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lucmoreau / ProvToolbox

Java toolkit to create and convert W3C PROV data model representations, and build provenance-enabled applications in a variety of programming languages (java, python, typescript, javascript)
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conversion to rdf doesn't preserve prefix #68

Closed satra closed 11 years ago

satra commented 11 years ago

i have a provn file that i convert using provconvert to ttl, but my prefix http://surfer.nmr.mgh.harvard.edu/fswiki/# is not encoded as one in the rdf file.

neither are these guys:

http://www.w3.org/2000/01/rdf-schema# http://www.w3.org/2001/XMLSchema# is this intended behavior or a bug?

@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix prim: <http://openprovenance.org/primitives#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema> .
@prefix xsi: <http://www.w3.org/2001/XMLSchema-instance> .
@prefix pc1: <http://www.ipaw.info/pc1/> .

<http://surfer.nmr.mgh.harvard.edu/fswiki/#fd2bd5d931546325b1eb57c2fb1fd6dc> a prov:Entity , prov:Collection , <
http://surfer.nmr.mgh.harvard.edu/fswiki/#stat_header> .

<http://surfer.nmr.mgh.harvard.edu/fswiki/#a0a2733414aec4b7943d54d501690ed1> a prov:Entity , <http://surfer.nmr.
mgh.harvard.edu/fswiki/#NTableCols> ;
        <http://www.w3.org/2000/01/rdf-schema#label> "NTableCols" ;
        <http://surfer.nmr.mgh.harvard.edu/fswiki/#value> "10"^^<http://www.w3.org/2001/XMLSchema#string> .

<http://surfer.nmr.mgh.harvard.edu/fswiki/#fd2bd5d931546325b1eb57c2fb1fd6dc> prov:hadMember <http://surfer.nmr.m
gh.harvard.edu/fswiki/#a0a2733414aec4b7943d54d501690ed1> .
lucmoreau commented 11 years ago

Hi Satraj

It's sesame that takes care of the rdf serialisation. It's not the prov toolbox.

Luc

Professor Luc Moreau Electronics and Computer Science University of Southampton Southampton SO17 1BJ United Kingdom

On 11 Feb 2013, at 23:26, "Satrajit Ghosh" notifications@github.com<mailto:notifications@github.com> wrote:

i have a provn file that i convert using provconvert to ttl, but my prefix http://surfer.nmr.mgh.harvard.edu/fswiki/# is not encoded as one in the rdf file.

neither are these guys:

http://www.w3.org/2000/01/rdf-schema# http://www.w3.org/2001/XMLSchema# is this intended behavior or a bug?

@prefix prov: http://www.w3.org/ns/prov# . @prefix prim: http://openprovenance.org/primitives# . @prefix xsd: http://www.w3.org/2001/XMLSchema . @prefix xsi: http://www.w3.org/2001/XMLSchema-instance . @prefix pc1: http://www.ipaw.info/pc1/ .

http://surfer.nmr.mgh.harvard.edu/fswiki/#fd2bd5d931546325b1eb57c2fb1fd6dc a prov:Entity , prov:Collection , < http://surfer.nmr.mgh.harvard.edu/fswiki/#stat_header> .

http://surfer.nmr.mgh.harvard.edu/fswiki/#a0a2733414aec4b7943d54d501690ed1 a prov:Entity , http://surfer.nmr. mgh.harvard.edu/fswiki/#NTableCols<http://mgh.harvard.edu/fswiki/#NTableCols> ; http://www.w3.org/2000/01/rdf-schema#label "NTableCols" ; http://surfer.nmr.mgh.harvard.edu/fswiki/#value "10"^^http://www.w3.org/2001/XMLSchema#string .

http://surfer.nmr.mgh.harvard.edu/fswiki/#fd2bd5d931546325b1eb57c2fb1fd6dc prov:hadMember http://surfer.nmr.m gh.harvard.edu/fswiki/#a0a2733414aec4b7943d54d501690ed1<http://gh.harvard.edu/fswiki/#a0a2733414aec4b7943d54d501690ed1> .

— Reply to this email directly or view it on GitHubhttps://github.com/lucmoreau/ProvToolbox/issues/68.

satra commented 11 years ago

alright, i'll take a look at that. closing this for now.

lucmoreau commented 11 years ago

Do you want to send your provn file. We can still see if we can configure sesame better.

Professor Luc Moreau Electronics and Computer Science tel: +44 23 8059 4487 University of Southampton fax: +44 23 8059 2865 Southampton SO17 1BJ email: l.moreau@ecs.soton.ac.uk United Kingdom http://www.ecs.soton.ac.uk/~lavm

From: Satrajit Ghosh [notifications@github.com] Sent: 12 February 2013 11:40 PM To: lucmoreau/ProvToolbox Cc: Luc Moreau Subject: {Disarmed} Re: [ProvToolbox] conversion to rdf doesn't preserve prefix (#68)

alright, i'll take a look at that. closing this for now.

— Reply to this email directly or view it on GitHubhttps://github.com/lucmoreau/ProvToolbox/issues/68#issuecomment-13466476.

satra commented 11 years ago

hi @lucmoreau,

here is a snippet of the provn file:

document
  prefix foaf <http://xmlns.com/foaf/0.1/>
  prefix dcterms <http://purl.org/dc/terms/>
  prefix nidm <http://nidm.nidash.org/#>
  prefix fs <http://surfer.nmr.mgh.harvard.edu/fswiki/#>

  entity(fs:cd0818be9cb95583c43bcbae448c5879, [prov:type='prov:Collection', prov:type='fs:directory', nidm:annotation="lex-READ", fs:subject_id="READ_4066"])
  entity(fs:a62381cc8c5c8a97e0461ec6ba7be6d1, [prov:type='fs:scripts', prov:label="scripts:build-stamp.txt", fs:relative_location="scripts/build-stamp.txt", nidm:file="file://computor.mit.edu/mindhive/xnat/surfaces/lex/READ/READ_4066/scripts/build-stamp.txt", nidm:md5sum="24644d03924b49d83db2b053959291bf"])
  hadMember(fs:cd0818be9cb95583c43bcbae448c5879, fs:a62381cc8c5c8a97e0461ec6ba7be6d1)
  entity(fs:3ceba1daea8e688375f24d2781f4929d, [prov:type='fs:scripts', prov:label="scripts:csurfdir", fs:relative_location="scripts/csurfdir", nidm:file="file://computor.mit.edu/mindhive/xnat/surfaces/lex/READ/READ_4066/scripts/csurfdir", nidm:md5sum="cc169bad1597e7a9ce10ea2085294730"])
  hadMember(fs:cd0818be9cb95583c43bcbae448c5879, fs:3ceba1daea8e688375f24d2781f4929d)
  entity(fs:df82e4125797837af93fd76046581834, [prov:type='fs:scripts', prov:label="scripts:ponscc.cut.log", fs:relative_location="scripts/ponscc.cut.log", nidm:file="file://computor.mit.edu/mindhive/xnat/surfaces/lex/READ/READ_4066/scripts/ponscc.cut.log", nidm:md5sum="67c55daf6d5859ac99916b8a7532c515"])
  hadMember(fs:cd0818be9cb95583c43bcbae448c5879, fs:df82e4125797837af93fd76046581834)
endDocument

and the corresponding ttl

@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix prim: <http://openprovenance.org/primitives#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema> .
@prefix xsi: <http://www.w3.org/2001/XMLSchema-instance> .
@prefix pc1: <http://www.ipaw.info/pc1/> .

<http://surfer.nmr.mgh.harvard.edu/fswiki/#cd0818be9cb95583c43bcbae448c5879> a prov:Entity , prov:Collection , <http://surfer.nmr.mgh.harvard.edu/fswiki/#directory> ;
        <http://nidm.nidash.org/#annotation> "lex-READ"^^<http://www.w3.org/2001/XMLSchema#string> ;
        <http://surfer.nmr.mgh.harvard.edu/fswiki/#subject_id> "READ_4066"^^<http://www.w3.org/2001/XMLSchema#string> .

<http://surfer.nmr.mgh.harvard.edu/fswiki/#a62381cc8c5c8a97e0461ec6ba7be6d1> a prov:Entity , <http://surfer.nmr.mgh.harvard.edu/fswiki/#scripts> ;
        <http://www.w3.org/2000/01/rdf-schema#label> "scripts:build-stamp.txt" ;
        <http://surfer.nmr.mgh.harvard.edu/fswiki/#relative_location> "scripts/build-stamp.txt"^^<http://www.w3.org/2001/XMLSchema#string> ;
        <http://nidm.nidash.org/#file> "file://computor.mit.edu/mindhive/xnat/surfaces/lex/READ/READ_4066/scripts/build-stamp.txt"^^<http://www.w3.org/2001/XMLSchema#string> ;
        <http://nidm.nidash.org/#md5sum> "24644d03924b49d83db2b053959291bf"^^<http://www.w3.org/2001/XMLSchema#string> .

<http://surfer.nmr.mgh.harvard.edu/fswiki/#cd0818be9cb95583c43bcbae448c5879> prov:hadMember <http://surfer.nmr.mgh.harvard.edu/fswiki/#a62381cc8c5c8a97e0461ec6ba7be6d1> .

<http://surfer.nmr.mgh.harvard.edu/fswiki/#3ceba1daea8e688375f24d2781f4929d> a prov:Entity , <http://surfer.nmr.mgh.harvard.edu/fswiki/#scripts> ;
        <http://www.w3.org/2000/01/rdf-schema#label> "scripts:csurfdir" ;
        <http://surfer.nmr.mgh.harvard.edu/fswiki/#relative_location> "scripts/csurfdir"^^<http://www.w3.org/2001/XMLSchema#string> ;
        <http://nidm.nidash.org/#file> "file://computor.mit.edu/mindhive/xnat/surfaces/lex/READ/READ_4066/scripts/csurfdir"^^<http://www.w3.org/2001/XMLSchema#string> ;
        <http://nidm.nidash.org/#md5sum> "cc169bad1597e7a9ce10ea2085294730"^^<http://www.w3.org/2001/XMLSchema#string> .

<http://surfer.nmr.mgh.harvard.edu/fswiki/#cd0818be9cb95583c43bcbae448c5879> prov:hadMember <http://surfer.nmr.mgh.harvard.edu/fswiki/#3ceba1daea8e688375f24d2781f4929d> .

<http://surfer.nmr.mgh.harvard.edu/fswiki/#df82e4125797837af93fd76046581834> a prov:Entity , <http://surfer.nmr.mgh.harvard.edu/fswiki/#scripts> ;
        <http://www.w3.org/2000/01/rdf-schema#label> "scripts:ponscc.cut.log" ;
        <http://surfer.nmr.mgh.harvard.edu/fswiki/#relative_location> "scripts/ponscc.cut.log"^^<http://www.w3.org/2001/XMLSchema#string> ;
        <http://nidm.nidash.org/#file> "file://computor.mit.edu/mindhive/xnat/surfaces/lex/READ/READ_4066/scripts/ponscc.cut.log"^^<http://www.w3.org/2001/XMLSchema#string> ;
        <http://nidm.nidash.org/#md5sum> "67c55daf6d5859ac99916b8a7532c515"^^<http://www.w3.org/2001/XMLSchema#string> .

<http://surfer.nmr.mgh.harvard.edu/fswiki/#cd0818be9cb95583c43bcbae448c5879> prov:hadMember <http://surfer.nmr.mgh.harvard.edu/fswiki/#df82e4125797837af93fd76046581834> .
lucmoreau commented 11 years ago

Hi Satra Thanks for pointing this out. The service (http://provenance.ecs.soton.ac.uk/validator/translator.html) was operating fine, but not the command line command. It's now fixed. I also predefine rdfs prefix. Cheers, Luc