gbic server for bbmri :

DB exists contains data but cannot be shown in the molgenis application forms. Try to uploda form UI , problems with :

• truncate tables : bbmri, ...

''Unknown column 'Contact.Affilication' in 'field list''''

'''Unknown column 'Contact.labworker' in 'field list''''

'''Unknown column 'Contact.Roles' in 'field list''''

• created the field in db bbmri table Contact & Roles .
• Try to mysql dumb form localhost & import in server .
  • Problem with bbmri table (!) There is no bbmri table
• Contact table is full -->
  • truncate, try to import ...
  • Unknown column 'Panel_individuals.individuals' in 'field list'
    • mysql> alter table Panel_individuals ADD individuals VARCHAR(60);
  • Unknown column 'BiobankInstitute?.Institutes' in 'field list'
    • mysql> alter table BiobankInstitute? ADD Institutes VARCHAR(60); Query OK, 0 rows affected (0.01 sec) Records: 0 Duplicates: 0 Warnings: 0
  • Unknown column 'Biobank_Publications.Publications' in 'field list'
    • * mysql> alter table Biobank_Publications ADD Publications VARCHAR(60);
    • Query OK, 0 rows affected (0.01 sec)
    • Records: 0 Duplicates: 0 Warnings: 0
  • Unknown column BiobankContact?.Contacts:
    • alter table BiobankContact ADD Contacts VARCHAR(60);
    • Query OK, 0 rows affected (0.02 sec)
    • Records: 0 Duplicates: 0 Warnings: 0
  • Unknown column Biobank_topics.Topics in fields list
    • mysql> alter table Biobank_Topics ADD Topics VARCHAR(60);
  • Unknown column 'Biobank_Materials.Materials' in 'field list
    • mysql> alter table Biobank_Materials ADD Materials VARCHAR(60);

• * mysql> alter table Biobank_Topics ADD Topics VARCHAR(60);
• Query OK, 0 rows affected (0.01 sec)
• Records: 0 Duplicates: 0 Warnings: 0

''antonak@gbic:~$ mysqlimport -u molgenis -p bbmri bbmri.sql ''

''Enter password: ''

''mysqlimport: Error: Table 'bbmri.bbmri' doesn't exist, when using table: bbmri''

Add the auth module in BBMRI

1. Include the auth_db in your properties file . (Skip this step for : pheno db is already in pheno_db.xml )
   1. For the pheno_db : Just update the entity inside the pheno_db from auth_db .
2. Copy the plugin (latest version) from svn : col7a1
3. Generate, Update the database (the tables are MolgenisUser? - MolgenisUserGroup? - MolgenisUserGroup_allowedToEdit - MolgenisUserGroup_allowedToView - MolgenisUserGroup_members)
4. Add plugin declaration in your ui file.
5. If the mechanism of the email does not work(firewall) make in the db active = true for the new created users .

Problem with debug session variable (default set to true) : fix file 

and add user in db 

• mysql> insert into MolgenisRole values('MolgenisUser', 1, 'despoina', 1, 1);
• mysql> insert into MolgenisUser values (1, 'despoina', 'despoina', 1, 1);
• mysql> commit;

Upload to gbic server