wiki:DespoinaLog/2010/12/07

Biobanks missing from server

Create from scratch (molgenis distro ) the Biobanks (BBMRI), Fill database

this will be faster and more complete : adjust pheno--> http://gbic.target.rug.nl:8080/Biobanks/molgenis.do

GCC project

  • Add gcc integrated bbmri project in gbic server.: http://gbic.target.rug.nl:8080/bbmri_gcc/molgenis.do
  • Database contents cannot be shown .!;
    • Table 'bbmri.observationelement' doesn't exist
    • Update db
    • TODO : insert DATA!
      • * mysql> INSERT INTO `Biobank` VALUES ('Agnes',34,'core','800','2010-11-25','see PLoS ONE 3(10): e3583. doi:10.1371/journal.pone.0003583',1);ERROR 1452 (23000): Cannot add or update a child row: a foreign key constraint fails (`bbmri`.`biobank`, CONSTRAINT `biobank_ibfk_1` FOREIGN KEY (`id`) REFERENCES `panel` (`id`) ON DELETE CASCADE) *
    • batch upload : keys are missing: OntologyTerm?.[name]

D2R on gcc model: : Materials conflict

$$$ mv molgenis-rdf-mapping.n3 molgenis-rdf-mapping_gcc.n3

$$$ d2r-server molgenis-rdf-mapping_gcc.n3

  • Fix missing classes: (despoina)
    • * de.fuberlin.wiwiss.d2rq.D2RQException: Object for d2rq:refersToClassMap not found at d2rq:PropertyBridge map:Biobank_materials (E21) *
    • Biobank material table exists in DB :
    • * mysql> describe Biobank_materials;
    • +-----------+---------+------+-----+---------+----------------+
    • | Field | Type | Null | Key | Default | Extra |
    • +-----------+---------+------+-----+---------+----------------+
    • | autoid | int(11) | NO | PRI | NULL | auto_increment |
    • | Materials | int(11) | NO | MUL | NULL | |
    • | Biobank | int(11) | NO | MUL | NULL | |
    • +-----------+---------+------+-----+---------+------------ *
  • In magetab_sdrf.xml :
 <entity name="Material" extends="!ObservationTarget">
  <field name="SourceMaterials" xref_name="SourceTarget" type="mref" xref_entity="Material"  description="The source materials that this material was derived from. These are the edges in the experimental design graph." />
  <field name="protocolApplications" type="mref" xref_entity="ProtocolApplication" description="The protocols used to produce this material" />	
  • The only reference in Material in the rdf mapping file is
    • * 1388 map:Biobank_materials a d2rq:PropertyBridge;
    • 1389 d2rq:belongsToClassMap map:Biobank;
    • 1390 d2rq:property vocab:Biobank_Materials;
    • 1391 d2rq:propertyDefinitionLabel "Materials";
    • 1392 d2rq:propertyDefinitionComment "Materials";
    • 1393 d2rq:refersToClassMap map:OntologyTerm;
    • 1394 d2rq:join "Biobank.id <= Biobank_Materials.Biobank";
    • 1395 d2rq:join "Biobank_Materials.Materials => OntologyTerm.id";
    • 1396 .
  • Add material in mappings file .
  • *
Last modified 13 years ago Last modified on 2010-12-07T16:44:24+01:00