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 .!;
  • 21400 ERROR [JDBCDatabase] executeQuery(select count(*) as num_rows FROM Biobank INNER JOIN Panel ON (Biobank.id = Panel.id) INNER JOIN ObservationTarget ON (Biobank.id = ObservationTarget.id) INNER JOIN ObservationElement ON (Biobank.id = ObservationElement.id) LEFT JOIN Investigation AS xref_Investigation ON xref_Investigation.id = ObservationElement.Investigation LEFT JOIN OntologyTerm AS xref_ontologyReference ON xref_ontologyReference.id = ObservationElement.ontologyReference LEFT JOIN OntologyTerm AS xref_Species ON xref_Species.id = Panel.Species LEFT JOIN OntologyTerm AS xref_PanelType ON xref_PanelType.id = Panel.PanelType LEFT JOIN OntologyTerm AS xref_Category ON xref_Category.id = Biobank.Category WHERE ObservationElement.__Type = 'Biobank')com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'bbmri.observationelement' doesn't exist
  • * mysql> create table ObservationElement (id int(11) NOT NULL);
  • Query OK, 0 rows affected (0.41 sec)

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 .
• *