wiki:DespoinaLog/2010/12/08

Version 13 (modified by antonak, 14 years ago) (diff)

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  • When importing bbmri mysql table , table structures change --> exception .
    • ​Try to export / import one table at a time : mysqldump5 -u root -p bbmri biobank >biobank.mysql / mysqldump5 -u root -p bbmri_old biobank >biobank.mysql / mysql5 -u root -p bbmri < biobank.mysql / mysql5 -u root -p bbmri < ontologyTerm.mysql
  • org.molgenis.framework.db.DatabaseException: Unknown column 'OntologyTerm.__Type' in 'where clause'
    • Was this produced after the import ? (generate gcc, update db -> test if it is shown --> import -> test if it's there)
    • So this is the PROBLEM for OntologyTerm :
    • * mysql> describe OntologyTerm;
    • +---------------+--------------------------------+------+-----+---------+----------------+
    • | Field | Type | Null | Key | Default | Extra |
    • +---------------+--------------------------------+------+-----+---------+----------------+
    • | id | int(11) | NO | PRI | NULL | auto_increment |
    • | name | varchar(127) | NO | | NULL | |
    • | __Type | enum('OntologyTerm','Species') | NO | | NULL | |
    • | ontology | int(11) | YES | MUL | NULL | |
    • | termAccession | varchar(255) | YES | | NULL | |
    • | definition | varchar(255) | YES | | NULL | |
    • | termPath | varchar(1024) | YES | | NULL | |
    • +---------------+--------------------------------+------+-----+---------+----------------+
    • 7 rows in set (0.04 sec)
    • mysql> describe bbmri_old.OntologyTerm;
    • +---------------+--------------+------+-----+---------+----------------+
    • | Field | Type | Null | Key | Default | Extra |
    • +---------------+--------------+------+-----+---------+----------------+
    • | id | int(11) | NO | PRI | NULL | auto_increment |
    • | term | varchar(255) | NO | | NULL | |
    • | ontology | int(11) | YES | MUL | NULL | |
    • | termAccession | varchar(255) | YES | | NULL | |
    • | definition | varchar(255) | YES | | NULL | |
    • +---------------+--------------+------+-----+---------+----------------+
    • 5 rows in set (0.01 sec)
    • SOLUTION
      • mysql> alter table bbmri_old.OntologyTerm change term name varchar(255) ;
      • mysql> alter table bbmri_old.OntologyTerm add column __Type enum('OntologyTerm','Species') ;
      • mysql> alter table bbmri_old.OntologyTerm add column termPath varchar(1024);
      • mysqldump5 -u root -p bbmri_old ontologyTerm > ontologyTerm.mysql
      • mysql5 -u root -p bbmri < ontologyTerm.mysql

STILL no data shown in molgenis forms :

mysql> update OntologyTerm set __Type="OntologyTerm"

problem solved !

  • * mysql> describe biobanks;
  • ERROR 1146 (42S02): Table 'bbmri.biobanks' doesn't exist
  • mysql> describe biobank;
  • +-------------+--------------------------------+------+-----+---------+-------+
  • | Field | Type | Null | Key | Default | Extra |
  • +-------------+--------------------------------+------+-----+---------+-------+
  • | Acronym | varchar(255) | YES | | NULL | |
  • | Category | int(11) | NO | MUL | NULL | |
  • | Type | enum('core','support','other') | NO | | NULL | |
  • | Size | varchar(255) | YES | | NULL | |
  • | LastUpdate | date | NO | | NULL | |
  • | Description | text | YES | | NULL | |
  • | id | int(11) | NO | PRI | NULL | |
  • +-------------+--------------------------------+------+-----+---------+-------+
  • 7 rows in set (0.00 sec)
  • mysql> describe bbmri_old.biobank;
  • +-------------+--------------------------------+------+-----+---------+-------+
  • | Field | Type | Null | Key | Default | Extra |
  • +-------------+--------------------------------+------+-----+---------+-------+
  • | Acronym | varchar(255) | YES | | NULL | |
  • | Category | int(11) | NO | MUL | NULL | |
  • | Type | enum('core','support','other') | NO | | NULL | |
  • | Size | varchar(255) | YES | | NULL | |
  • | LastUpdate | date | NO | | NULL | |
  • | Description | text | YES | | NULL | |
  • | id | int(11) | NO | PRI | NULL | |
  • +-------------+--------------------------------+------+-----+---------+-------+

Missing fields :  id name Investigation ontologyReference Individuals Species PanelType? FounderPanels? Acronym Institutes Publications Category Type Contacts Topics Materials Size LastUpdate? Description