• 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 | |
• +-------------+--------------------------------+------+-----+---------+-------+
• 7 rows in set (0.00 sec) *Note: See ​WikiFormatting and ​TracWiki for help on editing wiki content.Change informationComment about this change (optional):
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  Page is read-only Last modified by antonak, 12/08/10 13:50:50 (​6 minutes ago)