Details

      Description

      Bryan Thompson asked me to open a ticket.

      The problem is when performing a SERVICE query using the web interface from Blazegraph.

      I tried different queries that do not work.

      Unable to find source-code formatter for language: sparql. Available languages are: actionscript, html, java, javascript, none, sql, xhtml, xml
      PREFIX ssb:<http://csb.wur.nl/genome/>
      SELECT *
      WHERE {
        GRAPH ?G {?genome a ssb:Genome .
        SERVICE <http://sparql.uniprot.org/sparql/> {
          ?uniprot a <http://purl.uniprot.org/core/Taxon> .
          }
        }} LIMIT 10
      
      Unable to find source-code formatter for language: sparql. Available languages are: actionscript, html, java, javascript, none, sql, xhtml, xml
      PREFIX ssb:<http://csb.wur.nl/genome/>
      SELECT *
      WHERE {
      ?genome a ssb:Genome .
        SERVICE <http://sparql.uniprot.org/sparql/> {
          ?uniprot a <http://purl.uniprot.org/core/Taxon> .
          }
        } LIMIT 10
      

      Error file is attached as it is maybe to big for the description

      Blazegraph information
      Build Version=1.5.2
      Running on localhost, ubuntu 14.04 java 7

      1. BLAZEGRAPH.service
        11 kB
        Jasper Koehorst
      1. WebGuiError.png
        137 kB

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          Hide
          beebs Brad Bebee added a comment -

          This accept header does not work with the uniprot SPARQL endpoint:

          application/sparql-results+xml;q=0.8,application/xml;q=0.8,application/x-binary-rdf-results-table,application/sparql-results+json;q=0.8,application/json;q=0.8,text/csv;q=0.8,text/tab-separated-values;q=0.8
          

          This accept header does work with the uniprot SPARQL endpoint:

          application/sparql-results+xml;
          

          @igorkim Please track down if there is guidance in the SPEC for SERVICE and SPARQL endpoint regarding the required accept header. If so, we should explicitly set it to the SPEC by default. I suspect the uniprot endpoint may be misbehaving. It does not accept the output query parameter and uses the non-standard format query parameter.

          Show
          beebs Brad Bebee added a comment - This accept header does not work with the uniprot SPARQL endpoint: application/sparql-results+xml;q=0.8,application/xml;q=0.8,application/x-binary-rdf-results-table,application/sparql-results+json;q=0.8,application/json;q=0.8,text/csv;q=0.8,text/tab-separated-values;q=0.8 This accept header does work with the uniprot SPARQL endpoint: application/sparql-results+xml; @igorkim Please track down if there is guidance in the SPEC for SERVICE and SPARQL endpoint regarding the required accept header. If so, we should explicitly set it to the SPEC by default. I suspect the uniprot endpoint may be misbehaving. It does not accept the output query parameter and uses the non-standard format query parameter.
          Hide
          beebs Brad Bebee added a comment - - edited

          Jasper Koehorst The code-based work around is in Bryan's comment. The workbench workaround (no code changes) is to explicitly set the format query parameter in the SPARQL endpoint (<http://sparql.uniprot.org/sparql?format=xml>). Note this query takes a long time to run as it materializes a large number of entries from the uniport KB without any constraining graph pattern. See:

          PREFIX ssb:<http://csb.wur.nl/genome/>
          SELECT *
          WHERE {
          
            SERVICE <http://sparql.uniprot.org/sparql?format=xml> {
              ?s a <http://purl.uniprot.org/core/Taxon> .
              }
            } LIMIT 10
          
          Show
          beebs Brad Bebee added a comment - - edited Jasper Koehorst The code-based work around is in Bryan's comment. The workbench workaround (no code changes) is to explicitly set the format query parameter in the SPARQL endpoint (< http://sparql.uniprot.org/sparql?format=xml >). Note this query takes a long time to run as it materializes a large number of entries from the uniport KB without any constraining graph pattern. See: PREFIX ssb:<http: //csb.wur.nl/genome/> SELECT * WHERE { SERVICE <http: //sparql.uniprot.org/sparql?format=xml> { ?s a <http: //purl.uniprot.org/core/Taxon> . } } LIMIT 10
          Hide
          maria.krokhaleva maria.krokhaleva added a comment -

          Problem with the original query caused by missing dependency opencsv-2.3.jar needed to parse default response format of sparql.uniprot.org (text/csv).
          Fixed in branch Blzg 1398.
          Pull request: https://github.com/SYSTAP/bigdata/pull/126

          Show
          maria.krokhaleva maria.krokhaleva added a comment - Problem with the original query caused by missing dependency opencsv-2.3.jar needed to parse default response format of sparql.uniprot.org (text/csv). Fixed in branch Blzg 1398. Pull request: https://github.com/SYSTAP/bigdata/pull/126
          Hide
          bryanthompson bryanthompson added a comment -

          Please push another commit. I think that the failures in CI are random and unrelated, but I would like to confirm that.

          Show
          bryanthompson bryanthompson added a comment - Please push another commit. I think that the failures in CI are random and unrelated, but I would like to confirm that.
          Hide
          beebs Brad Bebee added a comment -
          Show
          beebs Brad Bebee added a comment - Merged down in https://github.com/SYSTAP/bigdata/pull/126

            People

            • Assignee:
              igorkim igorkim
              Reporter:
              jjkoehorst Jasper Koehorst
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              4 Start watching this issue

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              • Created:
                Updated:
                Resolved: