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Conrad Leonard
Mar 11, 2015, 1:26:21 AM3/11/15
to sta...@clarkparsia.com
Hi;
querying db then shows these as:
Now in the webconsole, browse to the first entity and click the 'Edit' widget, do nothing else, and click 'Save' button. Querying again gives:
Notice that the rdfs:label appears simply as "bwa 0.7.10", although the datatype is still given as xsd:string
I have noticed the following behaviour in the webconsole. I am using version 2.2.4:
Load a bunch of entities from .ttl file with datatypes explicit, e.g.:
aligner:bioscope a :Aligner; rdfs:label '''bioscope'''^^xsd:string .
aligner:bwa a :Aligner; rdfs:label '''bwa'''^^xsd:string .
aligner:lifescope a :Aligner; rdfs:label '''lifescope'''^^xsd:string .
aligner:mapsplice a :Aligner; rdfs:label '''mapsplice'''^^xsd:string .
aligner:rsem a :Aligner; rdfs:label '''rsem'''^^xsd:string .
aligner:tmap a :Aligner; rdfs:label '''tmap'''^^xsd:string .
etc...querying db then shows these as:
[conradL@qimr13054 ~]$ stardog query grafli "select ?s ?l (datatype(?l) as ?d) where {?s a :Aligner; rdfs:label ?l }"Picked up JAVA_TOOL_OPTIONS: -Djavax.net.ssl.trustStore=/opt/local/genomeinfo/java/truststore/keystore.jks+----------------------------+-----------------------------------------------------------------+------------+| s | l | d |+----------------------------+-----------------------------------------------------------------+------------+| aligner:bwa_0_7_10 | "bwa 0.7.10"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bwa | "bwa"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:rsem | "rsem"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bioscope | "bioscope"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:lifescope | "lifescope"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:mapsplice | "mapsplice"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:tmap | "tmap"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bioscope_1_2 | "bioscope-1.2"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bioscope_pairing | "bioscope-pairing"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bowtie2_2_0_2 | "bowtie2_2.0.2"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bowtie2_2_0_6 | "bowtie2_2.0.6"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bwa_0_6_1_r104 | "bwa_0.6.1-r104"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bwa_0_6_2_r126_tpx | "bwa_0.6.2-r126-tpx"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bwamem_0_7_10_r789 | "bwamem_0.7.10-r789"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bwamem_0_7_6a_r433 | "bwamem_0.7.6a-r433"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:isis | "isis"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:lifescope_2_0 | "lifescope_2.0"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:lifescope_2_1 | "lifescope_2.1"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:lifescope_2_5 | "lifescope_2.5"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:miseqreporter | "miseqreporter"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:novoalign_v2_08_02 | "novoalign_V2.08.02"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:novoalign_v3_00_02 | "novoalign_V3.00.02"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:tmap_0_2_3 | "tmap_0.2.3"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:tmap_0_3_7 | "tmap_0.3.7"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:tmap_3_2_0 | "tmap_3.2.0"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:tmap_3_4_0 | "tmap_3.4.0"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string |+----------------------------+-----------------------------------------------------------------+------------+
Now in the webconsole, browse to the first entity and click the 'Edit' widget, do nothing else, and click 'Save' button. Querying again gives:
[conradL@qimr13054 ~]$ stardog query grafli "select ?s ?l (datatype(?l) as ?d) where {?s a :Aligner; rdfs:label ?l }"Picked up JAVA_TOOL_OPTIONS: -Djavax.net.ssl.trustStore=/opt/local/genomeinfo/java/truststore/keystore.jks+----------------------------+-----------------------------------------------------------------+------------+| s | l | d |+----------------------------+-----------------------------------------------------------------+------------+| aligner:bwa_0_7_10 | "bwa 0.7.10" | xsd:string || aligner:bwa | "bwa"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:rsem | "rsem"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bioscope | "bioscope"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:lifescope | "lifescope"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:mapsplice | "mapsplice"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:tmap | "tmap"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bioscope_1_2 | "bioscope-1.2"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bioscope_pairing | "bioscope-pairing"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bowtie2_2_0_2 | "bowtie2_2.0.2"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bowtie2_2_0_6 | "bowtie2_2.0.6"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bwa_0_6_1_r104 | "bwa_0.6.1-r104"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bwa_0_6_2_r126_tpx | "bwa_0.6.2-r126-tpx"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bwamem_0_7_10_r789 | "bwamem_0.7.10-r789"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:bwamem_0_7_6a_r433 | "bwamem_0.7.6a-r433"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:isis | "isis"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:lifescope_2_0 | "lifescope_2.0"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:lifescope_2_1 | "lifescope_2.1"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:lifescope_2_5 | "lifescope_2.5"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:miseqreporter | "miseqreporter"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:novoalign_v2_08_02 | "novoalign_V2.08.02"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:novoalign_v3_00_02 | "novoalign_V3.00.02"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:tmap_0_2_3 | "tmap_0.2.3"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:tmap_0_3_7 | "tmap_0.3.7"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:tmap_3_2_0 | "tmap_3.2.0"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string || aligner:tmap_3_4_0 | "tmap_3.4.0"^^<http://www.w3.org/2001/XMLSchema#string> | xsd:string |+----------------------------+-----------------------------------------------------------------+------------+
Notice that the rdfs:label appears simply as "bwa 0.7.10", although the datatype is still given as xsd:string
Am I missing something about how datatypes are represented internally in the database, or is this a bug in the webconsole?
Edgar Rodriguez
Mar 11, 2015, 5:23:07 PM3/11/15
to sta...@clarkparsia.com
Hi Conrad,
Thank you for the report, this is a bug in the webconsole and I was able to reproduce it. The fix will be included in the next release.--
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