Add support for GraphDB triplestore about ld-r

[ali1k]

thanks for the clarification.
yes, I will check how I can add them to headers!

[ali1k]

@mathib looks nice! thanks for sharing. I will have a look to see how their SPARQl API works. Should be quite straightforward .

[mathib]

Great! Finally an easy way to share an LD-R app with some demo triples :)

[ali1k]

Great! Finally an easy way to share an LD-R app with some demo triples :)

yes! I added support for GraphDB there...

[mathib]

Did some quick tests:

• graph db on localhost: works (read+edit)
  in the default server.js config, there's a missing parameter graphName. The useReasoning function doesn't do anything (graphdb defaults to true)
• graph db on cloud version: only reading works for me...
  used settings in server.js config:
  host: 'rdf.ontotext.com', port: 80, path: '/<DB-number>/<DB-id>/repositories/<repo-id>', graphName: 'default', endpointType: 'graphdb'
  When I try to edit something, I get the following:

name: 'RequestError',
  message: 'Error: read ECONNRESET',
  cause: { Error: read ECONNRESET
    at TCP.onread (net.js:602:25) errno: 'ECONNRESET', code: 'ECONNRESET', syscall: 'read' },
  error: { Error: read ECONNRESET
    at TCP.onread (net.js:602:25) errno: 'ECONNRESET', code: 'ECONNRESET', syscall: 'read' },
  options:
   { uri: 'http://rdf.ontotext.com:443/<DB-number>/<DB-id>/repositories/<repo-id>?format=application%2Fsparql-results%2Bjson&query=%0A%20%20%20%20%20%20%20%20PREFIX%20xsd%3A%20%3Chttp%3A%2F%2Fwww.w3.org%2F2001%2FXMLSchema%23%3E%0A%20%20%20%20%20%20%20%20PREFIX%20ldr%3A%20%3Chttps%3A%2F%2Fgithub.com%2Fali1k%2Fld-reactor%2Fblob%2Fmaster%2Fvocabulary%2Findex.ttl%23%3E%0A%20%20%20%20%20%20%20%20PREFIX%20rdf%3A%20%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0A%20%20%20%20%20%20%20%20PREFIX%20rdfs%3A%20%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0A%20%20%20%20%20%20%20%20PREFIX%20owl%3A%20%3Chttp%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23%3E%0A%20%20%20%20%20%20%20%20PREFIX%20dcterms%3A%20%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Fterms%2F%3E%0A%20%20%20%20%20%20%20%20PREFIX%20void%3A%20%3Chttp%3A%2F%2Frdfs.org%2Fns%2Fvoid%23%3E%0A%20%20%20%20%20%20%20%20PREFIX%20foaf%3A%20%3Chttp%3A%2F%2Fxmlns.com%2Ffoaf%2F0.1%2F%3E%0A%20%20%20%20%20%20%20%20PREFIX%20skos%3A%20%3Chttp%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23%3E%0A%20%20%20%20%20%20%20%20PREFIX%20DBpedia%3A%20%3Chttp%3A%2F%2Fdbpedia.org%2Fontology%2F%3E%0A%20%20%20%20%20%20%20%20PREFIX%20Schema%3A%20%3Chttp%3A%2F%2Fschema.org%2F%3E%0A%20%20%20%20%20%20%20%20%0A%20%20%20%20%20%20%20%20%20%20%20%20SELECT%20%3Fp%20%3Fo%20%28count%28DISTINCT%20%3FextendedVal%29%20AS%20%3FhasExtendedValue%29%20%28SAMPLE%28%3Folb%29%20AS%20%3FoLabel%29%20%28SAMPLE%28%3Fotb%29%20AS%20%3FoTitle%29%20WHERE%20%7B%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%3Chttps%3A%2F%2Fwww.ugent.be%2FmyAwesomeFirstBIMProject%23site_7b7032cc-b822-417b-9aea-642906a29bd7%3E%20%3Fp%20%3Fo%20.%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20OPTIONAL%20%7B%3Fo%20%3Furi%20%3FextendedVal%20.%7D%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20OPTIONAL%20%7B%3Fo%20rdfs%3Alabel%20%3Fol%20.%7D%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20OPTIONAL%20%7B%3Fo%20dcterms%3Atitle%20%3Fot%20.%7D%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20BIND%20%28%20IF%20%28BOUND%20%28%3Fol%29%2C%20%3Fol%2C%20%27%27%20%29%20%20as%20%3Folb%20%20%29%20.%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20BIND%20%28%20IF%20%28BOUND%20%28%3Fot%29%2C%20%3Fot%2C%20%27%27%20%29%20%20as%20%3Fotb%20%20%29%20.%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%0A%20%20%20%20%20%20%20%20%20%20%20%20%7D%20GROUP%20BY%20%3Fp%20%3Fo%0A%20%20%20%20%20%20%20%20',
     headers: { Accept: 'application/sparql-results+json' },
     method: 'GET',
     callback: [Function: RP$callback],
     transform: undefined,
     simple: true,
     resolveWithFullResponse: false,
     transform2xxOnly: false },
  response: undefined }

