ?n3 }'
and see a simpler federated query:
SELECT * WHERE { {
SERVICE <S12> { ?x1 <p1> ?n1 }
SERVICE <S12> { ?x1 <p2> ?n2 }
SERVICE <S23> { ?x1 <p3> ?n3 }
} UNION {
SERVICE <S12> { ?x1 <p1> ?n1 }
SERVICE <S23> { ?x1 <p3> ?n3 }
SERVICE <S23> { ?x1 <p2> ?n2 }
} }
I got this related Q:
> Let's say we have two endpoints - S1 and S2 - registered with the federator.
>
> Triples in S1:
>
> ?x rdf:type ?y
>
> Triples in S2:
>
> ?a rdf:type foaf:person
> ?b foaf:mbox ?c
>
> Now, I get a query:
>
> Select ?x1
> Where {
> ?x1 rdf:type foaf:person
> ?x1 foaf:mbox ?y1
> }
>
> What does the mapper do in this instance? Is there a way to tell the
> mapper to look only at S2 (or only S1 to get bindings for the first
> triple in the where clause)? Or, is the federator expected to return
> the most complete answer by doing a union across both endpoints?
We can test this:
Query:
SPARQL -npq \
-M 'CONSTRUCT { ?x a ?y } WHERE { SERVICE <S1> { ?x a ?y } }' \
-M 'CONSTRUCT { ?a a <person> . ?b <mbox> ?c } WHERE { SERVICE <S2> { ?a a <person> . ?b <mbox> ?c } }' \
-e 'SELECT ?x1 WHERE { ?x1 a <person> . ?x1 <mbox> ?y1 }'
and get the expected UNION because two services can produce rdf:type
arcs:
Result (query):
SELECT ?x1
WHERE
{
{
SERVICE <S1>
{
?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <person> .
}
SERVICE <S2>
{
?_0x8580540_0_a <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <person> .
?x1 <mbox> ?y1 .
}
}
UNION
SERVICE <S2>
{
?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <person> .
?x1 <mbox> ?y1 .
}
}
> -Matt
>
>
--
-ericP
|
|
From: Eric Prud'h. <er...@w3...> - 2010-07-09 03:46:22
|
* Michael V. <mik...@ya...> [2010-03-30 14:19-0700] > Hi, > > My name is Michael Viana, I am the student currently working with Helen Chen on the COI demo. I was just wondering what the status of the JNI wrapper is and whether it is based on the SWTransformer or the new sparql.exe. I'd also be happy to lend a hand if need be, I'm not very familiar with JNI but I've been looking at the source code for SWtransformer and understand a little bit with respect to how the process would work. Hi, sorry for the late response; this got past me in my giant inbox. I've rolled the functionality of SWtransformer and SWserver into the SPARQL executable. I've also been working on a SWIG interface, but I don't have much to show on the java front. You can compile the SWIG python code: svn -q co https://swobjects.svn.sourceforge.net/svnroot/swobjects/branches/sparql11 swobjects-11 cd swobjects-11 make pytest but the SWIG java code doesn't compile. What would probably be the most effective path would be to get $(make jatest) to work in the attached skeleton code tree. Then I can apply the lessons learned to get the SWObjects java interface working. For reference, $(make pytest) works in this skeleton. > Michael Viana > > > > __________________________________________________________________ > The new Internet Explorer® 8 - Faster, safer, easier. Optimized for Yahoo! Get it Now for Free! at http://downloads.yahoo.com/ca/internetexplorer/ > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > SWObjects-devel mailing list > SWO...@li... > https://lists.sourceforge.net/lists/listinfo/swobjects-devel -- -ericP |
|
From: Eric Prud'h. <er...@w3...> - 2010-07-08 15:00:08
|
I believe I just subscribed you, and then passed your message on to distribution. I haven't seen your message yet, so I'm not confident. * Csaba Huszka <csa...@ag...> [2010-07-08 10:43-0400] > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > SWObjects-devel mailing list > SWO...@li... > https://lists.sourceforge.net/lists/listinfo/swobjects-devel -- -ericP |
|
From: Csaba H. <csa...@ag...> - 2010-07-08 14:43:46
|
