TODO:

• sent email to pheno group about the conflict of the entities : Institute & contact
  • This problem will be solved if the bbmri model is merged in the pheno model.
• update the ontocat jar in local & svn version (DONE)
  • commit to svn (DONE)
• ontologies directory changed: this is included in the project , so update the configuration file.
• update from svn . Eric has added the manuals inside the doc directory .
• merge the pheno model with the contents of teh bbmri model. delete the bbmri model and use only pheno model . (this is the solution to the 500 error -- or just add the module auth in the bbmri model . )
• The problem with the D2RQ server is a compatibility of the .n3 file and the database . The database that is used has a different scheme (pheno database ) with the one that is described in the model file) .
  • Model conflict problem that should be solved :
    • The pheno data model contains the auth module
    • The bbmri does not contain the auth module .
    • the bbmri_generate does not run without the module inside . More specifically I receive an error :
      • java.io.FileNotFoundException: /Users/despoina/Documents/molgenis4phenotypeWorkspace_helios_cocoa32/molgenis4phenotype_latest1/auth_db.xml (No such file or directory)
    • if the module is added the Exception in thread "main" java.lang.IllegalArgumentException: elements already exists with name = 'MolgenisUserGroup?' is shown.
• SVN conflict :
  • When committing the whole project : a lot of files seems to need to be committed , especially from the metadata folder. But in the comparison with the previous version this problem does not seem to appear . The only differences are in the classpath , the project and the current changes file.
• Sent an email to the Beheer-raetonline@… about the online system file that admins the paycheck . *

DONE:

• added <entity name="Biobank" extends="Panel"> in pheno_db.xml
• bbmri_db.xml is empty
• bbmri.molgenis.properties: removed the auth_db.xml
• molgenis.properties does not exist.
• created Semantic search plugin example configuration file.
• The Ontocat index is build correctly :
  • search working.
• Null exception in creation of (db) index. - resolved (DONE)
• Some fields were null
  • When retrieved from DB the table contact contains :
    • id,
    • FirstName,
    • MidInitials, LastName,
    • Affiliation, ,<---- this is strange. Is not contained in the DB , where does it come from ??
    • Address,
    • Phone, Email, Fax, tollFreePhone, labworker, xref_Affiliation.name AS Affiliation_name FROM Contact LEFT JOIN Institute AS xref_Affiliation ON xref_Affiliation.id....
• Affiliation exists in model? but not in db ! update database .
  • database now empty
  • upload xls ..ok
  • rebuild index.
• Search in the db index was not working for the field name

• name is not included in the model or the database, but data are here!
  • this creepy feature is because this column was created by the XLS IMPORT!
• Search inside the field description is WORKING : try "accurately" HIV .