I tried with port 443 as it graphdb cloud is served on https, but then I get the following error:

{ RequestError: Error: read ECONNRESET
    at new RequestError (C:\Users\<USER-NAME>\Desktop\ld-r\node_modules\request-promise-core\lib\errors.js:14:15)
    at Request.plumbing.callback (C:\Users\<USER-NAME>\Desktop\ld-r\node_modules\request-promise-core\lib\plumbing.js:87:29)
    at Request.RP$callback [as _callback] (C:\Users\<USER-NAME>\Desktop\ld-r\node_modules\request-promise-core\lib\plumbing.js:46:31)
    at self.callback (C:\Users\<USER-NAME>\Desktop\ld-r\node_modules\request\request.js:185:22)
    at Request.emit (events.js:180:13)
    at Request.onRequestError (C:\Users\<USER-NAME>\Desktop\ld-r\node_modules\request\request.js:881:8)
    at ClientRequest.emit (events.js:185:15)
    at Socket.socketErrorListener (_http_client.js:395:9)
    at Socket.emit (events.js:180:13)
    at emitErrorNT (internal/streams/destroy.js:64:8)
    at process._tickCallback (internal/process/next_tick.js:178:19)
From previous event:
    at Request.plumbing.init (C:\Users\<USER-NAME>\Desktop\ld-r\node_modules\request-promise-core\lib\plumbing.js:36:28)
    at Request.RP$initInterceptor [as init] (C:\Users\<USER-NAME>\Desktop\ld-r\node_modules\request-promise-core\configure\request2.js:41:27)
    at new Request (C:\Users\<USER-NAME>\Desktop\ld-r\node_modules\request\request.js:127:8)
    at request (C:\Users\<USER-NAME>\Desktop\ld-r\node_modules\request\index.js:53:10)
    at Function.post (C:\Users\<USER-NAME>\Desktop\ld-r\node_modules\request\index.js:61:12)
    at C:/Users/<USER-NAME>/Desktop/ld-r/services/facet.js:280:24
    at C:/Users/<USER-NAME>/Desktop/ld-r/services/utils/Configurator.js:61:13
    at DynamicConfigurator.prepareDynamicDatasetConfig (C:/Users/<USER-NAME>/Desktop/ld-r/plugins/dynamicConfiguration/DynamicConfigurator.js:479:13)
    at Configurator.prepareDatasetConfig (C:/Users/<USER-NAME>/Desktop/ld-r/services/utils/Configurator.js:47:29)
    at C:/Users/<USER-NAME>/Desktop/ld-r/services/facet.js:237:30
    at C:/Users/<USER-NAME>/Desktop/ld-r/services/utils/dynamicHelpers.js:72:13
    at C:/Users/<USER-NAME>/Desktop/ld-r/services/utils/dynamicHelpers.js:49:9
    at DynamicConfigurator.prepareDynamicServerConfig (C:/Users/<USER-NAME>/Desktop/ld-r/plugins/dynamicConfiguration/DynamicConfigurator.js:172:13)
    at prepareDGFunc (C:/Users/<USER-NAME>/Desktop/ld-r/services/utils/dynamicHelpers.js:15:25)
    at getDynamicEndpointParameters (C:/Users/<USER-NAME>/Desktop/ld-r/services/utils/dynamicHelpers.js:54:9)
    at Object.read (C:/Users/<USER-NAME>/Desktop/ld-r/services/facet.js:234:13)
    at Immediate.executeRequest (C:\Users\<USER-NAME>\Desktop\ld-r\node_modules\fetchr\libs\fetcher.js:229:21)
    at runCallback (timers.js:764:11)
    at tryOnImmediate (timers.js:734:5)
    at processImmediate (timers.js:716:5)
  name: 'RequestError',
  message: 'Error: read ECONNRESET',
  cause: { Error: read ECONNRESET
    at TCP.onread (net.js:602:25) errno: 'ECONNRESET', code: 'ECONNRESET', syscall: 'read' },
  error: { Error: read ECONNRESET
    at TCP.onread (net.js:602:25) errno: 'ECONNRESET', code: 'ECONNRESET', syscall: 'read' },
  options:
   { uri: 'http://rdf.ontotext.com:443/<DB-number>/<DB-id>/repositories/<repo-id>',
     form:
      { query: '\n        PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n        PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n        PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n        PREFIX owl: <http://www.w3.org/2002/07/owl#>\n        PREFIX dcterms: <http://purl.org/dc/terms/>\n        PREFIX void: <http://rdfs.org/ns/void#>\n        PREFIX foaf: <http://xmlns.com/foaf/0.1/>\n        PREFIX skos: <http://www.w3.org/2004/02/skos/core#>\n        \n        SELECT (count(DISTINCT ?s) AS ?total) WHERE {\n             \n                 ?s rdf:type ?type . FILTER (?type IN (<https://w3id.org/bot#Site>,<https://w3id.org/bot#Building>,<https://w3id.org/bot#Storey>,<https://w3id.org/bot#Space>,<https://w3id.org/bot#Element>)) \n                \n             \n        }\n        ',
        format: 'application/sparql-results+json' },
     headers: { Accept: 'application/sparql-results+json' },
     timeout: 10000,
     method: 'POST',
     callback: [Function: RP$callback],
     transform: undefined,
     simple: true,
     resolveWithFullResponse: false,
     transform2xxOnly: false },
  response: undefined }

