* When importing bbmri mysql table , table structures change --> exception . * [http://www.abbeyworkshop.com/howto/lamp/MySQL_Export_Backup/index.html 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 == Inconsistency with !OntologyTerm table == * 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 ! ''' === == Inconsistency with Biobanks table == * 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 | | * +-------------+--------------------------------+------+-----+---------+-------+ === But according to the model this is the complete list of fields : === === === * id * name * Investigation * ontologyReference * Individuals * Species * PanelType * FounderPanels * Acronym * Institutes * Publications * Category * Type * Contacts * Topics * Materials * Size * LastUpdate * Description {{{ ALTER TABLE biobank ADD name varchar(255); ALTER TABLE biobank ADD Investigation varchar(255); ALTER TABLE biobank ADD ontologyReference varchar(255); ALTER TABLE biobank ADD Individuals varchar(255); ALTER TABLE biobank ADD Species varchar(255); ALTER TABLE biobank ADD !PanelType varchar(255); ALTER TABLE biobank ADD !FounderPanels varchar(255); ALTER TABLE biobank ADD Institutes varchar(255); ALTER TABLE biobank ADD Publications varchar(255); ALTER TABLE biobank ADD Contacts varchar(255); ALTER TABLE biobank ADD Topics varchar(255); ALTER TABLE biobank ADD Materials varchar(255); }}} after import from old table , molgenis forms still not showing data .Only record id=1 is shown . mysql> select * from biobank where id=1; +---------+----------+------+------+------------+-------------------------------------------------------------+----+------+---------------+-------------------+-------------+---------+-----------+---------------+------------+--------------+----------+--------+-----------+ | Acronym | Category | Type | Size | !LastUpdate | Description | id | name | Investigation | ontologyReference | Individuals | Species | !PanelType | !FounderPanels | Institutes | Publications | Contacts | Topics | Materials | +---------+----------+------+------+------------+-------------------------------------------------------------+----+------+---------------+-------------------+-------------+---------+-----------+---------------+------------+--------------+----------+--------+-----------+ | Agnes | 34 | core | 800 | 2010-11-25 | see PLoS ONE 3(10): e3583. !doi:10.1371/journal.pone.0003583 | 1 | NULL | NULL | NULL | NULL | NULL | NULL | NULL | NULL | NULL | NULL | NULL | NULL | +---------+----------+------+------+------------+-------------------------------------------------------------+----+------+---------------+-------------------+-------------+---------+-----------+---------------+------------+--------------+----------+--------+-----------+ 1 row in set (0.00 sec) mysql> select * from biobank where id=2; +---------+----------+------+-------+------------+-------------+----+------+---------------+-------------------+-------------+---------+-----------+---------------+------------+--------------+----------+--------+-----------+ | Acronym | Category | Type | Size | !LastUpdate | Description | id | name | Investigation | ontologyReference | Individuals | Species | !PanelType | !FounderPanels | Institutes | Publications | Contacts | Topics | Materials | +---------+----------+------+-------+------------+-------------+----+------+---------------+-------------------+-------------+---------+-----------+---------------+------------+--------------+----------+--------+-----------+ | AGORA | 126 | core | 5,000 | 2010-11-25 | 1600 trio's | 2 | NULL | NULL | NULL | NULL | NULL | NULL | NULL | NULL | NULL | NULL | NULL | NULL | +---------+----------+------+-------+------------+-------------+----+------+---------------+-------------------+-------------+---------+-----------+---------------+------------+--------------+----------+--------+-----------+ 1 row in set (0.00 sec) 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 | | | name | varchar(255) | YES | | NULL | | | Investigation | varchar(255) | YES | | NULL | | | ontologyReference | varchar(255) | YES | | NULL | | | Individuals | varchar(255) | YES | | NULL | | | Species | varchar(255) | YES | | NULL | | | !PanelType | varchar(255) | YES | | NULL | | | !FounderPanels | varchar(255) | YES | | NULL | | | Institutes | varchar(255) | YES | | NULL | | | Publications | varchar(255) | YES | | NULL | | | Contacts | varchar(255) | YES | | NULL | | | Topics | varchar(255) | YES | | NULL | | | Materials | varchar(255) | YES | | NULL | | +-------------------+--------------------------------+------+-----+---------+-------+ 19 rows in set (0.00 sec)