[mathib]

it probably has something to do with authentication?

[mathib]

Some documentation that might come in handy:

• http://cloud-docs.ontotext.com/display/S4docs/NodeJS
• http://cloud-docs.ontotext.com/display/S4docs/GraphDB+Cloud+REST+APIs

[mathib]

@ali1k I've also did some testing with Postman to the graphdb cloud database and I've found out that I need indeed authentication to the SPARQL endpoint for this. I've also found that the request has to be modified in the case of SPARQL update:

• POST request instead of GET
• basic authentication (username/pw)
• endpoint changes from:
  host: 'rdf.ontotext.com', port: 80, path: '/<DB-number>/<DB-id>/repositories/<repo-id>
  in the case of reading the db into:
  host: 'rdf.ontotext.com', port: 80, path: '/<DB-number>/<DB-id>/repositories/<repo-id>/statements'
  when updating the db
• header parameter changes from query in the case of reading, into update when updating

Did you by any chance had some time to look into authentication-based access to SPARQL endpoints as mentioned here? If so, is there any documentation on how to use it? Thanks :)

[ali1k]

thanks for the comments. I have already added those changes for GraphDB:

https://github.com/ali1k/ld-r/blob/master/services/utils/helpers.js#L168-L177

you can use username and password attributes in your server.js file for HTTP-based authentication. Let me know if it works with that

[mathib]

Hi! Great, this works for me :) Think you can then close issue 18? Or does it need more testing on other kind of triplestores with authentication?

I'm no expert in this, but isn't it safer to add username and password as basic auth in the header, instead of adding it to the URL? I've also noted that the attribute reasoning has to be changed to infer in the case of graphdb

[ali1k]

great! I closed the issue #18
I don't think these credentials will be shared anywhere on the client as they are only shared on the server side of LD-R. However, it is still worth to further investigate that.

I also added support for infer when add useReasoning flag in server config.

[mathib]

I don't think these credentials will be shared anywhere on the client as they are only shared on the server side of LD-R

No, I meant that if you add credentials to the URL of the request, it is just plain and open (I think), while if you add it as an attribute in the header it is hashed?

I also added support for infer when add useReasoning flag in server config.

Thanks!

[lolostar]

Hi,

I try to configure ld-r but although I indicate graphDB in my config file, I still have ClioPatria in my ldr repository (graphDB) ... I think I got rid of all mention of ClioPatria in the config files.